Starting phenix.real_space_refine on Tue Nov 18 17:26:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz3_45052/11_2025/9bz3_45052_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz3_45052/11_2025/9bz3_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bz3_45052/11_2025/9bz3_45052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz3_45052/11_2025/9bz3_45052.map" model { file = "/net/cci-nas-00/data/ceres_data/9bz3_45052/11_2025/9bz3_45052_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz3_45052/11_2025/9bz3_45052_neut.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.98, per 1000 atoms: 0.25 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: 1.21 Conformation dependent library (CDL) restraints added in 727.8 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: 0.49 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: 3.16 Time building geometry restraints manager: 1.70 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=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.25e-02 6.40e+03 2.39e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.039 1.20e-02 6.94e+03 1.04e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.032 1.08e-02 8.57e+03 8.87e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.569 -0.032 1.17e-02 7.31e+03 7.33e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.573 -0.033 1.25e-02 6.40e+03 6.81e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21581 2.09 - 4.18: 511 4.18 - 6.27: 36 6.27 - 8.36: 2 8.36 - 10.45: 4 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.63 -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 - 35.80: 9468 35.80 - 71.59: 339 71.59 - 107.39: 37 107.39 - 143.19: 3 143.19 - 178.99: 3 Dihedral angle restraints: 9850 sinusoidal: 4092 harmonic: 5758 Sorted by residual: dihedral pdb=" C2 TTP A 803 " pdb=" C1' TTP A 803 " pdb=" N1 TTP A 803 " pdb=" O4' TTP A 803 " ideal model delta sinusoidal sigma weight residual -58.32 120.67 -178.99 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual 301.68 151.15 150.53 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" C5' TTP A 803 " pdb=" O5' TTP A 803 " pdb=" PA TTP A 803 " pdb=" O3A TTP A 803 " ideal model delta sinusoidal sigma weight residual 179.97 31.87 148.10 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 9847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2149 0.094 - 0.187: 178 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.250 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16386 Z= 0.315 Angle : 0.740 10.455 22134 Z= 0.463 Chirality : 0.058 0.469 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.952 178.987 6154 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 covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74040 (22134) hydrogen bonds : bond 0.15421 ( 871) hydrogen bonds : angle 6.51731 ( 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 : 0.598 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: 0.7539 (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: 0.9116 (mt) cc_final: 0.8820 (mt) REVERT: B 590 SER cc_start: 0.8860 (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: 0.1070 (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: 0.1355 time to fit residues: 159.5442 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 : 0.639 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.162837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.109776 restraints weight = 33626.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.113411 restraints weight = 16178.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.115810 restraints weight = 9789.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.117279 restraints weight = 6760.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.118285 restraints weight = 5130.763| |-----------------------------------------------------------------------------| 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 = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16386 Z= 0.223 Angle : 0.624 6.894 22134 Z= 0.334 Chirality : 0.043 0.238 2360 Planarity : 0.004 0.044 2818 Dihedral : 11.401 178.267 2242 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.12 % Allowed : 3.38 % Favored : 96.50 % 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: 1.42 (0.19), residues: 1932 helix: 1.43 (0.15), residues: 1128 sheet: -0.07 (0.41), residues: 146 loop : 0.53 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 90 TYR 0.021 0.002 TYR A 522 PHE 0.033 0.002 PHE C 227 TRP 0.015 0.002 TRP A 623 HIS 0.007 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00484 (16386) covalent geometry : angle 0.62397 (22134) hydrogen bonds : bond 0.04588 ( 871) hydrogen bonds : angle 5.04163 ( 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 623 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 621 time to evaluate : 0.583 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: 0.9332 (mt) cc_final: 0.9059 (mt) REVERT: A 150 GLN cc_start: 0.9054 (tm-30) cc_final: 0.8776 (tm-30) REVERT: A 179 LEU cc_start: 0.9327 (tp) cc_final: 0.9069 (tp) REVERT: A 188 ILE cc_start: 0.9601 (mt) cc_final: 0.9363 (mm) REVERT: A 202 ASN cc_start: 0.9283 (t0) cc_final: 0.9045 (t0) REVERT: A 204 SER cc_start: 0.9158 (m) cc_final: 0.8614 (t) REVERT: A 214 LYS cc_start: 0.8044 (tppt) cc_final: 0.7838 (tppt) REVERT: A 232 ASN cc_start: 0.8514 (m-40) cc_final: 0.8254 (m110) REVERT: A 286 ASP cc_start: 0.8032 (m-30) cc_final: 0.7648 (m-30) REVERT: A 308 LYS cc_start: 0.9591 (mtmt) cc_final: 0.9357 (mtmm) REVERT: A 362 ASP cc_start: 0.7296 (m-30) cc_final: 0.7054 (m-30) REVERT: A 367 VAL cc_start: 0.9708 (m) cc_final: 0.9489 (p) REVERT: A 447 ASN cc_start: 0.8394 (m-40) cc_final: 0.7260 (m-40) REVERT: A 458 MET cc_start: 0.9329 (mmm) cc_final: 0.8492 (mmm) REVERT: A 485 ARG cc_start: 0.8343 (mtm-85) cc_final: 0.7417 (mtm-85) REVERT: A 494 MET cc_start: 0.8739 (mtp) cc_final: 0.8385 (mtp) REVERT: A 496 ASN cc_start: 0.9338 (t0) cc_final: 0.9138 (t0) REVERT: A 576 LEU cc_start: 0.9018 (mt) cc_final: 0.8781 (mt) REVERT: A 583 SER cc_start: 0.9135 (m) cc_final: 0.8722 (t) REVERT: A 586 TYR cc_start: 0.8474 (m-80) cc_final: 0.8168 (m-10) REVERT: A 590 SER cc_start: 0.9254 (t) cc_final: 0.8906 (m) REVERT: A 602 GLU cc_start: 0.7222 (pt0) cc_final: 0.6509 (pt0) REVERT: A 606 TYR cc_start: 0.7964 (m-80) cc_final: 0.7685 (m-10) REVERT: A 630 TYR cc_start: 0.8619 (m-80) cc_final: 0.8415 (m-80) REVERT: A 640 MET cc_start: 0.9054 (tpp) cc_final: 0.8668 (tpp) REVERT: A 662 MET cc_start: 0.8433 (pmm) cc_final: 0.8187 (pmm) REVERT: A 667 LEU cc_start: 0.9041 (tt) cc_final: 0.8325 (tt) REVERT: A 668 ASN cc_start: 0.8926 (m110) cc_final: 0.8523 (m110) REVERT: B 51 LEU cc_start: 0.9061 (tp) cc_final: 0.8831 (tp) REVERT: B 108 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8691 (p) REVERT: B 147 GLN cc_start: 0.8792 (mt0) cc_final: 0.8497 (mt0) REVERT: B 156 PHE cc_start: 0.9191 (t80) cc_final: 0.8920 (t80) REVERT: B 190 MET cc_start: 0.9298 (mtm) cc_final: 0.9017 (mtm) REVERT: B 253 ILE cc_start: 0.9450 (tt) cc_final: 0.9221 (tt) REVERT: B 257 ASP cc_start: 0.8951 (m-30) cc_final: 0.8691 (m-30) REVERT: B 288 PHE cc_start: 0.9428 (t80) cc_final: 0.9181 (t80) REVERT: B 318 ASP cc_start: 0.8814 (t0) cc_final: 0.8561 (p0) REVERT: B 333 LYS cc_start: 0.8776 (tptp) cc_final: 0.8453 (tppt) REVERT: B 358 ILE cc_start: 0.9447 (mm) cc_final: 0.9229 (mm) REVERT: B 362 ASP cc_start: 0.8175 (m-30) cc_final: 0.7484 (m-30) REVERT: B 393 SER cc_start: 0.9537 (m) cc_final: 0.9244 (p) REVERT: B 471 TYR cc_start: 0.9038 (t80) cc_final: 0.8620 (t80) REVERT: B 493 MET cc_start: 0.9351 (tmm) cc_final: 0.9050 (tmm) REVERT: B 512 GLU cc_start: 0.8614 (pt0) cc_final: 0.8331 (pt0) REVERT: B 550 MET cc_start: 0.8377 (mtm) cc_final: 0.8113 (mtp) REVERT: B 561 LEU cc_start: 0.9390 (tp) cc_final: 0.9124 (tp) REVERT: B 615 MET cc_start: 0.9124 (mmp) cc_final: 0.8874 (mmm) REVERT: B 627 LYS cc_start: 0.9160 (tttt) cc_final: 0.8769 (tttp) REVERT: B 662 MET cc_start: 0.8249 (ptp) cc_final: 0.7940 (ptp) REVERT: C 74 MET cc_start: 0.7242 (mtt) cc_final: 0.6489 (mtt) REVERT: C 154 PHE cc_start: 0.8600 (t80) cc_final: 0.8312 (t80) REVERT: C 239 GLU cc_start: 0.9057 (tp30) cc_final: 0.8592 (tp30) REVERT: D 95 MET cc_start: 0.7141 (ttp) cc_final: 0.6832 (ttp) REVERT: D 242 TYR cc_start: 0.7845 (t80) cc_final: 0.7435 (t80) REVERT: D 245 ASP cc_start: 0.5027 (t0) cc_final: 0.4741 (m-30) outliers start: 2 outliers final: 0 residues processed: 622 average time/residue: 0.1256 time to fit residues: 116.6272 Evaluate side-chains 480 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 479 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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: 6.9990 chunk 131 optimal weight: 0.8980 chunk 164 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 182 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 91 optimal weight: 0.9980 chunk 150 optimal weight: 20.0000 chunk 63 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 158 optimal weight: 9.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 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 = 0.163471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.112957 restraints weight = 34184.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116612 restraints weight = 16530.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118862 restraints weight = 9862.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.120364 restraints weight = 6731.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.121130 restraints weight = 5062.706| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16386 Z= 0.222 Angle : 0.608 8.854 22134 Z= 0.321 Chirality : 0.042 0.191 2360 Planarity : 0.004 0.034 2818 Dihedral : 11.192 178.481 2242 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.12 % Allowed : 2.68 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.19), residues: 1932 helix: 1.44 (0.15), residues: 1133 sheet: 0.48 (0.44), residues: 110 loop : 0.33 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 669 TYR 0.016 0.002 TYR B 612 PHE 0.037 0.002 PHE C 109 TRP 0.014 0.002 TRP A 623 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00484 (16386) covalent geometry : angle 0.60772 (22134) hydrogen bonds : bond 0.04152 ( 871) hydrogen bonds : angle 4.85001 ( 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 569 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 567 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 158 ASN cc_start: 0.9024 (m110) cc_final: 0.8814 (m110) REVERT: A 188 ILE cc_start: 0.9598 (mt) cc_final: 0.9350 (mm) REVERT: A 214 LYS cc_start: 0.8184 (tppt) cc_final: 0.7915 (tppt) REVERT: A 232 ASN cc_start: 0.8514 (m-40) cc_final: 0.8202 (m110) REVERT: A 286 ASP cc_start: 0.8208 (m-30) cc_final: 0.7729 (m-30) REVERT: A 308 LYS cc_start: 0.9594 (mtmt) cc_final: 0.9369 (mtmm) REVERT: A 344 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8117 (mt-10) REVERT: A 362 ASP cc_start: 0.7377 (m-30) cc_final: 0.7131 (m-30) REVERT: A 383 SER cc_start: 0.8835 (p) cc_final: 0.8454 (t) REVERT: A 406 ASP cc_start: 0.8518 (m-30) cc_final: 0.8237 (m-30) REVERT: A 417 LEU cc_start: 0.9411 (tt) cc_final: 0.8387 (tt) REVERT: A 447 ASN cc_start: 0.8204 (m-40) cc_final: 0.7187 (m-40) REVERT: A 458 MET cc_start: 0.9275 (mmm) cc_final: 0.8358 (mtm) REVERT: A 494 MET cc_start: 0.8748 (mtp) cc_final: 0.8544 (mtp) REVERT: A 557 ASP cc_start: 0.8834 (m-30) cc_final: 0.8626 (m-30) REVERT: A 583 SER cc_start: 0.9138 (m) cc_final: 0.8813 (t) REVERT: A 602 GLU cc_start: 0.7049 (pt0) cc_final: 0.6755 (pt0) REVERT: A 604 ARG cc_start: 0.8470 (tpp-160) cc_final: 0.8158 (tpp-160) REVERT: A 634 MET cc_start: 0.9036 (mmp) cc_final: 0.8732 (mmp) REVERT: A 667 LEU cc_start: 0.9298 (tt) cc_final: 0.8751 (tt) REVERT: B 51 LEU cc_start: 0.9122 (tp) cc_final: 0.8849 (tp) REVERT: B 117 ARG cc_start: 0.8637 (mtt-85) cc_final: 0.8095 (mmm-85) REVERT: B 120 ASP cc_start: 0.8611 (m-30) cc_final: 0.8319 (m-30) REVERT: B 172 LEU cc_start: 0.9215 (mp) cc_final: 0.9012 (mp) REVERT: B 190 MET cc_start: 0.9258 (mtm) cc_final: 0.9046 (mtm) REVERT: B 253 ILE cc_start: 0.9432 (tt) cc_final: 0.9229 (tt) REVERT: B 266 LYS cc_start: 0.8655 (mtmm) cc_final: 0.8448 (mttm) REVERT: B 276 LYS cc_start: 0.8855 (ptmt) cc_final: 0.8429 (ptpp) REVERT: B 358 ILE cc_start: 0.9447 (mm) cc_final: 0.9224 (mm) REVERT: B 362 ASP cc_start: 0.8223 (m-30) cc_final: 0.7429 (m-30) REVERT: B 393 SER cc_start: 0.9548 (m) cc_final: 0.9202 (p) REVERT: B 471 TYR cc_start: 0.9144 (t80) cc_final: 0.8867 (t80) REVERT: B 493 MET cc_start: 0.9352 (tmm) cc_final: 0.9064 (tmm) REVERT: B 550 MET cc_start: 0.8427 (mtm) cc_final: 0.8150 (mtp) REVERT: B 627 LYS cc_start: 0.9113 (tttt) cc_final: 0.8912 (ttpp) REVERT: B 640 MET cc_start: 0.8923 (tpp) cc_final: 0.8226 (tpp) REVERT: B 662 MET cc_start: 0.8505 (ptp) cc_final: 0.8097 (ptp) REVERT: B 686 ARG cc_start: 0.7531 (mmt180) cc_final: 0.7275 (mmt180) REVERT: C 74 MET cc_start: 0.7139 (mtt) cc_final: 0.6451 (mtt) REVERT: C 154 PHE cc_start: 0.8636 (t80) cc_final: 0.8309 (t80) REVERT: C 239 GLU cc_start: 0.9035 (tp30) cc_final: 0.8536 (tp30) REVERT: D 21 PHE cc_start: 0.8449 (m-10) cc_final: 0.8135 (m-10) REVERT: D 95 MET cc_start: 0.7516 (ttp) cc_final: 0.7308 (ttp) REVERT: D 117 THR cc_start: 0.8649 (p) cc_final: 0.8372 (p) REVERT: D 173 TYR cc_start: 0.7191 (t80) cc_final: 0.6684 (t80) REVERT: D 242 TYR cc_start: 0.7748 (t80) cc_final: 0.7486 (t80) outliers start: 2 outliers final: 0 residues processed: 567 average time/residue: 0.1242 time to fit residues: 105.1280 Evaluate side-chains 454 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 454 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 0.9980 chunk 157 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 127 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 185 optimal weight: 5.9990 chunk 191 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 chunk 182 optimal weight: 30.0000 chunk 93 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.160309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.109407 restraints weight = 33595.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.112937 restraints weight = 16174.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.115048 restraints weight = 9761.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.116482 restraints weight = 6716.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.117521 restraints weight = 5125.736| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 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 = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16386 Z= 0.182 Angle : 0.577 7.268 22134 Z= 0.304 Chirality : 0.042 0.288 2360 Planarity : 0.003 0.034 2818 Dihedral : 10.886 175.752 2242 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.12 % Allowed : 2.33 % Favored : 97.55 % 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: 1.39 (0.19), residues: 1932 helix: 1.51 (0.15), residues: 1137 sheet: -0.55 (0.39), residues: 146 loop : 0.40 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 686 TYR 0.015 0.001 TYR D 130 PHE 0.033 0.002 PHE C 109 TRP 0.009 0.002 TRP A 623 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00401 (16386) covalent geometry : angle 0.57704 (22134) hydrogen bonds : bond 0.03833 ( 871) hydrogen bonds : angle 4.72876 ( 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 545 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 543 time to evaluate : 0.747 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: 0.8383 (mm-30) cc_final: 0.7684 (mp0) REVERT: A 214 LYS cc_start: 0.8270 (tppt) cc_final: 0.7992 (tppt) REVERT: A 232 ASN cc_start: 0.8689 (m-40) cc_final: 0.8412 (m110) REVERT: A 261 PHE cc_start: 0.8677 (t80) cc_final: 0.8460 (t80) REVERT: A 286 ASP cc_start: 0.8153 (m-30) cc_final: 0.7779 (m-30) REVERT: A 308 LYS cc_start: 0.9585 (mtmt) cc_final: 0.9354 (mtmm) REVERT: A 319 MET cc_start: 0.9238 (tpp) cc_final: 0.8966 (tpp) REVERT: A 344 GLU cc_start: 0.8577 (mt-10) cc_final: 0.8117 (mt-10) REVERT: A 406 ASP cc_start: 0.8504 (m-30) cc_final: 0.8174 (m-30) REVERT: A 417 LEU cc_start: 0.9421 (tt) cc_final: 0.8662 (tt) REVERT: A 447 ASN cc_start: 0.8123 (m-40) cc_final: 0.7118 (m-40) REVERT: A 458 MET cc_start: 0.9216 (mmm) cc_final: 0.8397 (mtm) REVERT: A 583 SER cc_start: 0.9124 (m) cc_final: 0.8879 (t) REVERT: A 604 ARG cc_start: 0.8275 (tpp-160) cc_final: 0.7639 (ttm-80) REVERT: A 667 LEU cc_start: 0.9207 (tt) cc_final: 0.8576 (tt) REVERT: B 51 LEU cc_start: 0.9097 (tp) cc_final: 0.8821 (tp) REVERT: B 102 ASN cc_start: 0.9291 (m110) cc_final: 0.8952 (m110) REVERT: B 117 ARG cc_start: 0.8717 (mtt-85) cc_final: 0.8151 (mmm-85) REVERT: B 120 ASP cc_start: 0.8624 (m-30) cc_final: 0.8374 (m-30) REVERT: B 147 GLN cc_start: 0.9071 (mt0) cc_final: 0.8574 (mt0) REVERT: B 190 MET cc_start: 0.9259 (mtm) cc_final: 0.9036 (mtm) REVERT: B 253 ILE cc_start: 0.9428 (tt) cc_final: 0.9163 (tt) REVERT: B 263 ASP cc_start: 0.8719 (m-30) cc_final: 0.8427 (m-30) REVERT: B 276 LYS cc_start: 0.8749 (ptmt) cc_final: 0.8385 (ptpp) REVERT: B 286 ASP cc_start: 0.8446 (m-30) cc_final: 0.8215 (m-30) REVERT: B 333 LYS cc_start: 0.9045 (tttm) cc_final: 0.8445 (tttp) REVERT: B 386 LEU cc_start: 0.9441 (mt) cc_final: 0.9181 (mp) REVERT: B 393 SER cc_start: 0.9567 (m) cc_final: 0.9236 (p) REVERT: B 396 ASP cc_start: 0.8133 (m-30) cc_final: 0.7849 (m-30) REVERT: B 447 ASN cc_start: 0.8459 (m-40) cc_final: 0.8029 (t0) REVERT: B 458 MET cc_start: 0.9063 (mmp) cc_final: 0.8813 (mmm) REVERT: B 467 ASN cc_start: 0.9304 (t0) cc_final: 0.8884 (t0) REVERT: B 493 MET cc_start: 0.9313 (tmm) cc_final: 0.9037 (tmm) REVERT: B 561 LEU cc_start: 0.9478 (tp) cc_final: 0.9250 (tp) REVERT: B 604 ARG cc_start: 0.8656 (tpp80) cc_final: 0.8305 (tpp80) REVERT: B 615 MET cc_start: 0.9144 (mmp) cc_final: 0.8895 (mmm) REVERT: B 627 LYS cc_start: 0.9168 (tttt) cc_final: 0.8687 (tttp) REVERT: B 640 MET cc_start: 0.8947 (tpp) cc_final: 0.8317 (tpp) REVERT: C 74 MET cc_start: 0.7275 (mtt) cc_final: 0.6745 (mtt) REVERT: C 89 VAL cc_start: 0.5690 (t) cc_final: 0.5389 (m) REVERT: C 208 LEU cc_start: 0.9338 (mt) cc_final: 0.9115 (mt) REVERT: C 239 GLU cc_start: 0.9010 (tp30) cc_final: 0.8641 (tp30) REVERT: D 173 TYR cc_start: 0.7128 (t80) cc_final: 0.6802 (t80) outliers start: 2 outliers final: 0 residues processed: 544 average time/residue: 0.1244 time to fit residues: 101.2294 Evaluate side-chains 453 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 453 time to evaluate : 0.591 ------------------------------------------------------------------------------- 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: 7.9990 chunk 46 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 37 optimal weight: 0.2980 chunk 126 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 115 optimal weight: 4.9990 chunk 168 optimal weight: 7.9990 chunk 157 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 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** ** 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 = 0.3982 r_free = 0.3982 target = 0.163474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.112942 restraints weight = 33561.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.116597 restraints weight = 16052.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.118869 restraints weight = 9480.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.120364 restraints weight = 6419.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.121285 restraints weight = 4809.964| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3351 r_free = 0.3351 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.5246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16386 Z= 0.131 Angle : 0.542 7.190 22134 Z= 0.286 Chirality : 0.041 0.192 2360 Planarity : 0.003 0.035 2818 Dihedral : 10.549 173.071 2242 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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: 1.59 (0.15), residues: 1127 sheet: -0.57 (0.40), residues: 148 loop : 0.31 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 686 TYR 0.018 0.001 TYR A 683 PHE 0.038 0.002 PHE C 109 TRP 0.039 0.002 TRP D 124 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00289 (16386) covalent geometry : angle 0.54225 (22134) hydrogen bonds : bond 0.03635 ( 871) hydrogen bonds : angle 4.61713 ( 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 567 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 567 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 PHE cc_start: 0.8819 (t80) cc_final: 0.8575 (t80) REVERT: A 179 LEU cc_start: 0.9300 (tp) cc_final: 0.8997 (tt) REVERT: A 188 ILE cc_start: 0.9562 (mt) cc_final: 0.9321 (mm) REVERT: A 214 LYS cc_start: 0.8194 (tppt) cc_final: 0.7901 (tppt) REVERT: A 228 LYS cc_start: 0.9035 (mmmt) cc_final: 0.8687 (mmtt) REVERT: A 257 ASP cc_start: 0.8867 (m-30) cc_final: 0.8555 (m-30) REVERT: A 308 LYS cc_start: 0.9582 (mtmt) cc_final: 0.9362 (mtmm) REVERT: A 344 GLU cc_start: 0.8637 (mt-10) cc_final: 0.8431 (mt-10) REVERT: A 406 ASP cc_start: 0.8467 (m-30) cc_final: 0.8077 (m-30) REVERT: A 417 LEU cc_start: 0.9362 (tt) cc_final: 0.8478 (tt) REVERT: A 447 ASN cc_start: 0.8071 (m-40) cc_final: 0.7579 (m-40) REVERT: A 458 MET cc_start: 0.9174 (mmm) cc_final: 0.8423 (mtm) REVERT: A 583 SER cc_start: 0.9062 (m) cc_final: 0.8861 (t) REVERT: A 584 ILE cc_start: 0.8994 (pt) cc_final: 0.8765 (pt) REVERT: A 667 LEU cc_start: 0.9200 (tt) cc_final: 0.8605 (tt) REVERT: B 51 LEU cc_start: 0.9017 (tp) cc_final: 0.8601 (tp) REVERT: B 71 LEU cc_start: 0.9469 (mm) cc_final: 0.9134 (mp) REVERT: B 95 MET cc_start: 0.8471 (tpp) cc_final: 0.8223 (tpp) REVERT: B 102 ASN cc_start: 0.9300 (m110) cc_final: 0.8970 (m110) REVERT: B 190 MET cc_start: 0.9234 (mtm) cc_final: 0.8991 (mtm) REVERT: B 191 GLN cc_start: 0.8830 (mm-40) cc_final: 0.8271 (mm-40) REVERT: B 263 ASP cc_start: 0.8589 (m-30) cc_final: 0.8373 (m-30) REVERT: B 276 LYS cc_start: 0.8726 (ptmt) cc_final: 0.8352 (ptpp) REVERT: B 286 ASP cc_start: 0.8421 (m-30) cc_final: 0.8188 (m-30) REVERT: B 288 PHE cc_start: 0.9434 (t80) cc_final: 0.9105 (t80) REVERT: B 333 LYS cc_start: 0.9014 (tttm) cc_final: 0.8671 (tttp) REVERT: B 379 SER cc_start: 0.8706 (t) cc_final: 0.8504 (t) REVERT: B 392 SER cc_start: 0.9285 (m) cc_final: 0.8984 (m) REVERT: B 393 SER cc_start: 0.9521 (m) cc_final: 0.9277 (p) REVERT: B 399 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8269 (mm-30) REVERT: B 467 ASN cc_start: 0.9234 (t0) cc_final: 0.8736 (t0) REVERT: B 493 MET cc_start: 0.9273 (tmm) cc_final: 0.8995 (tmm) REVERT: B 561 LEU cc_start: 0.9486 (tp) cc_final: 0.9267 (tp) REVERT: B 604 ARG cc_start: 0.8596 (tpp80) cc_final: 0.7937 (tpp80) REVERT: B 615 MET cc_start: 0.9115 (mmp) cc_final: 0.8827 (mmm) REVERT: B 627 LYS cc_start: 0.9210 (tttt) cc_final: 0.8916 (tttp) REVERT: B 640 MET cc_start: 0.8962 (tpp) cc_final: 0.8392 (tpp) REVERT: C 74 MET cc_start: 0.7738 (mtt) cc_final: 0.7261 (mtp) REVERT: C 89 VAL cc_start: 0.6446 (t) cc_final: 0.5885 (t) REVERT: C 239 GLU cc_start: 0.8971 (tp30) cc_final: 0.8630 (tp30) outliers start: 0 outliers final: 0 residues processed: 567 average time/residue: 0.1213 time to fit residues: 102.8278 Evaluate side-chains 456 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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: 6.9990 chunk 183 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN B 232 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.159249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.109078 restraints weight = 33572.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.112510 restraints weight = 16690.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.114719 restraints weight = 9973.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.116215 restraints weight = 6773.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.117133 restraints weight = 5072.640| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3303 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7627 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16386 Z= 0.192 Angle : 0.590 10.284 22134 Z= 0.310 Chirality : 0.042 0.153 2360 Planarity : 0.003 0.037 2818 Dihedral : 10.592 171.393 2242 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.42 (0.15), residues: 1142 sheet: -0.62 (0.40), residues: 148 loop : 0.19 (0.24), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 686 TYR 0.042 0.002 TYR D 130 PHE 0.039 0.002 PHE C 109 TRP 0.031 0.002 TRP D 124 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00423 (16386) covalent geometry : angle 0.58988 (22134) hydrogen bonds : bond 0.03759 ( 871) hydrogen bonds : angle 4.72946 ( 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 526 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 526 time to evaluate : 0.600 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: A 65 GLU cc_start: 0.8399 (mm-30) cc_final: 0.7798 (mp0) REVERT: A 109 ASN cc_start: 0.8868 (m110) cc_final: 0.8546 (m-40) REVERT: A 188 ILE cc_start: 0.9606 (mt) cc_final: 0.9318 (mm) REVERT: A 204 SER cc_start: 0.9218 (m) cc_final: 0.8837 (t) REVERT: A 214 LYS cc_start: 0.8287 (tppt) cc_final: 0.8045 (tppt) REVERT: A 228 LYS cc_start: 0.8998 (mmmt) cc_final: 0.8675 (mmtt) REVERT: A 286 ASP cc_start: 0.8175 (m-30) cc_final: 0.7768 (m-30) REVERT: A 308 LYS cc_start: 0.9580 (mtmt) cc_final: 0.9342 (mtmm) REVERT: A 319 MET cc_start: 0.9277 (tpp) cc_final: 0.9038 (tpp) REVERT: A 344 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8421 (mt-10) REVERT: A 362 ASP cc_start: 0.7257 (m-30) cc_final: 0.6968 (m-30) REVERT: A 406 ASP cc_start: 0.8536 (m-30) cc_final: 0.8152 (m-30) REVERT: A 417 LEU cc_start: 0.9409 (tt) cc_final: 0.8631 (tt) REVERT: A 427 LYS cc_start: 0.9177 (ttmm) cc_final: 0.8972 (tttm) REVERT: A 447 ASN cc_start: 0.8098 (m-40) cc_final: 0.7324 (m-40) REVERT: A 456 LYS cc_start: 0.8925 (ptpp) cc_final: 0.8588 (ptpp) REVERT: A 458 MET cc_start: 0.9185 (mmm) cc_final: 0.8449 (mtm) REVERT: A 494 MET cc_start: 0.8750 (mtm) cc_final: 0.8486 (ptm) REVERT: A 606 TYR cc_start: 0.8098 (m-80) cc_final: 0.7658 (m-80) REVERT: A 667 LEU cc_start: 0.9267 (tt) cc_final: 0.8689 (tt) REVERT: A 686 ARG cc_start: 0.8431 (mtp-110) cc_final: 0.7907 (mtp-110) REVERT: B 95 MET cc_start: 0.8528 (tpp) cc_final: 0.8296 (tpp) REVERT: B 102 ASN cc_start: 0.9236 (m110) cc_final: 0.8904 (m110) REVERT: B 120 ASP cc_start: 0.8674 (m-30) cc_final: 0.8422 (m-30) REVERT: B 147 GLN cc_start: 0.9340 (mt0) cc_final: 0.9074 (mt0) REVERT: B 190 MET cc_start: 0.9276 (mtm) cc_final: 0.9036 (mtm) REVERT: B 191 GLN cc_start: 0.8893 (mm-40) cc_final: 0.8065 (mm-40) REVERT: B 235 ARG cc_start: 0.8561 (ttm110) cc_final: 0.8102 (mtm110) REVERT: B 253 ILE cc_start: 0.9401 (tt) cc_final: 0.9188 (tt) REVERT: B 258 ILE cc_start: 0.9524 (tp) cc_final: 0.9232 (tp) REVERT: B 276 LYS cc_start: 0.8607 (ptmt) cc_final: 0.8274 (ptpp) REVERT: B 288 PHE cc_start: 0.9459 (t80) cc_final: 0.9125 (t80) REVERT: B 333 LYS cc_start: 0.9043 (tttm) cc_final: 0.8510 (tttp) REVERT: B 359 MET cc_start: 0.9170 (ttp) cc_final: 0.8731 (tmm) REVERT: B 362 ASP cc_start: 0.8035 (m-30) cc_final: 0.7095 (m-30) REVERT: B 392 SER cc_start: 0.9285 (m) cc_final: 0.9054 (m) REVERT: B 393 SER cc_start: 0.9498 (m) cc_final: 0.9253 (p) REVERT: B 396 ASP cc_start: 0.8110 (m-30) cc_final: 0.7693 (m-30) REVERT: B 467 ASN cc_start: 0.9276 (t0) cc_final: 0.8738 (t0) REVERT: B 493 MET cc_start: 0.9320 (tmm) cc_final: 0.9015 (tmm) REVERT: B 550 MET cc_start: 0.8554 (mtp) cc_final: 0.7607 (mtp) REVERT: B 590 SER cc_start: 0.9109 (p) cc_final: 0.8867 (p) REVERT: B 604 ARG cc_start: 0.8649 (tpp80) cc_final: 0.7786 (tpp80) REVERT: B 615 MET cc_start: 0.9117 (mmp) cc_final: 0.8913 (mmm) REVERT: B 627 LYS cc_start: 0.9221 (tttt) cc_final: 0.8766 (tttp) REVERT: B 634 MET cc_start: 0.9333 (mmm) cc_final: 0.8907 (mmm) REVERT: B 640 MET cc_start: 0.8964 (tpp) cc_final: 0.8268 (tpp) REVERT: C 74 MET cc_start: 0.7854 (mtt) cc_final: 0.7592 (mtt) REVERT: C 109 PHE cc_start: 0.6429 (m-80) cc_final: 0.6056 (m-80) REVERT: D 56 MET cc_start: -0.1295 (mmm) cc_final: -0.1585 (mmm) REVERT: D 108 ILE cc_start: 0.8328 (tp) cc_final: 0.8076 (pt) outliers start: 0 outliers final: 0 residues processed: 526 average time/residue: 0.1200 time to fit residues: 95.4280 Evaluate side-chains 435 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 435 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 186 optimal weight: 20.0000 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.160493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.111007 restraints weight = 33024.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.114514 restraints weight = 16194.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.116687 restraints weight = 9569.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.117999 restraints weight = 6529.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.119115 restraints weight = 4997.864| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3334 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3334 r_free = 0.3334 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 = 0.3334 r_free = 0.3334 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3334 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.5720 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= 0.161 Angle : 0.593 14.679 22134 Z= 0.307 Chirality : 0.042 0.151 2360 Planarity : 0.003 0.035 2818 Dihedral : 10.436 169.155 2242 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % 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: 1.20 (0.19), residues: 1932 helix: 1.45 (0.15), residues: 1139 sheet: -0.62 (0.41), residues: 148 loop : 0.12 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 686 TYR 0.036 0.002 TYR D 130 PHE 0.031 0.002 PHE C 109 TRP 0.041 0.002 TRP D 124 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00357 (16386) covalent geometry : angle 0.59330 (22134) hydrogen bonds : bond 0.03748 ( 871) hydrogen bonds : angle 4.70130 ( 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 532 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 532 time to evaluate : 0.544 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: A 65 GLU cc_start: 0.8393 (mm-30) cc_final: 0.7793 (mp0) REVERT: A 109 ASN cc_start: 0.8826 (m110) cc_final: 0.8547 (m-40) REVERT: A 188 ILE cc_start: 0.9615 (mt) cc_final: 0.9388 (mm) REVERT: A 214 LYS cc_start: 0.8195 (tppt) cc_final: 0.7920 (tppt) REVERT: A 228 LYS cc_start: 0.8995 (mmmt) cc_final: 0.8724 (mmtt) REVERT: A 286 ASP cc_start: 0.8120 (m-30) cc_final: 0.7729 (m-30) REVERT: A 308 LYS cc_start: 0.9565 (mtmt) cc_final: 0.9349 (mtmm) REVERT: A 319 MET cc_start: 0.9259 (tpp) cc_final: 0.8993 (tpp) REVERT: A 344 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8310 (mt-10) REVERT: A 362 ASP cc_start: 0.7248 (m-30) cc_final: 0.7010 (m-30) REVERT: A 406 ASP cc_start: 0.8493 (m-30) cc_final: 0.8128 (m-30) REVERT: A 417 LEU cc_start: 0.9383 (tt) cc_final: 0.8444 (tt) REVERT: A 458 MET cc_start: 0.9176 (mmm) cc_final: 0.8421 (mtm) REVERT: A 493 MET cc_start: 0.8762 (tmm) cc_final: 0.8343 (tmm) REVERT: A 494 MET cc_start: 0.8755 (mtm) cc_final: 0.8518 (ptm) REVERT: A 584 ILE cc_start: 0.9028 (pt) cc_final: 0.8781 (pt) REVERT: A 667 LEU cc_start: 0.9270 (tt) cc_final: 0.8669 (tt) REVERT: A 686 ARG cc_start: 0.8466 (mtp-110) cc_final: 0.7925 (mtp-110) REVERT: B 95 MET cc_start: 0.8509 (tpp) cc_final: 0.8095 (tpp) REVERT: B 102 ASN cc_start: 0.9308 (m110) cc_final: 0.8963 (m110) REVERT: B 120 ASP cc_start: 0.8680 (m-30) cc_final: 0.8431 (m-30) REVERT: B 190 MET cc_start: 0.9275 (mtm) cc_final: 0.9040 (mtm) REVERT: B 191 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8280 (mm-40) REVERT: B 235 ARG cc_start: 0.8514 (ttm110) cc_final: 0.8014 (mtm110) REVERT: B 253 ILE cc_start: 0.9389 (tt) cc_final: 0.9188 (tt) REVERT: B 276 LYS cc_start: 0.8620 (ptmt) cc_final: 0.8288 (ptpp) REVERT: B 286 ASP cc_start: 0.8397 (m-30) cc_final: 0.8097 (m-30) REVERT: B 288 PHE cc_start: 0.9444 (t80) cc_final: 0.9140 (t80) REVERT: B 322 MET cc_start: 0.8869 (mmt) cc_final: 0.8084 (mpp) REVERT: B 333 LYS cc_start: 0.9037 (tttm) cc_final: 0.8701 (tttp) REVERT: B 358 ILE cc_start: 0.9439 (mm) cc_final: 0.9186 (mm) REVERT: B 359 MET cc_start: 0.9111 (ttp) cc_final: 0.8728 (tmm) REVERT: B 386 LEU cc_start: 0.9451 (mp) cc_final: 0.9242 (mp) REVERT: B 393 SER cc_start: 0.9463 (m) cc_final: 0.9166 (p) REVERT: B 467 ASN cc_start: 0.9200 (t0) cc_final: 0.8636 (t0) REVERT: B 493 MET cc_start: 0.9270 (tmm) cc_final: 0.8965 (tmm) REVERT: B 550 MET cc_start: 0.8499 (mtp) cc_final: 0.7633 (mtp) REVERT: B 586 TYR cc_start: 0.8521 (m-80) cc_final: 0.8189 (m-10) REVERT: B 602 GLU cc_start: 0.7370 (pt0) cc_final: 0.7110 (pt0) REVERT: B 604 ARG cc_start: 0.8617 (tpp80) cc_final: 0.7733 (tpp80) REVERT: B 615 MET cc_start: 0.9138 (mmp) cc_final: 0.8893 (mmm) REVERT: B 627 LYS cc_start: 0.9192 (tttt) cc_final: 0.8758 (tttp) REVERT: B 634 MET cc_start: 0.9324 (mmm) cc_final: 0.8907 (mmm) REVERT: B 640 MET cc_start: 0.8985 (tpp) cc_final: 0.8282 (tpp) REVERT: C 74 MET cc_start: 0.7611 (mtt) cc_final: 0.7400 (mtp) REVERT: C 89 VAL cc_start: 0.5591 (m) cc_final: 0.5054 (m) REVERT: C 109 PHE cc_start: 0.6582 (m-80) cc_final: 0.6000 (m-80) REVERT: D 56 MET cc_start: -0.1063 (mmm) cc_final: -0.1307 (mmm) REVERT: D 108 ILE cc_start: 0.8268 (tp) cc_final: 0.8009 (pt) REVERT: D 173 TYR cc_start: 0.6190 (t80) cc_final: 0.5899 (t80) outliers start: 0 outliers final: 0 residues processed: 532 average time/residue: 0.1255 time to fit residues: 99.9709 Evaluate side-chains 431 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 431 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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: 2.9990 chunk 99 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 134 optimal weight: 7.9990 chunk 153 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 151 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN B 25 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 201 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.155924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.106605 restraints weight = 34089.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.110057 restraints weight = 16967.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.112232 restraints weight = 10020.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.113489 restraints weight = 6859.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.114587 restraints weight = 5270.080| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3267 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3267 r_free = 0.3267 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3267 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 16386 Z= 0.255 Angle : 0.659 11.667 22134 Z= 0.344 Chirality : 0.044 0.161 2360 Planarity : 0.004 0.038 2818 Dihedral : 10.548 167.663 2242 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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: 1.05 (0.19), residues: 1932 helix: 1.31 (0.15), residues: 1128 sheet: 0.09 (0.46), residues: 110 loop : -0.09 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 274 TYR 0.036 0.002 TYR D 130 PHE 0.029 0.002 PHE D 178 TRP 0.045 0.003 TRP D 124 HIS 0.006 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00557 (16386) covalent geometry : angle 0.65891 (22134) hydrogen bonds : bond 0.04029 ( 871) hydrogen bonds : angle 4.85933 ( 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 508 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 508 time to evaluate : 0.537 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: 0.8489 (mm-30) cc_final: 0.7847 (mp0) REVERT: A 188 ILE cc_start: 0.9622 (mt) cc_final: 0.9375 (mm) REVERT: A 204 SER cc_start: 0.9220 (m) cc_final: 0.8890 (t) REVERT: A 214 LYS cc_start: 0.8436 (tppt) cc_final: 0.8185 (tppt) REVERT: A 286 ASP cc_start: 0.8138 (m-30) cc_final: 0.7723 (m-30) REVERT: A 308 LYS cc_start: 0.9590 (mtmt) cc_final: 0.9371 (mtmm) REVERT: A 319 MET cc_start: 0.9248 (tpp) cc_final: 0.8957 (tpp) REVERT: A 344 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8407 (mt-10) REVERT: A 362 ASP cc_start: 0.7416 (m-30) cc_final: 0.7125 (m-30) REVERT: A 458 MET cc_start: 0.9224 (mmm) cc_final: 0.8490 (mtm) REVERT: A 584 ILE cc_start: 0.8977 (pt) cc_final: 0.8750 (pt) REVERT: A 604 ARG cc_start: 0.7652 (ptp-110) cc_final: 0.7343 (ptp-110) REVERT: A 667 LEU cc_start: 0.9344 (tt) cc_final: 0.8719 (tt) REVERT: A 686 ARG cc_start: 0.8486 (mtp-110) cc_final: 0.7913 (mtp-110) REVERT: B 51 LEU cc_start: 0.9070 (tp) cc_final: 0.8835 (tp) REVERT: B 95 MET cc_start: 0.8516 (tpp) cc_final: 0.8213 (tpp) REVERT: B 102 ASN cc_start: 0.9280 (m110) cc_final: 0.8919 (m110) REVERT: B 114 ILE cc_start: 0.9629 (mt) cc_final: 0.9370 (mp) REVERT: B 120 ASP cc_start: 0.8715 (m-30) cc_final: 0.8420 (m-30) REVERT: B 125 VAL cc_start: 0.9296 (t) cc_final: 0.9085 (p) REVERT: B 147 GLN cc_start: 0.9109 (mt0) cc_final: 0.8820 (mt0) REVERT: B 218 ASN cc_start: 0.8775 (t0) cc_final: 0.8497 (t0) REVERT: B 253 ILE cc_start: 0.9426 (tt) cc_final: 0.9183 (tt) REVERT: B 274 ARG cc_start: 0.8188 (ttm-80) cc_final: 0.7441 (ttm110) REVERT: B 276 LYS cc_start: 0.8808 (ptmt) cc_final: 0.8442 (ptpp) REVERT: B 322 MET cc_start: 0.8914 (mmt) cc_final: 0.8155 (mpp) REVERT: B 333 LYS cc_start: 0.9051 (tttm) cc_final: 0.8507 (tttp) REVERT: B 359 MET cc_start: 0.9177 (ttp) cc_final: 0.8687 (tmm) REVERT: B 362 ASP cc_start: 0.8129 (m-30) cc_final: 0.7252 (m-30) REVERT: B 467 ASN cc_start: 0.9252 (t0) cc_final: 0.8774 (t0) REVERT: B 493 MET cc_start: 0.9327 (tmm) cc_final: 0.8972 (tmm) REVERT: B 550 MET cc_start: 0.8517 (mtp) cc_final: 0.7575 (mtp) REVERT: B 604 ARG cc_start: 0.8642 (tpp80) cc_final: 0.7661 (tpp80) REVERT: B 627 LYS cc_start: 0.9218 (tttt) cc_final: 0.8775 (tttp) REVERT: B 640 MET cc_start: 0.8932 (tpp) cc_final: 0.8281 (tpp) REVERT: C 90 LEU cc_start: 0.7731 (mt) cc_final: 0.7290 (tt) REVERT: C 154 PHE cc_start: 0.8529 (t80) cc_final: 0.7522 (t80) REVERT: C 269 MET cc_start: 0.7868 (tmm) cc_final: 0.7576 (mmp) REVERT: D 108 ILE cc_start: 0.8280 (tp) cc_final: 0.8026 (pt) REVERT: D 173 TYR cc_start: 0.6024 (t80) cc_final: 0.5800 (t80) outliers start: 0 outliers final: 0 residues processed: 508 average time/residue: 0.1226 time to fit residues: 93.9617 Evaluate side-chains 427 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 427 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 158 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 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 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.161123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.112146 restraints weight = 33564.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.115636 restraints weight = 16448.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.117897 restraints weight = 9776.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.119382 restraints weight = 6607.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.120167 restraints weight = 4926.508| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 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 = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.6052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16386 Z= 0.144 Angle : 0.647 18.639 22134 Z= 0.333 Chirality : 0.042 0.208 2360 Planarity : 0.003 0.037 2818 Dihedral : 10.204 163.106 2242 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.04 (0.19), residues: 1932 helix: 1.26 (0.15), residues: 1142 sheet: 0.12 (0.48), residues: 106 loop : -0.05 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 274 TYR 0.024 0.002 TYR C 174 PHE 0.049 0.002 PHE C 109 TRP 0.045 0.002 TRP D 124 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00321 (16386) covalent geometry : angle 0.64669 (22134) hydrogen bonds : bond 0.03898 ( 871) hydrogen bonds : angle 4.83649 ( 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 524 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 524 time to evaluate : 0.435 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: 0.8445 (mm-30) cc_final: 0.7843 (mp0) REVERT: A 109 ASN cc_start: 0.8936 (m110) cc_final: 0.8668 (m-40) REVERT: A 172 LEU cc_start: 0.9049 (mp) cc_final: 0.8754 (mp) REVERT: A 179 LEU cc_start: 0.9380 (tp) cc_final: 0.9167 (tp) REVERT: A 188 ILE cc_start: 0.9590 (mt) cc_final: 0.9234 (mm) REVERT: A 214 LYS cc_start: 0.8200 (tppt) cc_final: 0.7932 (tppt) REVERT: A 228 LYS cc_start: 0.9007 (mmmt) cc_final: 0.8601 (mmtt) REVERT: A 286 ASP cc_start: 0.8111 (m-30) cc_final: 0.7755 (m-30) REVERT: A 308 LYS cc_start: 0.9561 (mtmt) cc_final: 0.9332 (mtmm) REVERT: A 319 MET cc_start: 0.9247 (tpp) cc_final: 0.8962 (tpp) REVERT: A 341 LYS cc_start: 0.8627 (pttp) cc_final: 0.8327 (pttm) REVERT: A 344 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8414 (mt-10) REVERT: A 357 TYR cc_start: 0.8306 (m-80) cc_final: 0.7946 (m-80) REVERT: A 362 ASP cc_start: 0.7295 (m-30) cc_final: 0.7053 (m-30) REVERT: A 458 MET cc_start: 0.9165 (mmm) cc_final: 0.8450 (mtm) REVERT: A 584 ILE cc_start: 0.8994 (pt) cc_final: 0.8786 (pt) REVERT: A 606 TYR cc_start: 0.7606 (m-10) cc_final: 0.7234 (m-10) REVERT: A 667 LEU cc_start: 0.9264 (tt) cc_final: 0.8605 (tt) REVERT: A 686 ARG cc_start: 0.8440 (mtp-110) cc_final: 0.8012 (mtp-110) REVERT: B 95 MET cc_start: 0.8450 (tpp) cc_final: 0.8191 (tpp) REVERT: B 102 ASN cc_start: 0.9251 (m110) cc_final: 0.8896 (m110) REVERT: B 117 ARG cc_start: 0.8689 (mtt-85) cc_final: 0.8252 (mtp85) REVERT: B 120 ASP cc_start: 0.8550 (m-30) cc_final: 0.8288 (m-30) REVERT: B 147 GLN cc_start: 0.9050 (mt0) cc_final: 0.8684 (mt0) REVERT: B 172 LEU cc_start: 0.9088 (mp) cc_final: 0.8863 (mp) REVERT: B 235 ARG cc_start: 0.8509 (ttm110) cc_final: 0.7946 (mtm110) REVERT: B 253 ILE cc_start: 0.9366 (tt) cc_final: 0.9089 (tt) REVERT: B 262 LEU cc_start: 0.9441 (mm) cc_final: 0.9239 (mm) REVERT: B 276 LYS cc_start: 0.8726 (ptmt) cc_final: 0.8387 (ptpp) REVERT: B 288 PHE cc_start: 0.9436 (t80) cc_final: 0.9165 (t80) REVERT: B 322 MET cc_start: 0.8917 (mmt) cc_final: 0.8108 (mpp) REVERT: B 333 LYS cc_start: 0.9077 (tttm) cc_final: 0.8748 (tttp) REVERT: B 362 ASP cc_start: 0.8008 (m-30) cc_final: 0.7066 (m-30) REVERT: B 447 ASN cc_start: 0.8525 (m-40) cc_final: 0.8296 (m-40) REVERT: B 467 ASN cc_start: 0.9180 (t0) cc_final: 0.8632 (t0) REVERT: B 550 MET cc_start: 0.8456 (mtp) cc_final: 0.7589 (mtp) REVERT: B 576 LEU cc_start: 0.9257 (mt) cc_final: 0.9013 (mt) REVERT: B 604 ARG cc_start: 0.8533 (tpp80) cc_final: 0.7513 (tpp80) REVERT: B 627 LYS cc_start: 0.9249 (tttt) cc_final: 0.8807 (tttp) REVERT: B 634 MET cc_start: 0.9288 (mmm) cc_final: 0.8874 (mmm) REVERT: B 640 MET cc_start: 0.8955 (tpp) cc_final: 0.8278 (tpp) REVERT: C 90 LEU cc_start: 0.7739 (mt) cc_final: 0.7391 (tt) REVERT: C 154 PHE cc_start: 0.8645 (t80) cc_final: 0.7644 (t80) REVERT: C 269 MET cc_start: 0.7911 (tmm) cc_final: 0.7528 (mmp) REVERT: D 21 PHE cc_start: 0.8107 (m-80) cc_final: 0.7752 (m-80) REVERT: D 108 ILE cc_start: 0.8382 (tp) cc_final: 0.8109 (pt) outliers start: 0 outliers final: 0 residues processed: 524 average time/residue: 0.1240 time to fit residues: 98.1372 Evaluate side-chains 444 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 0.522 ------------------------------------------------------------------------------- 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: 3.9990 chunk 62 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 189 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 165 optimal weight: 1.9990 chunk 16 optimal weight: 0.0370 chunk 54 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.159855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.111242 restraints weight = 33768.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.114608 restraints weight = 16659.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.116798 restraints weight = 9900.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.118232 restraints weight = 6789.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.119069 restraints weight = 5073.593| |-----------------------------------------------------------------------------| r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3331 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3331 r_free = 0.3331 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 = 0.3331 r_free = 0.3331 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3331 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.6183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16386 Z= 0.159 Angle : 0.633 9.914 22134 Z= 0.329 Chirality : 0.044 0.349 2360 Planarity : 0.003 0.041 2818 Dihedral : 10.075 161.442 2242 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.19), residues: 1932 helix: 1.29 (0.15), residues: 1139 sheet: 0.03 (0.48), residues: 106 loop : -0.04 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 274 TYR 0.044 0.002 TYR B 118 PHE 0.048 0.002 PHE C 109 TRP 0.046 0.002 TRP D 124 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00356 (16386) covalent geometry : angle 0.63304 (22134) hydrogen bonds : bond 0.03887 ( 871) hydrogen bonds : angle 4.81370 ( 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 495 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 495 time to evaluate : 0.590 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: 0.8455 (mm-30) cc_final: 0.7829 (mp0) REVERT: A 214 LYS cc_start: 0.8179 (tppt) cc_final: 0.7905 (tppt) REVERT: A 250 TYR cc_start: 0.8855 (m-80) cc_final: 0.8561 (m-80) REVERT: A 286 ASP cc_start: 0.8096 (m-30) cc_final: 0.7755 (m-30) REVERT: A 308 LYS cc_start: 0.9559 (mtmt) cc_final: 0.9334 (mtmm) REVERT: A 319 MET cc_start: 0.9215 (tpp) cc_final: 0.8818 (tpp) REVERT: A 341 LYS cc_start: 0.8634 (pttp) cc_final: 0.8313 (pttm) REVERT: A 344 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8382 (mt-10) REVERT: A 362 ASP cc_start: 0.7321 (m-30) cc_final: 0.7100 (m-30) REVERT: A 458 MET cc_start: 0.9165 (mmm) cc_final: 0.8480 (mtm) REVERT: A 615 MET cc_start: 0.8927 (mmm) cc_final: 0.8654 (mmm) REVERT: A 667 LEU cc_start: 0.9284 (tt) cc_final: 0.8655 (tt) REVERT: A 686 ARG cc_start: 0.8540 (mtp-110) cc_final: 0.8134 (mtp-110) REVERT: B 95 MET cc_start: 0.8458 (tpp) cc_final: 0.8215 (tpp) REVERT: B 117 ARG cc_start: 0.8691 (mtt-85) cc_final: 0.8241 (mtp85) REVERT: B 120 ASP cc_start: 0.8533 (m-30) cc_final: 0.8271 (m-30) REVERT: B 147 GLN cc_start: 0.9052 (mt0) cc_final: 0.8722 (mt0) REVERT: B 150 GLN cc_start: 0.9111 (tp40) cc_final: 0.8826 (tp-100) REVERT: B 235 ARG cc_start: 0.8455 (ttm110) cc_final: 0.7854 (mtm110) REVERT: B 253 ILE cc_start: 0.9371 (tt) cc_final: 0.9162 (tt) REVERT: B 276 LYS cc_start: 0.8905 (ptmt) cc_final: 0.8419 (ptpp) REVERT: B 288 PHE cc_start: 0.9454 (t80) cc_final: 0.9228 (t80) REVERT: B 333 LYS cc_start: 0.9031 (tttm) cc_final: 0.8515 (tttp) REVERT: B 359 MET cc_start: 0.9123 (ttp) cc_final: 0.8836 (tmm) REVERT: B 362 ASP cc_start: 0.7957 (m-30) cc_final: 0.7054 (m-30) REVERT: B 447 ASN cc_start: 0.8573 (m-40) cc_final: 0.8345 (m-40) REVERT: B 467 ASN cc_start: 0.9162 (t0) cc_final: 0.8665 (t0) REVERT: B 550 MET cc_start: 0.8405 (mtp) cc_final: 0.7551 (mtp) REVERT: B 561 LEU cc_start: 0.9423 (tp) cc_final: 0.9217 (tp) REVERT: B 576 LEU cc_start: 0.9251 (mt) cc_final: 0.8980 (mt) REVERT: B 604 ARG cc_start: 0.8602 (tpp80) cc_final: 0.7628 (tpp80) REVERT: B 640 MET cc_start: 0.8966 (tpp) cc_final: 0.8277 (tpp) REVERT: C 90 LEU cc_start: 0.7782 (mt) cc_final: 0.7487 (tt) REVERT: C 154 PHE cc_start: 0.8723 (t80) cc_final: 0.7660 (t80) REVERT: C 157 MET cc_start: 0.8616 (mtm) cc_final: 0.8157 (ptp) REVERT: C 269 MET cc_start: 0.7871 (tmm) cc_final: 0.7533 (mmp) REVERT: D 108 ILE cc_start: 0.8418 (tp) cc_final: 0.8158 (pt) outliers start: 0 outliers final: 0 residues processed: 495 average time/residue: 0.1219 time to fit residues: 90.8682 Evaluate side-chains 425 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 7.9990 chunk 25 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 125 optimal weight: 0.0000 chunk 28 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 475 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 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 = 0.3965 r_free = 0.3965 target = 0.160672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.112068 restraints weight = 33499.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.115360 restraints weight = 16321.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.117479 restraints weight = 9729.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.118888 restraints weight = 6686.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.119633 restraints weight = 5023.970| |-----------------------------------------------------------------------------| r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3345 r_free = 0.3345 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.6313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 16386 Z= 0.147 Angle : 0.627 9.081 22134 Z= 0.326 Chirality : 0.043 0.270 2360 Planarity : 0.003 0.041 2818 Dihedral : 9.853 152.216 2242 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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: 1.09 (0.19), residues: 1932 helix: 1.30 (0.15), residues: 1138 sheet: 0.43 (0.50), residues: 96 loop : -0.08 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 604 TYR 0.024 0.001 TYR D 130 PHE 0.048 0.002 PHE C 109 TRP 0.044 0.002 TRP D 124 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00328 (16386) covalent geometry : angle 0.62664 (22134) hydrogen bonds : bond 0.03801 ( 871) hydrogen bonds : angle 4.81317 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3439.66 seconds wall clock time: 60 minutes 17.94 seconds (3617.94 seconds total)