Starting phenix.real_space_refine on Sun Aug 24 01:12:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byy_45048/08_2025/9byy_45048_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byy_45048/08_2025/9byy_45048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9byy_45048/08_2025/9byy_45048_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byy_45048/08_2025/9byy_45048_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9byy_45048/08_2025/9byy_45048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byy_45048/08_2025/9byy_45048.map" } resolution = 4.07 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 4.11, per 1000 atoms: 0.26 Number of scatterers: 16038 At special positions: 0 Unit cell: (97.632, 124.074, 132.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.55 Conformation dependent library (CDL) restraints added in 707.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.985A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.954A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.665A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.695A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.627A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.073A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.677A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.878A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.027A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.068A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.567A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.668A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.360A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.477A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.185A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.049A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.13 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4819 1.34 - 1.46: 3057 1.46 - 1.58: 8329 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.600 -0.060 1.25e-02 6.40e+03 2.29e+01 bond pdb=" 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 1.06e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.574 -0.032 1.08e-02 8.57e+03 8.59e+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 7.50e+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 7.07e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21577 2.09 - 4.18: 515 4.18 - 6.27: 37 6.27 - 8.36: 1 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 2.01e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.14 -4.43 1.15e+00 7.56e-01 1.48e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.20 -3.92 1.09e+00 8.42e-01 1.29e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.81 -4.31 1.23e+00 6.61e-01 1.23e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.68 -3.97 1.15e+00 7.56e-01 1.19e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 9468 35.81 - 71.62: 339 71.62 - 107.43: 37 107.43 - 143.24: 3 143.24 - 179.05: 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 -58.32 120.73 -179.05 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 301.68 151.20 150.48 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 31.91 148.06 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 9847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2144 0.093 - 0.186: 184 0.186 - 0.279: 27 0.279 - 0.372: 3 0.372 - 0.465: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.42e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.67e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.68e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " 0.017 2.00e-02 2.50e+03 1.11e-02 2.14e+00 pdb=" CG PHE D 92 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 169 " 0.017 2.00e-02 2.50e+03 9.71e-03 1.88e+00 pdb=" CG TYR C 169 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 169 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 169 " 0.008 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 129 2.51 - 3.11: 11557 3.11 - 3.70: 27052 3.70 - 4.30: 41529 4.30 - 4.90: 65421 Nonbonded interactions: 145688 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.012 3.040 ... (remaining 145683 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.520 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 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 0.060 16386 Z= 0.315 Angle : 0.740 10.449 22134 Z= 0.463 Chirality : 0.058 0.465 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.952 179.051 6154 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.34 % Allowed : 15.33 % Favored : 83.33 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.18), residues: 1932 helix: 0.59 (0.14), residues: 1151 sheet: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.009 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74007 (22134) hydrogen bonds : bond 0.15421 ( 871) hydrogen bonds : angle 6.51807 ( 2571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 860 time to evaluate : 0.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8904 (mm) cc_final: 0.8689 (mm) REVERT: A 109 ASN cc_start: 0.8043 (m-40) cc_final: 0.7604 (p0) REVERT: A 116 GLU cc_start: 0.7207 (mt-10) cc_final: 0.6838 (mt-10) REVERT: A 118 TYR cc_start: 0.8114 (t80) cc_final: 0.7890 (t80) REVERT: A 147 GLN cc_start: 0.8293 (mt0) cc_final: 0.7243 (mt0) REVERT: A 149 TYR cc_start: 0.8380 (t80) cc_final: 0.8010 (t80) REVERT: A 155 THR cc_start: 0.9239 (m) cc_final: 0.8920 (m) REVERT: A 162 LYS cc_start: 0.7625 (ttpt) cc_final: 0.7293 (ttmm) REVERT: A 190 MET cc_start: 0.8182 (mtt) cc_final: 0.7777 (mtt) REVERT: A 192 LEU cc_start: 0.9213 (mt) cc_final: 0.8681 (mt) REVERT: A 204 SER cc_start: 0.9231 (m) cc_final: 0.8698 (t) REVERT: A 227 MET cc_start: 0.8479 (mtp) cc_final: 0.8231 (mtp) REVERT: A 345 LYS cc_start: 0.8579 (tttt) cc_final: 0.8187 (tttt) REVERT: A 373 ILE cc_start: 0.8878 (mt) cc_final: 0.8624 (mt) REVERT: A 377 LYS cc_start: 0.8860 (mttt) cc_final: 0.8375 (mttp) REVERT: A 436 LEU cc_start: 0.8997 (mt) cc_final: 0.8616 (mm) REVERT: A 500 ILE cc_start: 0.9355 (mt) cc_final: 0.9153 (mt) REVERT: A 588 GLN cc_start: 0.7615 (mm-40) cc_final: 0.7289 (mm-40) REVERT: A 598 MET cc_start: 0.7525 (mtm) cc_final: 0.6965 (mtm) REVERT: A 606 TYR cc_start: 0.6927 (m-80) cc_final: 0.6616 (m-10) REVERT: A 610 LYS cc_start: 0.7098 (ttmm) cc_final: 0.6876 (ttmm) REVERT: A 634 MET cc_start: 0.8405 (mmp) cc_final: 0.8098 (mmm) REVERT: B 12 LEU cc_start: 0.8929 (mt) cc_final: 0.8462 (mt) REVERT: B 51 LEU cc_start: 0.8150 (tp) cc_final: 0.7910 (tp) REVERT: B 99 LYS cc_start: 0.9088 (mmtt) cc_final: 0.8632 (mmtt) REVERT: B 147 GLN cc_start: 0.8069 (mt0) cc_final: 0.7384 (mt0) REVERT: B 161 ARG cc_start: 0.7152 (mtt180) cc_final: 0.6931 (mtt180) REVERT: B 181 ASP cc_start: 0.8428 (m-30) cc_final: 0.8064 (m-30) REVERT: B 211 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7302 (mm-30) REVERT: B 264 THR cc_start: 0.8338 (p) cc_final: 0.8067 (p) REVERT: B 286 ASP cc_start: 0.6259 (OUTLIER) cc_final: 0.5864 (m-30) REVERT: B 288 PHE cc_start: 0.7851 (t80) cc_final: 0.7546 (t80) REVERT: B 319 MET cc_start: 0.8079 (tpp) cc_final: 0.7481 (tpp) REVERT: B 394 TYR cc_start: 0.8003 (m-80) cc_final: 0.7679 (m-80) REVERT: B 425 ILE cc_start: 0.9175 (mt) cc_final: 0.8898 (mt) REVERT: B 436 LEU cc_start: 0.9111 (mt) cc_final: 0.8900 (mt) REVERT: B 460 SER cc_start: 0.8467 (t) cc_final: 0.8144 (p) REVERT: B 570 MET cc_start: 0.7289 (mtm) cc_final: 0.6929 (mtm) REVERT: B 584 ILE cc_start: 0.8989 (tp) cc_final: 0.8771 (tp) REVERT: B 585 SER cc_start: 0.9094 (p) cc_final: 0.8611 (t) REVERT: B 588 GLN cc_start: 0.7635 (mm-40) cc_final: 0.6500 (mm-40) REVERT: B 589 SER cc_start: 0.7889 (m) cc_final: 0.7527 (m) REVERT: B 640 MET cc_start: 0.7717 (tpp) cc_final: 0.7082 (tpp) REVERT: B 644 ILE cc_start: 0.8889 (mt) cc_final: 0.8581 (mt) outliers start: 23 outliers final: 7 residues processed: 874 average time/residue: 0.1553 time to fit residues: 193.7265 Evaluate side-chains 587 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 579 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 0.0370 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 0.9980 overall best weight: 2.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 259 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 44 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 HIS B 313 HIS B 387 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN B 676 HIS ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN C 84 HIS C 210 GLN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN D 71 ASN D 80 HIS D 127 GLN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.138700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.104091 restraints weight = 33599.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.106765 restraints weight = 18563.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.109366 restraints weight = 12319.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.110689 restraints weight = 8977.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.111615 restraints weight = 7087.737| |-----------------------------------------------------------------------------| 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) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16386 Z= 0.215 Angle : 0.663 12.064 22134 Z= 0.351 Chirality : 0.044 0.336 2360 Planarity : 0.004 0.045 2818 Dihedral : 11.441 173.059 2242 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.29 % Allowed : 2.74 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.19), residues: 1932 helix: 1.29 (0.15), residues: 1123 sheet: 0.22 (0.43), residues: 138 loop : 0.52 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 350 TYR 0.023 0.002 TYR A 522 PHE 0.028 0.002 PHE D 320 TRP 0.012 0.002 TRP B 9 HIS 0.008 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00466 (16386) covalent geometry : angle 0.66318 (22134) hydrogen bonds : bond 0.04736 ( 871) hydrogen bonds : angle 5.06866 ( 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 692 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 687 time to evaluate : 0.493 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 99 LYS cc_start: 0.9113 (mmtt) cc_final: 0.8904 (mmtm) REVERT: A 117 ARG cc_start: 0.8386 (mtp85) cc_final: 0.8176 (mtp85) REVERT: A 147 GLN cc_start: 0.8684 (mt0) cc_final: 0.8151 (mt0) REVERT: A 163 ARG cc_start: 0.8358 (mmm160) cc_final: 0.8069 (mtp180) REVERT: A 266 LYS cc_start: 0.8623 (mtmm) cc_final: 0.8420 (mttp) REVERT: A 276 LYS cc_start: 0.9206 (pttp) cc_final: 0.8967 (ptpp) REVERT: A 405 LEU cc_start: 0.8956 (mt) cc_final: 0.8734 (mp) REVERT: A 444 ASP cc_start: 0.8275 (t0) cc_final: 0.7368 (t0) REVERT: A 446 ARG cc_start: 0.7771 (mmm160) cc_final: 0.6885 (mmt180) REVERT: A 493 MET cc_start: 0.9011 (tmm) cc_final: 0.8698 (tmm) REVERT: A 588 GLN cc_start: 0.8866 (mm-40) cc_final: 0.8299 (mm-40) REVERT: A 640 MET cc_start: 0.9116 (ttm) cc_final: 0.8527 (ttm) REVERT: A 683 TYR cc_start: 0.8429 (t80) cc_final: 0.8157 (t80) REVERT: B 8 LYS cc_start: 0.8745 (tptp) cc_final: 0.8125 (tppt) REVERT: B 12 LEU cc_start: 0.9494 (mt) cc_final: 0.9106 (mt) REVERT: B 96 SER cc_start: 0.9511 (m) cc_final: 0.9244 (p) REVERT: B 147 GLN cc_start: 0.8855 (mt0) cc_final: 0.8189 (mt0) REVERT: B 181 ASP cc_start: 0.8839 (m-30) cc_final: 0.8175 (m-30) REVERT: B 200 SER cc_start: 0.8940 (t) cc_final: 0.8657 (t) REVERT: B 253 ILE cc_start: 0.9527 (tt) cc_final: 0.9292 (tt) REVERT: B 263 ASP cc_start: 0.9024 (m-30) cc_final: 0.8729 (m-30) REVERT: B 276 LYS cc_start: 0.9192 (pttt) cc_final: 0.8780 (pttm) REVERT: B 282 VAL cc_start: 0.9571 (t) cc_final: 0.9355 (m) REVERT: B 288 PHE cc_start: 0.9225 (t80) cc_final: 0.8854 (t80) REVERT: B 291 LEU cc_start: 0.9494 (mt) cc_final: 0.8924 (mt) REVERT: B 312 GLN cc_start: 0.8767 (mt0) cc_final: 0.8247 (mt0) REVERT: B 348 MET cc_start: 0.7932 (tpt) cc_final: 0.7304 (tpp) REVERT: B 386 LEU cc_start: 0.9172 (mt) cc_final: 0.8962 (mt) REVERT: B 393 SER cc_start: 0.9526 (m) cc_final: 0.9031 (p) REVERT: B 394 TYR cc_start: 0.8903 (m-80) cc_final: 0.7911 (m-80) REVERT: B 413 SER cc_start: 0.7968 (p) cc_final: 0.6637 (t) REVERT: B 425 ILE cc_start: 0.9625 (mt) cc_final: 0.9386 (mt) REVERT: B 493 MET cc_start: 0.9402 (tmm) cc_final: 0.9150 (tmm) REVERT: B 526 GLU cc_start: 0.8103 (tp30) cc_final: 0.7726 (tp30) REVERT: B 550 MET cc_start: 0.7818 (mtp) cc_final: 0.7234 (ttm) REVERT: B 588 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8323 (mm-40) REVERT: B 589 SER cc_start: 0.9270 (m) cc_final: 0.9030 (p) REVERT: B 602 GLU cc_start: 0.7990 (pt0) cc_final: 0.7519 (pt0) REVERT: B 640 MET cc_start: 0.9041 (tpp) cc_final: 0.8560 (tpp) REVERT: C 53 ASP cc_start: 0.8277 (t0) cc_final: 0.8020 (t0) REVERT: C 93 MET cc_start: 0.9234 (mtm) cc_final: 0.9033 (mtm) REVERT: C 212 ILE cc_start: 0.8540 (mm) cc_final: 0.8080 (mm) REVERT: D 95 MET cc_start: 0.9265 (tmm) cc_final: 0.9044 (tmm) REVERT: D 96 MET cc_start: 0.7839 (mmm) cc_final: 0.7503 (tpt) REVERT: D 100 VAL cc_start: 0.7804 (t) cc_final: 0.7424 (t) REVERT: D 149 ASP cc_start: 0.8335 (m-30) cc_final: 0.8091 (m-30) REVERT: D 178 PHE cc_start: 0.8124 (m-80) cc_final: 0.7859 (m-80) REVERT: D 189 GLU cc_start: 0.7209 (tm-30) cc_final: 0.6455 (pt0) REVERT: D 224 LEU cc_start: 0.8491 (mt) cc_final: 0.8221 (mt) REVERT: D 235 LEU cc_start: 0.8977 (mt) cc_final: 0.8599 (pp) REVERT: D 259 PHE cc_start: 0.7577 (t80) cc_final: 0.7218 (t80) REVERT: D 318 ASP cc_start: 0.8326 (m-30) cc_final: 0.7816 (m-30) outliers start: 5 outliers final: 2 residues processed: 689 average time/residue: 0.1195 time to fit residues: 122.2807 Evaluate side-chains 532 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 530 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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: 4.9990 chunk 131 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 182 optimal weight: 8.9990 chunk 159 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 158 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 338 ASN ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS A 645 GLN B 11 GLN B 61 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN C 233 ASN D 23 ASN D 28 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.126586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.091065 restraints weight = 38672.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.094308 restraints weight = 20044.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.096561 restraints weight = 12291.074| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.098051 restraints weight = 8543.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.099038 restraints weight = 6539.829| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.5328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 16386 Z= 0.317 Angle : 0.717 12.742 22134 Z= 0.380 Chirality : 0.046 0.161 2360 Planarity : 0.004 0.044 2818 Dihedral : 11.482 172.930 2242 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.29 % Allowed : 3.26 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.19), residues: 1932 helix: 1.01 (0.15), residues: 1141 sheet: -0.07 (0.44), residues: 134 loop : 0.46 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 196 TYR 0.026 0.002 TYR C 169 PHE 0.030 0.002 PHE B 37 TRP 0.037 0.002 TRP D 124 HIS 0.007 0.002 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00682 (16386) covalent geometry : angle 0.71744 (22134) hydrogen bonds : bond 0.04470 ( 871) hydrogen bonds : angle 5.07866 ( 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 637 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 632 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8640 (m-10) cc_final: 0.8343 (m-10) REVERT: A 40 TYR cc_start: 0.8936 (t80) cc_final: 0.8504 (t80) REVERT: A 95 MET cc_start: 0.8660 (mmm) cc_final: 0.8444 (tpp) REVERT: A 99 LYS cc_start: 0.9234 (mmtt) cc_final: 0.9023 (mmtm) REVERT: A 117 ARG cc_start: 0.8533 (mtp85) cc_final: 0.8142 (mtp85) REVERT: A 147 GLN cc_start: 0.8888 (mt0) cc_final: 0.8556 (mt0) REVERT: A 204 SER cc_start: 0.9334 (t) cc_final: 0.8922 (t) REVERT: A 286 ASP cc_start: 0.8598 (m-30) cc_final: 0.7967 (m-30) REVERT: A 290 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8200 (tm-30) REVERT: A 348 MET cc_start: 0.8257 (tpt) cc_final: 0.7906 (tpt) REVERT: A 352 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7766 (mt-10) REVERT: A 362 ASP cc_start: 0.7386 (m-30) cc_final: 0.6751 (m-30) REVERT: A 437 THR cc_start: 0.9405 (m) cc_final: 0.9116 (p) REVERT: A 458 MET cc_start: 0.9258 (mmm) cc_final: 0.8684 (mmm) REVERT: A 493 MET cc_start: 0.8954 (tmm) cc_final: 0.8498 (tmm) REVERT: A 573 SER cc_start: 0.9317 (p) cc_final: 0.8794 (p) REVERT: B 31 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8668 (mt-10) REVERT: B 119 GLU cc_start: 0.8936 (mp0) cc_final: 0.8483 (mp0) REVERT: B 143 LEU cc_start: 0.9448 (tp) cc_final: 0.9217 (tp) REVERT: B 147 GLN cc_start: 0.9003 (mt0) cc_final: 0.8265 (mt0) REVERT: B 157 LEU cc_start: 0.9178 (tp) cc_final: 0.8814 (tp) REVERT: B 211 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7467 (mm-30) REVERT: B 238 ASP cc_start: 0.6923 (p0) cc_final: 0.6094 (p0) REVERT: B 253 ILE cc_start: 0.9559 (tt) cc_final: 0.9350 (tt) REVERT: B 263 ASP cc_start: 0.9002 (m-30) cc_final: 0.8754 (m-30) REVERT: B 276 LYS cc_start: 0.9247 (pttt) cc_final: 0.9000 (pttt) REVERT: B 282 VAL cc_start: 0.9629 (t) cc_final: 0.9375 (m) REVERT: B 288 PHE cc_start: 0.9407 (t80) cc_final: 0.9064 (t80) REVERT: B 348 MET cc_start: 0.7997 (tpt) cc_final: 0.7257 (tpp) REVERT: B 359 MET cc_start: 0.8815 (ttp) cc_final: 0.8612 (tmm) REVERT: B 373 ILE cc_start: 0.9680 (mt) cc_final: 0.9409 (mt) REVERT: B 394 TYR cc_start: 0.9000 (m-80) cc_final: 0.8240 (m-80) REVERT: B 425 ILE cc_start: 0.9627 (mt) cc_final: 0.9397 (mt) REVERT: B 467 ASN cc_start: 0.9285 (t0) cc_final: 0.8428 (t0) REVERT: B 493 MET cc_start: 0.9448 (tmm) cc_final: 0.9134 (tmm) REVERT: B 526 GLU cc_start: 0.8015 (tp30) cc_final: 0.7567 (tp30) REVERT: B 550 MET cc_start: 0.8212 (mtp) cc_final: 0.7911 (ttm) REVERT: B 588 GLN cc_start: 0.9217 (mm-40) cc_final: 0.8437 (mm-40) REVERT: B 590 SER cc_start: 0.8931 (p) cc_final: 0.8400 (t) REVERT: B 640 MET cc_start: 0.9167 (tpp) cc_final: 0.8564 (tpp) REVERT: B 667 LEU cc_start: 0.9530 (tp) cc_final: 0.9225 (tp) REVERT: B 668 ASN cc_start: 0.9148 (m-40) cc_final: 0.8933 (m-40) REVERT: B 671 ASP cc_start: 0.8611 (m-30) cc_final: 0.8366 (m-30) REVERT: C 27 LYS cc_start: 0.9019 (mtmm) cc_final: 0.8617 (tptt) REVERT: C 31 LEU cc_start: 0.9232 (mt) cc_final: 0.9029 (mt) REVERT: C 154 PHE cc_start: 0.8529 (t80) cc_final: 0.7913 (t80) REVERT: C 157 MET cc_start: 0.9081 (ptp) cc_final: 0.8862 (ptt) REVERT: C 169 TYR cc_start: 0.7824 (m-10) cc_final: 0.7591 (m-10) REVERT: C 212 ILE cc_start: 0.8678 (mm) cc_final: 0.8318 (mm) REVERT: D 16 ASP cc_start: 0.4390 (m-30) cc_final: 0.3959 (t0) REVERT: D 42 LEU cc_start: 0.5889 (pp) cc_final: 0.5626 (pp) REVERT: D 46 TYR cc_start: 0.8475 (m-80) cc_final: 0.8215 (m-80) REVERT: D 56 MET cc_start: 0.6130 (mpp) cc_final: 0.5723 (mpp) REVERT: D 149 ASP cc_start: 0.8573 (m-30) cc_final: 0.8317 (m-30) REVERT: D 179 TYR cc_start: 0.8492 (t80) cc_final: 0.8287 (t80) REVERT: D 233 ASN cc_start: 0.8680 (m110) cc_final: 0.8453 (m110) REVERT: D 240 LEU cc_start: 0.8750 (mt) cc_final: 0.8539 (mt) REVERT: D 259 PHE cc_start: 0.7647 (t80) cc_final: 0.7311 (t80) REVERT: D 282 ILE cc_start: 0.3494 (OUTLIER) cc_final: 0.3207 (mm) outliers start: 5 outliers final: 1 residues processed: 634 average time/residue: 0.1138 time to fit residues: 108.3860 Evaluate side-chains 502 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 500 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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: 3.9990 chunk 157 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 89 optimal weight: 0.0370 chunk 127 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 191 optimal weight: 0.0670 chunk 159 optimal weight: 20.0000 chunk 182 optimal weight: 8.9990 chunk 93 optimal weight: 0.8980 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN B 232 ASN B 370 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN D 23 ASN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.130574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.094696 restraints weight = 37451.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.098140 restraints weight = 19272.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.100396 restraints weight = 11808.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.102031 restraints weight = 8179.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.103025 restraints weight = 6179.583| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16386 Z= 0.181 Angle : 0.615 9.547 22134 Z= 0.325 Chirality : 0.043 0.209 2360 Planarity : 0.004 0.053 2818 Dihedral : 10.996 165.679 2242 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.23 % Allowed : 2.21 % 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 aren not related in a simple way. whole: 0.93 (0.19), residues: 1932 helix: 1.04 (0.15), residues: 1130 sheet: -0.35 (0.44), residues: 134 loop : 0.33 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 686 TYR 0.026 0.002 TYR A 118 PHE 0.027 0.002 PHE D 109 TRP 0.042 0.002 TRP D 124 HIS 0.008 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00399 (16386) covalent geometry : angle 0.61502 (22134) hydrogen bonds : bond 0.04069 ( 871) hydrogen bonds : angle 4.92322 ( 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 628 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 624 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.9658 (mm) cc_final: 0.9293 (mm) REVERT: A 40 TYR cc_start: 0.8925 (t80) cc_final: 0.8510 (t80) REVERT: A 91 PHE cc_start: 0.9225 (m-80) cc_final: 0.8959 (m-80) REVERT: A 117 ARG cc_start: 0.8418 (mtp85) cc_final: 0.8215 (mtp85) REVERT: A 131 ASN cc_start: 0.9061 (t0) cc_final: 0.8718 (t0) REVERT: A 147 GLN cc_start: 0.8771 (mt0) cc_final: 0.8486 (mt0) REVERT: A 150 GLN cc_start: 0.8909 (tp40) cc_final: 0.8019 (tm-30) REVERT: A 163 ARG cc_start: 0.8181 (mtp180) cc_final: 0.7854 (ttt90) REVERT: A 204 SER cc_start: 0.9214 (t) cc_final: 0.8800 (t) REVERT: A 286 ASP cc_start: 0.8724 (m-30) cc_final: 0.8109 (m-30) REVERT: A 290 GLU cc_start: 0.8413 (tm-30) cc_final: 0.8178 (tm-30) REVERT: A 315 ASP cc_start: 0.8964 (p0) cc_final: 0.8724 (p0) REVERT: A 348 MET cc_start: 0.8118 (tpt) cc_final: 0.7699 (tpt) REVERT: A 352 GLU cc_start: 0.8448 (mt-10) cc_final: 0.7777 (mt-10) REVERT: A 360 PHE cc_start: 0.8661 (m-80) cc_final: 0.8430 (m-80) REVERT: A 362 ASP cc_start: 0.7289 (m-30) cc_final: 0.6547 (m-30) REVERT: A 458 MET cc_start: 0.9229 (mmm) cc_final: 0.8652 (mmm) REVERT: A 493 MET cc_start: 0.8960 (tmm) cc_final: 0.8564 (tmm) REVERT: A 573 SER cc_start: 0.9324 (p) cc_final: 0.8781 (p) REVERT: A 599 GLU cc_start: 0.8304 (mp0) cc_final: 0.8093 (mp0) REVERT: A 634 MET cc_start: 0.8897 (mmm) cc_final: 0.8654 (mmm) REVERT: A 640 MET cc_start: 0.9076 (ttm) cc_final: 0.8568 (ttm) REVERT: B 8 LYS cc_start: 0.8881 (tptp) cc_final: 0.8544 (tppt) REVERT: B 12 LEU cc_start: 0.9504 (mt) cc_final: 0.9217 (mt) REVERT: B 119 GLU cc_start: 0.8894 (mp0) cc_final: 0.8479 (mp0) REVERT: B 147 GLN cc_start: 0.8959 (mt0) cc_final: 0.8309 (mt0) REVERT: B 157 LEU cc_start: 0.9165 (tp) cc_final: 0.8772 (tp) REVERT: B 158 ASN cc_start: 0.8994 (m110) cc_final: 0.8646 (m-40) REVERT: B 211 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7447 (mm-30) REVERT: B 253 ILE cc_start: 0.9587 (tt) cc_final: 0.9367 (tt) REVERT: B 263 ASP cc_start: 0.8995 (m-30) cc_final: 0.8699 (m-30) REVERT: B 282 VAL cc_start: 0.9619 (t) cc_final: 0.9400 (m) REVERT: B 288 PHE cc_start: 0.9323 (t80) cc_final: 0.8978 (t80) REVERT: B 312 GLN cc_start: 0.8934 (mt0) cc_final: 0.8548 (tt0) REVERT: B 316 GLU cc_start: 0.8750 (tt0) cc_final: 0.8502 (tt0) REVERT: B 348 MET cc_start: 0.7921 (tpt) cc_final: 0.7203 (tpp) REVERT: B 373 ILE cc_start: 0.9678 (mt) cc_final: 0.8892 (mt) REVERT: B 393 SER cc_start: 0.9360 (m) cc_final: 0.8875 (m) REVERT: B 394 TYR cc_start: 0.9002 (m-80) cc_final: 0.8346 (m-80) REVERT: B 425 ILE cc_start: 0.9621 (mt) cc_final: 0.9372 (mt) REVERT: B 467 ASN cc_start: 0.9334 (t0) cc_final: 0.8384 (t0) REVERT: B 493 MET cc_start: 0.9472 (tmm) cc_final: 0.9117 (tmm) REVERT: B 526 GLU cc_start: 0.7934 (tp30) cc_final: 0.7472 (tp30) REVERT: B 588 GLN cc_start: 0.9150 (mm-40) cc_final: 0.8439 (mm-40) REVERT: B 590 SER cc_start: 0.9103 (p) cc_final: 0.8207 (t) REVERT: B 602 GLU cc_start: 0.8048 (pt0) cc_final: 0.7833 (pt0) REVERT: B 610 LYS cc_start: 0.8530 (tmtt) cc_final: 0.8193 (tptp) REVERT: B 615 MET cc_start: 0.9484 (mmm) cc_final: 0.9134 (mmm) REVERT: B 640 MET cc_start: 0.9142 (tpp) cc_final: 0.8443 (tpp) REVERT: B 644 ILE cc_start: 0.9596 (mt) cc_final: 0.9135 (mp) REVERT: B 667 LEU cc_start: 0.9431 (tp) cc_final: 0.9139 (tp) REVERT: C 27 LYS cc_start: 0.9006 (mtmm) cc_final: 0.8698 (tptt) REVERT: C 53 ASP cc_start: 0.7810 (t0) cc_final: 0.7588 (t0) REVERT: C 55 TYR cc_start: 0.7064 (t80) cc_final: 0.6120 (t80) REVERT: C 154 PHE cc_start: 0.8494 (t80) cc_final: 0.7870 (t80) REVERT: C 157 MET cc_start: 0.9006 (ptp) cc_final: 0.8780 (ptt) REVERT: C 196 ARG cc_start: 0.8245 (ttp80) cc_final: 0.8037 (ttp80) REVERT: C 243 THR cc_start: 0.7227 (p) cc_final: 0.6574 (p) REVERT: D 20 MET cc_start: 0.8806 (ptp) cc_final: 0.8484 (ptp) REVERT: D 24 GLN cc_start: 0.8191 (mp-120) cc_final: 0.7489 (tp-100) REVERT: D 42 LEU cc_start: 0.5989 (pp) cc_final: 0.5645 (pp) REVERT: D 46 TYR cc_start: 0.8537 (m-80) cc_final: 0.8160 (m-80) REVERT: D 56 MET cc_start: 0.5899 (mpp) cc_final: 0.5568 (mpp) REVERT: D 79 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.6251 (pm20) REVERT: D 149 ASP cc_start: 0.8443 (m-30) cc_final: 0.8141 (m-30) REVERT: D 154 PHE cc_start: 0.8497 (t80) cc_final: 0.8270 (t80) REVERT: D 179 TYR cc_start: 0.8354 (t80) cc_final: 0.8120 (t80) REVERT: D 185 MET cc_start: 0.7718 (mmm) cc_final: 0.6201 (pmm) REVERT: D 189 GLU cc_start: 0.7428 (tm-30) cc_final: 0.6710 (pt0) REVERT: D 208 LEU cc_start: 0.9356 (mt) cc_final: 0.9146 (mt) REVERT: D 233 ASN cc_start: 0.8651 (m110) cc_final: 0.8428 (m110) REVERT: D 259 PHE cc_start: 0.7554 (t80) cc_final: 0.7174 (t80) outliers start: 4 outliers final: 0 residues processed: 626 average time/residue: 0.1324 time to fit residues: 124.2504 Evaluate side-chains 514 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 513 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 120 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 126 optimal weight: 0.9990 chunk 129 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 122 optimal weight: 0.0570 chunk 115 optimal weight: 0.9990 chunk 168 optimal weight: 10.0000 chunk 157 optimal weight: 10.0000 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN A 365 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN B 180 ASN B 232 ASN B 361 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.134443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.098437 restraints weight = 37505.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.101962 restraints weight = 18872.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.104307 restraints weight = 11367.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.105767 restraints weight = 7790.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.106801 restraints weight = 5944.970| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16386 Z= 0.127 Angle : 0.593 15.308 22134 Z= 0.309 Chirality : 0.041 0.238 2360 Planarity : 0.003 0.036 2818 Dihedral : 10.616 161.604 2242 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 2.45 % 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 aren not related in a simple way. whole: 0.99 (0.19), residues: 1932 helix: 1.12 (0.15), residues: 1130 sheet: -0.47 (0.43), residues: 130 loop : 0.30 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 686 TYR 0.019 0.001 TYR B 531 PHE 0.029 0.002 PHE A 129 TRP 0.042 0.001 TRP D 124 HIS 0.007 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00279 (16386) covalent geometry : angle 0.59278 (22134) hydrogen bonds : bond 0.03868 ( 871) hydrogen bonds : angle 4.85328 ( 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 650 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 650 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.8490 (m-80) cc_final: 0.8175 (m-10) REVERT: A 40 TYR cc_start: 0.8877 (t80) cc_final: 0.8404 (t80) REVERT: A 99 LYS cc_start: 0.8852 (mmtp) cc_final: 0.8539 (mmtp) REVERT: A 117 ARG cc_start: 0.8008 (mtp85) cc_final: 0.7775 (mtp85) REVERT: A 131 ASN cc_start: 0.9106 (t0) cc_final: 0.8790 (t0) REVERT: A 147 GLN cc_start: 0.8691 (mt0) cc_final: 0.8389 (mt0) REVERT: A 150 GLN cc_start: 0.8804 (tp40) cc_final: 0.8131 (tm-30) REVERT: A 184 ARG cc_start: 0.8705 (mmm160) cc_final: 0.8379 (mmm-85) REVERT: A 204 SER cc_start: 0.9165 (t) cc_final: 0.8891 (p) REVERT: A 263 ASP cc_start: 0.8344 (m-30) cc_final: 0.8090 (m-30) REVERT: A 286 ASP cc_start: 0.8734 (m-30) cc_final: 0.8139 (m-30) REVERT: A 290 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8133 (tm-30) REVERT: A 291 LEU cc_start: 0.9301 (mp) cc_final: 0.8837 (mp) REVERT: A 348 MET cc_start: 0.8110 (tpt) cc_final: 0.7300 (tpt) REVERT: A 352 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8100 (mp0) REVERT: A 362 ASP cc_start: 0.7257 (m-30) cc_final: 0.6619 (m-30) REVERT: A 493 MET cc_start: 0.8952 (tmm) cc_final: 0.8538 (tmm) REVERT: A 494 MET cc_start: 0.8868 (mtm) cc_final: 0.8075 (ptp) REVERT: A 640 MET cc_start: 0.9050 (ttm) cc_final: 0.8563 (ttm) REVERT: B 8 LYS cc_start: 0.8876 (tptp) cc_final: 0.8475 (tppt) REVERT: B 12 LEU cc_start: 0.9471 (mt) cc_final: 0.9070 (mt) REVERT: B 71 LEU cc_start: 0.9516 (mm) cc_final: 0.9311 (mm) REVERT: B 98 PHE cc_start: 0.9396 (t80) cc_final: 0.8842 (t80) REVERT: B 147 GLN cc_start: 0.9009 (mt0) cc_final: 0.8164 (mt0) REVERT: B 157 LEU cc_start: 0.9118 (tp) cc_final: 0.8736 (tp) REVERT: B 158 ASN cc_start: 0.8916 (m110) cc_final: 0.8576 (m-40) REVERT: B 173 LEU cc_start: 0.9529 (mt) cc_final: 0.9316 (mt) REVERT: B 211 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7283 (mm-30) REVERT: B 235 ARG cc_start: 0.8271 (mmm-85) cc_final: 0.7840 (mmt90) REVERT: B 253 ILE cc_start: 0.9550 (tt) cc_final: 0.9342 (tt) REVERT: B 263 ASP cc_start: 0.8968 (m-30) cc_final: 0.8693 (m-30) REVERT: B 288 PHE cc_start: 0.9288 (t80) cc_final: 0.8876 (t80) REVERT: B 348 MET cc_start: 0.7933 (tpt) cc_final: 0.7198 (tpp) REVERT: B 359 MET cc_start: 0.8860 (ttp) cc_final: 0.8622 (tmm) REVERT: B 379 SER cc_start: 0.8759 (t) cc_final: 0.8533 (t) REVERT: B 393 SER cc_start: 0.9395 (m) cc_final: 0.8975 (m) REVERT: B 394 TYR cc_start: 0.9064 (m-80) cc_final: 0.8319 (m-80) REVERT: B 425 ILE cc_start: 0.9595 (mt) cc_final: 0.9377 (mt) REVERT: B 467 ASN cc_start: 0.9191 (t0) cc_final: 0.8289 (t0) REVERT: B 493 MET cc_start: 0.9443 (tmm) cc_final: 0.9079 (tmm) REVERT: B 526 GLU cc_start: 0.7894 (tp30) cc_final: 0.7399 (tp30) REVERT: B 588 GLN cc_start: 0.9143 (mm-40) cc_final: 0.8285 (mm-40) REVERT: B 590 SER cc_start: 0.8956 (p) cc_final: 0.8181 (t) REVERT: B 601 ILE cc_start: 0.8984 (mm) cc_final: 0.8685 (mm) REVERT: B 615 MET cc_start: 0.9439 (mmm) cc_final: 0.9186 (mmm) REVERT: B 635 PHE cc_start: 0.8971 (m-80) cc_final: 0.8548 (m-80) REVERT: B 640 MET cc_start: 0.9110 (tpp) cc_final: 0.8445 (tpp) REVERT: B 644 ILE cc_start: 0.9568 (mt) cc_final: 0.9135 (mp) REVERT: B 667 LEU cc_start: 0.9498 (tp) cc_final: 0.9169 (tp) REVERT: C 21 PHE cc_start: 0.9313 (m-10) cc_final: 0.9076 (m-10) REVERT: C 27 LYS cc_start: 0.9033 (mtmm) cc_final: 0.8635 (tptp) REVERT: C 154 PHE cc_start: 0.8393 (t80) cc_final: 0.7765 (t80) REVERT: C 196 ARG cc_start: 0.8206 (ttp80) cc_final: 0.7981 (ttp80) REVERT: C 247 TYR cc_start: 0.8135 (m-10) cc_final: 0.7923 (m-80) REVERT: C 313 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8629 (mt-10) REVERT: D 42 LEU cc_start: 0.5994 (pp) cc_final: 0.5636 (pp) REVERT: D 46 TYR cc_start: 0.8534 (m-80) cc_final: 0.8183 (m-80) REVERT: D 56 MET cc_start: 0.6089 (mpp) cc_final: 0.5644 (mpp) REVERT: D 95 MET cc_start: 0.9132 (tmm) cc_final: 0.8754 (tmm) REVERT: D 96 MET cc_start: 0.8455 (tpt) cc_final: 0.7413 (mmm) REVERT: D 149 ASP cc_start: 0.8431 (m-30) cc_final: 0.8173 (m-30) REVERT: D 154 PHE cc_start: 0.8452 (t80) cc_final: 0.7883 (t80) REVERT: D 185 MET cc_start: 0.7833 (mmm) cc_final: 0.6524 (pmm) REVERT: D 189 GLU cc_start: 0.7568 (tm-30) cc_final: 0.6883 (pt0) REVERT: D 233 ASN cc_start: 0.8658 (m110) cc_final: 0.8444 (m110) REVERT: D 259 PHE cc_start: 0.7407 (t80) cc_final: 0.7062 (t80) outliers start: 0 outliers final: 0 residues processed: 650 average time/residue: 0.1354 time to fit residues: 131.9525 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 : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 172 optimal weight: 9.9990 chunk 52 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 27 optimal weight: 5.9990 chunk 136 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN A 361 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN A 645 GLN B 180 ASN B 232 ASN B 361 GLN B 365 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN C 24 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 ASN D 24 GLN D 69 GLN D 132 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.128950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.093710 restraints weight = 37895.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.097040 restraints weight = 19274.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.099258 restraints weight = 11859.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.100639 restraints weight = 8209.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.101687 restraints weight = 6296.263| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.6267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16386 Z= 0.227 Angle : 0.667 12.301 22134 Z= 0.350 Chirality : 0.043 0.171 2360 Planarity : 0.004 0.041 2818 Dihedral : 10.784 165.459 2242 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.12 % Allowed : 2.21 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.19), residues: 1932 helix: 0.92 (0.15), residues: 1141 sheet: -0.68 (0.41), residues: 142 loop : 0.23 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 261 TYR 0.022 0.002 TYR D 142 PHE 0.034 0.002 PHE D 178 TRP 0.054 0.002 TRP D 124 HIS 0.006 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00500 (16386) covalent geometry : angle 0.66690 (22134) hydrogen bonds : bond 0.04033 ( 871) hydrogen bonds : angle 5.02963 ( 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 605 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 603 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8949 (t80) cc_final: 0.8332 (t80) REVERT: A 117 ARG cc_start: 0.8286 (mtp85) cc_final: 0.8071 (mtp85) REVERT: A 131 ASN cc_start: 0.9108 (t0) cc_final: 0.8873 (t0) REVERT: A 147 GLN cc_start: 0.8901 (mt0) cc_final: 0.8527 (mt0) REVERT: A 204 SER cc_start: 0.9329 (t) cc_final: 0.8840 (t) REVERT: A 263 ASP cc_start: 0.8319 (m-30) cc_final: 0.8092 (m-30) REVERT: A 286 ASP cc_start: 0.8769 (m-30) cc_final: 0.8141 (m-30) REVERT: A 290 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8159 (tm-30) REVERT: A 315 ASP cc_start: 0.8918 (p0) cc_final: 0.8706 (p0) REVERT: A 362 ASP cc_start: 0.7193 (m-30) cc_final: 0.6518 (m-30) REVERT: A 396 ASP cc_start: 0.8074 (p0) cc_final: 0.7121 (p0) REVERT: A 444 ASP cc_start: 0.8461 (t70) cc_final: 0.7477 (t0) REVERT: A 493 MET cc_start: 0.8954 (tmm) cc_final: 0.8489 (tmm) REVERT: A 494 MET cc_start: 0.8971 (mtm) cc_final: 0.8107 (ptp) REVERT: A 634 MET cc_start: 0.8887 (mmm) cc_final: 0.8662 (mmm) REVERT: B 71 LEU cc_start: 0.9503 (mm) cc_final: 0.9152 (mp) REVERT: B 119 GLU cc_start: 0.8775 (mp0) cc_final: 0.8399 (mp0) REVERT: B 140 TYR cc_start: 0.9310 (m-10) cc_final: 0.9037 (m-10) REVERT: B 143 LEU cc_start: 0.9528 (tp) cc_final: 0.9241 (tp) REVERT: B 147 GLN cc_start: 0.9086 (mt0) cc_final: 0.8406 (mt0) REVERT: B 157 LEU cc_start: 0.9105 (tp) cc_final: 0.8701 (tp) REVERT: B 158 ASN cc_start: 0.8951 (m110) cc_final: 0.8607 (m-40) REVERT: B 211 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7450 (mm-30) REVERT: B 232 ASN cc_start: 0.7855 (t160) cc_final: 0.7528 (t0) REVERT: B 235 ARG cc_start: 0.8294 (mmm-85) cc_final: 0.7853 (mtt-85) REVERT: B 253 ILE cc_start: 0.9583 (tt) cc_final: 0.9343 (tt) REVERT: B 263 ASP cc_start: 0.9041 (m-30) cc_final: 0.8700 (m-30) REVERT: B 288 PHE cc_start: 0.9379 (t80) cc_final: 0.9033 (t80) REVERT: B 348 MET cc_start: 0.7944 (tpt) cc_final: 0.7236 (tpp) REVERT: B 373 ILE cc_start: 0.9643 (mt) cc_final: 0.9024 (mt) REVERT: B 393 SER cc_start: 0.9406 (m) cc_final: 0.9060 (m) REVERT: B 394 TYR cc_start: 0.9081 (m-80) cc_final: 0.8345 (m-80) REVERT: B 425 ILE cc_start: 0.9599 (mt) cc_final: 0.9319 (mt) REVERT: B 467 ASN cc_start: 0.9307 (t0) cc_final: 0.8439 (t0) REVERT: B 493 MET cc_start: 0.9480 (tmm) cc_final: 0.9157 (tmm) REVERT: B 509 GLU cc_start: 0.8729 (tt0) cc_final: 0.8444 (tm-30) REVERT: B 526 GLU cc_start: 0.7981 (tp30) cc_final: 0.7478 (tp30) REVERT: B 588 GLN cc_start: 0.9220 (mm-40) cc_final: 0.8597 (mm-40) REVERT: B 590 SER cc_start: 0.9139 (p) cc_final: 0.8444 (t) REVERT: B 595 MET cc_start: 0.8970 (mmm) cc_final: 0.8290 (mmm) REVERT: B 601 ILE cc_start: 0.9193 (mm) cc_final: 0.8881 (mm) REVERT: B 615 MET cc_start: 0.9444 (mmm) cc_final: 0.9148 (mmm) REVERT: B 635 PHE cc_start: 0.8949 (m-80) cc_final: 0.8697 (m-80) REVERT: B 667 LEU cc_start: 0.9483 (tp) cc_final: 0.9137 (tp) REVERT: C 27 LYS cc_start: 0.9024 (mtmm) cc_final: 0.8671 (tptp) REVERT: C 28 GLN cc_start: 0.7677 (mt0) cc_final: 0.7432 (mt0) REVERT: C 49 LYS cc_start: 0.9096 (mttp) cc_final: 0.8834 (tmtt) REVERT: C 154 PHE cc_start: 0.8494 (t80) cc_final: 0.7995 (t80) REVERT: C 196 ARG cc_start: 0.8355 (ttp80) cc_final: 0.8124 (ttp80) REVERT: C 243 THR cc_start: 0.7239 (p) cc_final: 0.6900 (t) REVERT: C 247 TYR cc_start: 0.8199 (m-10) cc_final: 0.7992 (m-80) REVERT: C 313 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8565 (mt-10) REVERT: D 42 LEU cc_start: 0.6028 (pp) cc_final: 0.5658 (pp) REVERT: D 46 TYR cc_start: 0.8704 (m-80) cc_final: 0.8351 (m-80) REVERT: D 56 MET cc_start: 0.5799 (mpp) cc_final: 0.5377 (mpp) REVERT: D 95 MET cc_start: 0.9111 (tmm) cc_final: 0.8789 (tmm) REVERT: D 96 MET cc_start: 0.8443 (tpp) cc_final: 0.7617 (mmm) REVERT: D 138 ILE cc_start: 0.8929 (mm) cc_final: 0.8719 (mm) REVERT: D 142 TYR cc_start: 0.8520 (m-80) cc_final: 0.8211 (m-80) REVERT: D 149 ASP cc_start: 0.8534 (m-30) cc_final: 0.8260 (m-30) REVERT: D 154 PHE cc_start: 0.8301 (t80) cc_final: 0.8091 (t80) REVERT: D 185 MET cc_start: 0.8083 (mmm) cc_final: 0.6792 (pmm) REVERT: D 192 ASN cc_start: 0.8636 (t0) cc_final: 0.8084 (m-40) REVERT: D 233 ASN cc_start: 0.8699 (m110) cc_final: 0.8425 (m110) REVERT: D 241 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7277 (tm-30) REVERT: D 259 PHE cc_start: 0.7602 (t80) cc_final: 0.7177 (t80) outliers start: 2 outliers final: 0 residues processed: 604 average time/residue: 0.1303 time to fit residues: 118.2771 Evaluate side-chains 483 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 483 time to evaluate : 0.692 ------------------------------------------------------------------------------- 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: 6.9990 chunk 51 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 105 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 156 optimal weight: 8.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN B 232 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 467 ASN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.130194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.094574 restraints weight = 37726.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.097974 restraints weight = 19211.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.100094 restraints weight = 11686.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.101730 restraints weight = 8176.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.102796 restraints weight = 6160.038| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.6482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16386 Z= 0.197 Angle : 0.656 15.812 22134 Z= 0.339 Chirality : 0.043 0.225 2360 Planarity : 0.003 0.042 2818 Dihedral : 10.695 163.851 2242 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % 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 aren not related in a simple way. whole: 0.68 (0.19), residues: 1932 helix: 0.94 (0.15), residues: 1138 sheet: -0.82 (0.41), residues: 142 loop : 0.11 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 446 TYR 0.026 0.002 TYR A 118 PHE 0.036 0.002 PHE A 129 TRP 0.055 0.002 TRP D 124 HIS 0.008 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00442 (16386) covalent geometry : angle 0.65570 (22134) hydrogen bonds : bond 0.03979 ( 871) hydrogen bonds : angle 4.96526 ( 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 608 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 608 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8981 (t80) cc_final: 0.8349 (t80) REVERT: A 117 ARG cc_start: 0.8279 (mtp85) cc_final: 0.8021 (mtp85) REVERT: A 131 ASN cc_start: 0.9181 (t0) cc_final: 0.8916 (t0) REVERT: A 147 GLN cc_start: 0.8876 (mt0) cc_final: 0.8488 (mt0) REVERT: A 204 SER cc_start: 0.9338 (t) cc_final: 0.9016 (t) REVERT: A 263 ASP cc_start: 0.8320 (m-30) cc_final: 0.8079 (m-30) REVERT: A 286 ASP cc_start: 0.8841 (m-30) cc_final: 0.8260 (m-30) REVERT: A 290 GLU cc_start: 0.8414 (tm-30) cc_final: 0.8127 (tm-30) REVERT: A 315 ASP cc_start: 0.8992 (p0) cc_final: 0.8755 (p0) REVERT: A 362 ASP cc_start: 0.7153 (m-30) cc_final: 0.6430 (m-30) REVERT: A 396 ASP cc_start: 0.7896 (p0) cc_final: 0.6899 (p0) REVERT: A 399 GLU cc_start: 0.7980 (mt-10) cc_final: 0.7767 (mt-10) REVERT: A 479 TYR cc_start: 0.9224 (t80) cc_final: 0.8749 (t80) REVERT: A 493 MET cc_start: 0.8954 (tmm) cc_final: 0.8459 (tmm) REVERT: A 632 MET cc_start: 0.8722 (mtm) cc_final: 0.7970 (mtm) REVERT: A 640 MET cc_start: 0.9085 (ttm) cc_final: 0.8838 (ttm) REVERT: B 8 LYS cc_start: 0.8933 (tptp) cc_final: 0.8596 (tppt) REVERT: B 12 LEU cc_start: 0.9511 (mt) cc_final: 0.9236 (mt) REVERT: B 119 GLU cc_start: 0.8816 (mp0) cc_final: 0.8431 (mp0) REVERT: B 127 LEU cc_start: 0.9497 (mm) cc_final: 0.9269 (mm) REVERT: B 147 GLN cc_start: 0.9044 (mt0) cc_final: 0.8222 (mt0) REVERT: B 157 LEU cc_start: 0.9071 (tp) cc_final: 0.8690 (tp) REVERT: B 158 ASN cc_start: 0.8962 (m110) cc_final: 0.8598 (m-40) REVERT: B 211 GLU cc_start: 0.7711 (mm-30) cc_final: 0.7410 (mm-30) REVERT: B 232 ASN cc_start: 0.7893 (t160) cc_final: 0.7598 (t0) REVERT: B 235 ARG cc_start: 0.8285 (mmm-85) cc_final: 0.7878 (mtt-85) REVERT: B 253 ILE cc_start: 0.9594 (tt) cc_final: 0.9372 (tt) REVERT: B 263 ASP cc_start: 0.9006 (m-30) cc_final: 0.8656 (m-30) REVERT: B 288 PHE cc_start: 0.9412 (t80) cc_final: 0.9007 (t80) REVERT: B 348 MET cc_start: 0.8006 (tpt) cc_final: 0.7264 (tpp) REVERT: B 373 ILE cc_start: 0.9601 (mt) cc_final: 0.9300 (mt) REVERT: B 393 SER cc_start: 0.9418 (m) cc_final: 0.9022 (m) REVERT: B 394 TYR cc_start: 0.9079 (m-80) cc_final: 0.8409 (m-80) REVERT: B 425 ILE cc_start: 0.9607 (mt) cc_final: 0.9285 (mt) REVERT: B 441 GLU cc_start: 0.8650 (mp0) cc_final: 0.8426 (mp0) REVERT: B 493 MET cc_start: 0.9452 (tmm) cc_final: 0.9118 (tmm) REVERT: B 526 GLU cc_start: 0.8095 (tp30) cc_final: 0.7617 (tp30) REVERT: B 550 MET cc_start: 0.8387 (mtp) cc_final: 0.7858 (mtm) REVERT: B 588 GLN cc_start: 0.9212 (mm-40) cc_final: 0.8543 (mm-40) REVERT: B 601 ILE cc_start: 0.9191 (mm) cc_final: 0.8899 (mm) REVERT: B 640 MET cc_start: 0.9183 (tpp) cc_final: 0.8836 (tpp) REVERT: B 644 ILE cc_start: 0.9485 (mp) cc_final: 0.9160 (mp) REVERT: B 667 LEU cc_start: 0.9483 (tp) cc_final: 0.9140 (tp) REVERT: C 21 PHE cc_start: 0.9350 (m-10) cc_final: 0.9138 (m-80) REVERT: C 27 LYS cc_start: 0.9030 (mtmm) cc_final: 0.8658 (tptp) REVERT: C 49 LYS cc_start: 0.9107 (mttp) cc_final: 0.8862 (tmtt) REVERT: C 55 TYR cc_start: 0.7322 (t80) cc_final: 0.6533 (t80) REVERT: C 154 PHE cc_start: 0.8502 (t80) cc_final: 0.8039 (t80) REVERT: C 196 ARG cc_start: 0.8379 (ttp80) cc_final: 0.8120 (ttp80) REVERT: C 243 THR cc_start: 0.7271 (p) cc_final: 0.6821 (t) REVERT: C 313 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8562 (mt-10) REVERT: D 42 LEU cc_start: 0.6038 (pp) cc_final: 0.5640 (pp) REVERT: D 46 TYR cc_start: 0.8767 (m-80) cc_final: 0.8342 (m-80) REVERT: D 95 MET cc_start: 0.9046 (tmm) cc_final: 0.8624 (tmm) REVERT: D 96 MET cc_start: 0.8514 (tpp) cc_final: 0.7631 (mmm) REVERT: D 119 ASN cc_start: 0.9249 (m-40) cc_final: 0.8899 (t0) REVERT: D 149 ASP cc_start: 0.8486 (m-30) cc_final: 0.8217 (m-30) REVERT: D 154 PHE cc_start: 0.8216 (t80) cc_final: 0.7931 (t80) REVERT: D 179 TYR cc_start: 0.8219 (t80) cc_final: 0.7936 (t80) REVERT: D 185 MET cc_start: 0.8162 (mmm) cc_final: 0.6789 (pmm) REVERT: D 192 ASN cc_start: 0.8746 (t0) cc_final: 0.8215 (m110) REVERT: D 195 LEU cc_start: 0.8896 (tt) cc_final: 0.8298 (tt) REVERT: D 205 VAL cc_start: 0.9578 (t) cc_final: 0.9175 (t) REVERT: D 224 LEU cc_start: 0.8950 (mt) cc_final: 0.8701 (mt) REVERT: D 233 ASN cc_start: 0.8657 (m110) cc_final: 0.8419 (m110) REVERT: D 235 LEU cc_start: 0.9170 (mt) cc_final: 0.8847 (pp) REVERT: D 241 GLU cc_start: 0.7709 (tm-30) cc_final: 0.7395 (tm-30) REVERT: D 259 PHE cc_start: 0.7565 (t80) cc_final: 0.7216 (t80) outliers start: 0 outliers final: 0 residues processed: 608 average time/residue: 0.1346 time to fit residues: 122.2801 Evaluate side-chains 483 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 483 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 134 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 158 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 62 GLN A 191 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN ** C 210 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 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.126913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.091889 restraints weight = 38632.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.095107 restraints weight = 19666.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.097319 restraints weight = 11966.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.098853 restraints weight = 8292.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.099691 restraints weight = 6307.724| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.6692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 16386 Z= 0.259 Angle : 0.707 14.680 22134 Z= 0.370 Chirality : 0.045 0.173 2360 Planarity : 0.004 0.064 2818 Dihedral : 10.777 164.011 2242 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 0.06 % Allowed : 1.05 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.19), residues: 1932 helix: 0.77 (0.15), residues: 1128 sheet: -0.72 (0.41), residues: 142 loop : 0.03 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 446 TYR 0.025 0.002 TYR D 142 PHE 0.043 0.002 PHE A 129 TRP 0.059 0.002 TRP D 124 HIS 0.007 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00569 (16386) covalent geometry : angle 0.70656 (22134) hydrogen bonds : bond 0.04102 ( 871) hydrogen bonds : angle 5.14866 ( 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 570 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 569 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.9093 (mp0) cc_final: 0.8759 (mp0) REVERT: A 40 TYR cc_start: 0.8961 (t80) cc_final: 0.8458 (t80) REVERT: A 99 LYS cc_start: 0.8827 (mmtp) cc_final: 0.8522 (mmtp) REVERT: A 117 ARG cc_start: 0.8430 (mtp85) cc_final: 0.8184 (mtp85) REVERT: A 131 ASN cc_start: 0.9146 (t0) cc_final: 0.8873 (t0) REVERT: A 147 GLN cc_start: 0.8904 (mt0) cc_final: 0.8611 (mt0) REVERT: A 204 SER cc_start: 0.9337 (t) cc_final: 0.8919 (t) REVERT: A 236 TYR cc_start: 0.8658 (t80) cc_final: 0.8263 (t80) REVERT: A 263 ASP cc_start: 0.8320 (m-30) cc_final: 0.8029 (m-30) REVERT: A 286 ASP cc_start: 0.8768 (m-30) cc_final: 0.8272 (m-30) REVERT: A 290 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8146 (tm-30) REVERT: A 362 ASP cc_start: 0.7169 (m-30) cc_final: 0.6489 (m-30) REVERT: A 396 ASP cc_start: 0.7940 (p0) cc_final: 0.6978 (p0) REVERT: A 437 THR cc_start: 0.9361 (m) cc_final: 0.9094 (p) REVERT: A 479 TYR cc_start: 0.8991 (t80) cc_final: 0.8635 (t80) REVERT: A 494 MET cc_start: 0.9008 (mtm) cc_final: 0.8228 (mtt) REVERT: A 640 MET cc_start: 0.9144 (ttm) cc_final: 0.8828 (ttm) REVERT: B 71 LEU cc_start: 0.9451 (mm) cc_final: 0.9124 (mp) REVERT: B 119 GLU cc_start: 0.8959 (mp0) cc_final: 0.8580 (mp0) REVERT: B 147 GLN cc_start: 0.8988 (mt0) cc_final: 0.8252 (mt0) REVERT: B 157 LEU cc_start: 0.9124 (tp) cc_final: 0.8776 (tp) REVERT: B 158 ASN cc_start: 0.9005 (m110) cc_final: 0.8665 (m-40) REVERT: B 211 GLU cc_start: 0.7844 (mm-30) cc_final: 0.7534 (mm-30) REVERT: B 217 GLU cc_start: 0.8252 (tm-30) cc_final: 0.8021 (tm-30) REVERT: B 232 ASN cc_start: 0.7979 (t160) cc_final: 0.7549 (t0) REVERT: B 253 ILE cc_start: 0.9572 (tt) cc_final: 0.9323 (tt) REVERT: B 263 ASP cc_start: 0.9006 (m-30) cc_final: 0.8665 (m-30) REVERT: B 288 PHE cc_start: 0.9408 (t80) cc_final: 0.9030 (t80) REVERT: B 348 MET cc_start: 0.7907 (tpt) cc_final: 0.7180 (tpp) REVERT: B 373 ILE cc_start: 0.9651 (mt) cc_final: 0.9323 (mt) REVERT: B 393 SER cc_start: 0.9398 (m) cc_final: 0.8951 (m) REVERT: B 394 TYR cc_start: 0.9072 (m-80) cc_final: 0.8758 (m-80) REVERT: B 425 ILE cc_start: 0.9617 (mt) cc_final: 0.9337 (mt) REVERT: B 441 GLU cc_start: 0.8661 (mp0) cc_final: 0.8448 (mp0) REVERT: B 493 MET cc_start: 0.9453 (tmm) cc_final: 0.9244 (tmm) REVERT: B 509 GLU cc_start: 0.8753 (tt0) cc_final: 0.8529 (tm-30) REVERT: B 526 GLU cc_start: 0.8095 (tp30) cc_final: 0.7625 (tp30) REVERT: B 588 GLN cc_start: 0.9166 (mm-40) cc_final: 0.8500 (mm-40) REVERT: B 595 MET cc_start: 0.8897 (mmm) cc_final: 0.8265 (mmm) REVERT: B 602 GLU cc_start: 0.8220 (pt0) cc_final: 0.7897 (pt0) REVERT: B 615 MET cc_start: 0.9452 (mmp) cc_final: 0.9076 (mmm) REVERT: B 636 LYS cc_start: 0.9635 (mmtm) cc_final: 0.9378 (mmmm) REVERT: B 667 LEU cc_start: 0.9510 (tp) cc_final: 0.9153 (tp) REVERT: B 671 ASP cc_start: 0.8692 (m-30) cc_final: 0.8491 (m-30) REVERT: C 27 LYS cc_start: 0.9022 (mtmm) cc_final: 0.8736 (tptp) REVERT: C 55 TYR cc_start: 0.7317 (t80) cc_final: 0.6492 (t80) REVERT: C 154 PHE cc_start: 0.8539 (t80) cc_final: 0.8151 (t80) REVERT: C 313 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8556 (mt-10) REVERT: D 46 TYR cc_start: 0.8888 (m-80) cc_final: 0.8371 (m-80) REVERT: D 56 MET cc_start: 0.5776 (mpp) cc_final: 0.5455 (mpp) REVERT: D 95 MET cc_start: 0.9175 (tmm) cc_final: 0.8678 (tmm) REVERT: D 96 MET cc_start: 0.8653 (tpp) cc_final: 0.7667 (mmm) REVERT: D 119 ASN cc_start: 0.9360 (m-40) cc_final: 0.9065 (t0) REVERT: D 149 ASP cc_start: 0.8461 (m-30) cc_final: 0.8188 (m-30) REVERT: D 179 TYR cc_start: 0.8186 (t80) cc_final: 0.7863 (t80) REVERT: D 185 MET cc_start: 0.8224 (mmm) cc_final: 0.6805 (pmm) REVERT: D 192 ASN cc_start: 0.8814 (t0) cc_final: 0.8290 (m-40) REVERT: D 195 LEU cc_start: 0.8715 (tt) cc_final: 0.8490 (tt) REVERT: D 205 VAL cc_start: 0.9420 (t) cc_final: 0.9125 (t) REVERT: D 214 ASN cc_start: 0.9320 (m-40) cc_final: 0.9116 (m-40) REVERT: D 233 ASN cc_start: 0.8735 (m110) cc_final: 0.8524 (m110) REVERT: D 235 LEU cc_start: 0.9256 (mt) cc_final: 0.8865 (pp) REVERT: D 259 PHE cc_start: 0.7546 (t80) cc_final: 0.7109 (t80) outliers start: 1 outliers final: 1 residues processed: 569 average time/residue: 0.1377 time to fit residues: 117.3646 Evaluate side-chains 482 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 481 time to evaluate : 0.626 ------------------------------------------------------------------------------- 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: 1.9990 chunk 133 optimal weight: 0.8980 chunk 149 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 86 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN B 232 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 GLN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** 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 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.133099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.097886 restraints weight = 37355.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.101342 restraints weight = 18846.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.103588 restraints weight = 11401.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.105078 restraints weight = 7840.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.106020 restraints weight = 5888.136| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.6876 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= 0.138 Angle : 0.661 14.892 22134 Z= 0.341 Chirality : 0.043 0.278 2360 Planarity : 0.003 0.040 2818 Dihedral : 10.431 156.397 2242 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.59 (0.19), residues: 1932 helix: 0.88 (0.15), residues: 1125 sheet: -0.85 (0.40), residues: 138 loop : 0.04 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 446 TYR 0.032 0.001 TYR A 118 PHE 0.037 0.002 PHE A 129 TRP 0.061 0.002 TRP D 124 HIS 0.008 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00308 (16386) covalent geometry : angle 0.66141 (22134) hydrogen bonds : bond 0.03949 ( 871) hydrogen bonds : angle 4.98363 ( 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 622 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 622 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8968 (mp0) cc_final: 0.8628 (mp0) REVERT: A 40 TYR cc_start: 0.8960 (t80) cc_final: 0.8480 (t80) REVERT: A 117 ARG cc_start: 0.8247 (mtp85) cc_final: 0.8036 (mtp85) REVERT: A 131 ASN cc_start: 0.9100 (t0) cc_final: 0.8840 (t0) REVERT: A 147 GLN cc_start: 0.8724 (mt0) cc_final: 0.8379 (mt0) REVERT: A 188 ILE cc_start: 0.9440 (mm) cc_final: 0.9133 (mm) REVERT: A 204 SER cc_start: 0.9294 (t) cc_final: 0.8985 (t) REVERT: A 217 GLU cc_start: 0.8871 (tp30) cc_final: 0.8629 (tp30) REVERT: A 218 ASN cc_start: 0.9210 (m-40) cc_final: 0.9010 (m-40) REVERT: A 274 ARG cc_start: 0.8134 (ttm110) cc_final: 0.7740 (ptp-110) REVERT: A 286 ASP cc_start: 0.8669 (m-30) cc_final: 0.8312 (m-30) REVERT: A 290 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7988 (tm-30) REVERT: A 360 PHE cc_start: 0.8657 (m-80) cc_final: 0.8141 (m-80) REVERT: A 361 GLN cc_start: 0.8146 (tp40) cc_final: 0.7639 (tp-100) REVERT: A 362 ASP cc_start: 0.6962 (m-30) cc_final: 0.6246 (m-30) REVERT: A 365 ASN cc_start: 0.8471 (m110) cc_final: 0.7721 (m110) REVERT: A 479 TYR cc_start: 0.8871 (t80) cc_final: 0.8266 (t80) REVERT: A 493 MET cc_start: 0.8944 (tmm) cc_final: 0.8710 (tmm) REVERT: A 494 MET cc_start: 0.9008 (mtm) cc_final: 0.8263 (mtp) REVERT: A 640 MET cc_start: 0.9074 (ttm) cc_final: 0.8646 (ttm) REVERT: B 8 LYS cc_start: 0.8966 (tptp) cc_final: 0.8608 (tppt) REVERT: B 12 LEU cc_start: 0.9526 (mt) cc_final: 0.9235 (mt) REVERT: B 95 MET cc_start: 0.9090 (tpp) cc_final: 0.8824 (mmm) REVERT: B 98 PHE cc_start: 0.9398 (t80) cc_final: 0.9046 (t80) REVERT: B 119 GLU cc_start: 0.8774 (mp0) cc_final: 0.8467 (mp0) REVERT: B 127 LEU cc_start: 0.9512 (mm) cc_final: 0.9212 (mm) REVERT: B 140 TYR cc_start: 0.9196 (m-10) cc_final: 0.8930 (m-10) REVERT: B 147 GLN cc_start: 0.8923 (mt0) cc_final: 0.7908 (mt0) REVERT: B 157 LEU cc_start: 0.9020 (tp) cc_final: 0.8654 (tp) REVERT: B 158 ASN cc_start: 0.8961 (m110) cc_final: 0.8578 (m-40) REVERT: B 211 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7391 (mm-30) REVERT: B 263 ASP cc_start: 0.8992 (m-30) cc_final: 0.8487 (m-30) REVERT: B 288 PHE cc_start: 0.9332 (t80) cc_final: 0.9018 (t80) REVERT: B 348 MET cc_start: 0.7968 (tpt) cc_final: 0.7240 (tpp) REVERT: B 375 LYS cc_start: 0.8816 (mttm) cc_final: 0.8616 (mttm) REVERT: B 381 LEU cc_start: 0.8792 (tp) cc_final: 0.8512 (tp) REVERT: B 393 SER cc_start: 0.9371 (m) cc_final: 0.9076 (m) REVERT: B 394 TYR cc_start: 0.9038 (m-80) cc_final: 0.8355 (m-80) REVERT: B 425 ILE cc_start: 0.9604 (mt) cc_final: 0.9389 (mt) REVERT: B 493 MET cc_start: 0.9424 (tmm) cc_final: 0.9025 (tmm) REVERT: B 526 GLU cc_start: 0.7896 (tp30) cc_final: 0.7317 (tp30) REVERT: B 585 SER cc_start: 0.9236 (p) cc_final: 0.8909 (t) REVERT: B 588 GLN cc_start: 0.9146 (mm-40) cc_final: 0.8233 (mm-40) REVERT: B 595 MET cc_start: 0.8840 (mmm) cc_final: 0.8175 (mmm) REVERT: B 601 ILE cc_start: 0.8953 (mm) cc_final: 0.8536 (mm) REVERT: B 602 GLU cc_start: 0.8097 (pt0) cc_final: 0.7870 (pt0) REVERT: B 615 MET cc_start: 0.9459 (mmp) cc_final: 0.9065 (mmm) REVERT: B 667 LEU cc_start: 0.9480 (tp) cc_final: 0.9153 (tp) REVERT: C 27 LYS cc_start: 0.8982 (mtmm) cc_final: 0.8726 (tptp) REVERT: C 55 TYR cc_start: 0.7250 (t80) cc_final: 0.6476 (t80) REVERT: C 154 PHE cc_start: 0.8453 (t80) cc_final: 0.8017 (t80) REVERT: D 56 MET cc_start: 0.5951 (mpp) cc_final: 0.5727 (mpp) REVERT: D 95 MET cc_start: 0.9093 (tmm) cc_final: 0.8747 (tmm) REVERT: D 96 MET cc_start: 0.8575 (tpp) cc_final: 0.7570 (mmt) REVERT: D 119 ASN cc_start: 0.9296 (m-40) cc_final: 0.8938 (t0) REVERT: D 149 ASP cc_start: 0.8440 (m-30) cc_final: 0.8212 (m-30) REVERT: D 192 ASN cc_start: 0.8736 (t0) cc_final: 0.8258 (m-40) REVERT: D 196 ARG cc_start: 0.8341 (tpm170) cc_final: 0.8087 (tpm170) REVERT: D 214 ASN cc_start: 0.9304 (m-40) cc_final: 0.9098 (m-40) REVERT: D 224 LEU cc_start: 0.8950 (mt) cc_final: 0.8682 (mt) REVERT: D 233 ASN cc_start: 0.8708 (m110) cc_final: 0.8447 (m110) REVERT: D 241 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7182 (tm-30) REVERT: D 259 PHE cc_start: 0.7724 (t80) cc_final: 0.7378 (t80) outliers start: 0 outliers final: 0 residues processed: 622 average time/residue: 0.1307 time to fit residues: 122.2996 Evaluate side-chains 500 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 500 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 165 optimal weight: 0.0770 chunk 16 optimal weight: 6.9990 chunk 54 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS A 447 ASN B 232 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 GLN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.131865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.097260 restraints weight = 37511.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.100637 restraints weight = 18976.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.102791 restraints weight = 11493.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.104330 restraints weight = 7992.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.105159 restraints weight = 6009.898| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.7042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16386 Z= 0.158 Angle : 0.674 13.642 22134 Z= 0.348 Chirality : 0.044 0.320 2360 Planarity : 0.004 0.040 2818 Dihedral : 10.365 156.039 2242 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.06 % Allowed : 0.23 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.19), residues: 1932 helix: 0.84 (0.15), residues: 1137 sheet: -0.41 (0.43), residues: 122 loop : -0.16 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 446 TYR 0.030 0.001 TYR A 522 PHE 0.033 0.002 PHE C 21 TRP 0.061 0.002 TRP D 124 HIS 0.010 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00357 (16386) covalent geometry : angle 0.67439 (22134) hydrogen bonds : bond 0.03925 ( 871) hydrogen bonds : angle 4.97987 ( 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 591 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 590 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.8992 (mp0) cc_final: 0.8600 (mp0) REVERT: A 40 TYR cc_start: 0.8974 (t80) cc_final: 0.8477 (t80) REVERT: A 99 LYS cc_start: 0.8702 (mmtp) cc_final: 0.8490 (mttt) REVERT: A 101 TYR cc_start: 0.9248 (m-10) cc_final: 0.8936 (m-10) REVERT: A 131 ASN cc_start: 0.9162 (t0) cc_final: 0.8906 (t0) REVERT: A 147 GLN cc_start: 0.8777 (mt0) cc_final: 0.8465 (mt0) REVERT: A 188 ILE cc_start: 0.9446 (mm) cc_final: 0.9203 (mm) REVERT: A 204 SER cc_start: 0.9351 (t) cc_final: 0.8914 (t) REVERT: A 217 GLU cc_start: 0.8890 (tp30) cc_final: 0.8642 (tp30) REVERT: A 218 ASN cc_start: 0.9199 (m-40) cc_final: 0.8996 (m-40) REVERT: A 286 ASP cc_start: 0.8776 (m-30) cc_final: 0.8342 (m-30) REVERT: A 290 GLU cc_start: 0.8398 (tm-30) cc_final: 0.8055 (tm-30) REVERT: A 360 PHE cc_start: 0.8677 (m-80) cc_final: 0.8203 (m-80) REVERT: A 361 GLN cc_start: 0.8282 (tp40) cc_final: 0.7824 (tp-100) REVERT: A 362 ASP cc_start: 0.6893 (m-30) cc_final: 0.6213 (m-30) REVERT: A 365 ASN cc_start: 0.8340 (m110) cc_final: 0.7653 (m110) REVERT: A 493 MET cc_start: 0.8934 (tmm) cc_final: 0.8667 (tmm) REVERT: A 494 MET cc_start: 0.8969 (mtm) cc_final: 0.8248 (mtp) REVERT: A 640 MET cc_start: 0.9030 (ttm) cc_final: 0.8715 (ttm) REVERT: B 98 PHE cc_start: 0.9324 (t80) cc_final: 0.8982 (t80) REVERT: B 119 GLU cc_start: 0.8835 (mp0) cc_final: 0.8509 (mp0) REVERT: B 140 TYR cc_start: 0.9211 (m-10) cc_final: 0.8992 (m-10) REVERT: B 147 GLN cc_start: 0.8947 (mt0) cc_final: 0.7959 (mt0) REVERT: B 211 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7450 (mm-30) REVERT: B 217 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7919 (tm-30) REVERT: B 235 ARG cc_start: 0.8128 (mmm-85) cc_final: 0.7911 (mmm-85) REVERT: B 253 ILE cc_start: 0.9518 (tt) cc_final: 0.9292 (tt) REVERT: B 259 ASN cc_start: 0.9106 (m-40) cc_final: 0.8626 (m-40) REVERT: B 263 ASP cc_start: 0.8885 (m-30) cc_final: 0.8455 (m-30) REVERT: B 288 PHE cc_start: 0.9229 (t80) cc_final: 0.8983 (t80) REVERT: B 348 MET cc_start: 0.7995 (tpt) cc_final: 0.7304 (tpp) REVERT: B 379 SER cc_start: 0.8595 (t) cc_final: 0.8127 (t) REVERT: B 393 SER cc_start: 0.9408 (m) cc_final: 0.8988 (m) REVERT: B 394 TYR cc_start: 0.9068 (m-80) cc_final: 0.8374 (m-80) REVERT: B 410 ASN cc_start: 0.8906 (m-40) cc_final: 0.8659 (m-40) REVERT: B 425 ILE cc_start: 0.9602 (mt) cc_final: 0.9309 (mt) REVERT: B 493 MET cc_start: 0.9426 (tmm) cc_final: 0.9209 (tmm) REVERT: B 526 GLU cc_start: 0.7908 (tp30) cc_final: 0.7325 (tp30) REVERT: B 585 SER cc_start: 0.9208 (p) cc_final: 0.8903 (t) REVERT: B 588 GLN cc_start: 0.9176 (mm-40) cc_final: 0.8275 (mm-40) REVERT: B 595 MET cc_start: 0.8856 (mmm) cc_final: 0.8190 (mmm) REVERT: B 601 ILE cc_start: 0.8952 (mm) cc_final: 0.8633 (mm) REVERT: B 602 GLU cc_start: 0.8092 (pt0) cc_final: 0.7847 (pt0) REVERT: B 615 MET cc_start: 0.9435 (mmp) cc_final: 0.9041 (mmm) REVERT: B 667 LEU cc_start: 0.9498 (tp) cc_final: 0.9149 (tp) REVERT: C 27 LYS cc_start: 0.8982 (mtmm) cc_final: 0.8741 (tptp) REVERT: C 55 TYR cc_start: 0.7193 (t80) cc_final: 0.6371 (t80) REVERT: C 66 ASP cc_start: 0.5502 (m-30) cc_final: 0.5248 (m-30) REVERT: C 103 LYS cc_start: 0.7180 (tppt) cc_final: 0.6863 (tppt) REVERT: C 154 PHE cc_start: 0.8443 (t80) cc_final: 0.8022 (t80) REVERT: D 56 MET cc_start: 0.5993 (mpp) cc_final: 0.5665 (mpp) REVERT: D 76 ILE cc_start: 0.8856 (mt) cc_final: 0.8630 (pt) REVERT: D 87 LYS cc_start: 0.7922 (mmtt) cc_final: 0.7487 (mmtt) REVERT: D 95 MET cc_start: 0.9095 (tmm) cc_final: 0.8638 (tmm) REVERT: D 96 MET cc_start: 0.8510 (tpp) cc_final: 0.7459 (mmt) REVERT: D 149 ASP cc_start: 0.8320 (m-30) cc_final: 0.8066 (m-30) REVERT: D 189 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7456 (pt0) REVERT: D 190 ILE cc_start: 0.8322 (mt) cc_final: 0.7987 (mt) REVERT: D 192 ASN cc_start: 0.8771 (t0) cc_final: 0.8286 (m-40) REVERT: D 205 VAL cc_start: 0.9402 (t) cc_final: 0.9166 (t) REVERT: D 214 ASN cc_start: 0.9282 (m-40) cc_final: 0.9061 (m-40) REVERT: D 233 ASN cc_start: 0.8713 (m110) cc_final: 0.8483 (m110) REVERT: D 235 LEU cc_start: 0.9063 (mt) cc_final: 0.8808 (pp) REVERT: D 241 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7176 (tm-30) REVERT: D 259 PHE cc_start: 0.7725 (t80) cc_final: 0.7410 (t80) outliers start: 1 outliers final: 0 residues processed: 591 average time/residue: 0.1299 time to fit residues: 115.1653 Evaluate side-chains 487 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 487 time to evaluate : 0.654 ------------------------------------------------------------------------------- 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: 9.9990 chunk 1 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 148 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 28 optimal weight: 0.0980 chunk 34 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS A 447 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN B 232 ASN B 370 ASN B 467 ASN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 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 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.132912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.098873 restraints weight = 37400.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.102078 restraints weight = 19423.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.104154 restraints weight = 11937.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.105699 restraints weight = 8343.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.106535 restraints weight = 6309.979| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.7185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16386 Z= 0.152 Angle : 0.674 13.640 22134 Z= 0.349 Chirality : 0.044 0.275 2360 Planarity : 0.003 0.040 2818 Dihedral : 10.273 154.327 2242 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % 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 aren not related in a simple way. whole: 0.51 (0.19), residues: 1932 helix: 0.85 (0.15), residues: 1136 sheet: -0.55 (0.42), residues: 118 loop : -0.20 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 446 TYR 0.030 0.001 TYR A 522 PHE 0.035 0.002 PHE C 21 TRP 0.062 0.002 TRP D 124 HIS 0.008 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00344 (16386) covalent geometry : angle 0.67382 (22134) hydrogen bonds : bond 0.03934 ( 871) hydrogen bonds : angle 4.99924 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3315.98 seconds wall clock time: 58 minutes 26.95 seconds (3506.95 seconds total)