Starting phenix.real_space_refine on Sun Aug 24 01:10:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzd_45064/08_2025/9bzd_45064_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzd_45064/08_2025/9bzd_45064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bzd_45064/08_2025/9bzd_45064_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzd_45064/08_2025/9bzd_45064_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bzd_45064/08_2025/9bzd_45064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzd_45064/08_2025/9bzd_45064.map" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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: 3.98, per 1000 atoms: 0.25 Number of scatterers: 16038 At special positions: 0 Unit cell: (93.288, 128.778, 129.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 668.6 milliseconds Enol-peptide restraints added in 953.7 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: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.984A 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: 3.953A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.664A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.128A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.694A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.850A 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: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.677A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.878A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A 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: 3.544A 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: 4.934A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.668A 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: 6.359A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A 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: 6.716A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.478A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.185A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.063A 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: 7.906A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.72 Time building geometry restraints manager: 1.91 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: 4892 1.34 - 1.46: 3091 1.46 - 1.58: 8222 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.060 1.25e-02 6.40e+03 2.34e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.579 -0.039 1.20e-02 6.94e+03 1.07e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.033 1.08e-02 8.57e+03 9.08e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.568 -0.031 1.17e-02 7.31e+03 7.11e+00 bond pdb=" CA ILE C 35 " pdb=" CB ILE C 35 " ideal model delta sigma weight residual 1.537 1.568 -0.031 1.21e-02 6.83e+03 6.69e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 21579 2.10 - 4.19: 513 4.19 - 6.29: 37 6.29 - 8.38: 1 8.38 - 10.48: 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 110.54 116.60 -6.06 1.36e+00 5.41e-01 1.99e+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 111.28 115.22 -3.94 1.09e+00 8.42e-01 1.31e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.82 -4.32 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 111.71 115.73 -4.02 1.15e+00 7.56e-01 1.22e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 9470 35.80 - 71.60: 337 71.60 - 107.40: 37 107.40 - 143.20: 3 143.20 - 178.99: 3 Dihedral angle restraints: 9850 sinusoidal: 4092 harmonic: 5758 Sorted by residual: dihedral pdb=" C2 TTP A 803 " pdb=" C1' TTP A 803 " pdb=" N1 TTP A 803 " pdb=" O4' TTP A 803 " ideal model delta sinusoidal sigma weight residual -58.32 120.68 -178.99 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual 301.68 151.21 150.47 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 31.93 148.04 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: 2147 0.093 - 0.187: 180 0.187 - 0.280: 28 0.280 - 0.373: 3 0.373 - 0.467: 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 5.44e+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 4.58e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.017 2.00e-02 2.50e+03 1.10e-02 2.13e+00 pdb=" CG PHE D 92 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.009 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 1.01e-02 2.04e+00 pdb=" CG TYR C 169 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " -0.003 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: 131 2.51 - 3.11: 11547 3.11 - 3.70: 27037 3.70 - 4.30: 41565 4.30 - 4.90: 65447 Nonbonded interactions: 145727 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.911 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.962 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.012 3.040 ... (remaining 145722 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.560 Find NCS groups from input model: 0.300 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 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= 0.316 Angle : 0.740 10.479 22134 Z= 0.463 Chirality : 0.058 0.467 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.948 178.994 6154 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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: 0.57 (0.18), residues: 1932 helix: 0.59 (0.14), residues: 1149 sheet: 0.46 (0.42), residues: 124 loop : 0.24 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 196 TYR 0.021 0.002 TYR D 179 PHE 0.021 0.002 PHE C 168 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 0.74031 (22134) hydrogen bonds : bond 0.15424 ( 871) hydrogen bonds : angle 6.51733 ( 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 1098 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 1075 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLN cc_start: 0.8048 (mt0) cc_final: 0.7539 (mt0) REVERT: A 12 LEU cc_start: 0.7978 (mt) cc_final: 0.7773 (mp) REVERT: A 28 LYS cc_start: 0.8502 (mmtm) cc_final: 0.8297 (tppp) REVERT: A 76 ASP cc_start: 0.7984 (m-30) cc_final: 0.7351 (m-30) REVERT: A 127 LEU cc_start: 0.8536 (mt) cc_final: 0.8223 (mt) REVERT: A 179 LEU cc_start: 0.8732 (tp) cc_final: 0.8515 (tp) REVERT: A 181 ASP cc_start: 0.7596 (m-30) cc_final: 0.7212 (m-30) REVERT: A 204 SER cc_start: 0.8470 (m) cc_final: 0.8039 (t) REVERT: A 265 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8590 (mmmt) REVERT: A 280 ILE cc_start: 0.8960 (pt) cc_final: 0.8670 (pt) REVERT: A 348 MET cc_start: 0.7366 (tmm) cc_final: 0.6798 (tmm) REVERT: A 352 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6376 (mt-10) REVERT: A 362 ASP cc_start: 0.5957 (m-30) cc_final: 0.5559 (m-30) REVERT: A 598 MET cc_start: 0.7520 (mtm) cc_final: 0.6916 (mtp) REVERT: A 604 ARG cc_start: 0.7657 (mmp80) cc_final: 0.6307 (mmt90) REVERT: A 606 TYR cc_start: 0.6419 (m-80) cc_final: 0.5936 (m-80) REVERT: A 645 GLN cc_start: 0.8195 (tp40) cc_final: 0.7666 (tp40) REVERT: B 11 GLN cc_start: 0.7881 (mt0) cc_final: 0.7483 (mt0) REVERT: B 12 LEU cc_start: 0.8243 (mt) cc_final: 0.7942 (mt) REVERT: B 33 VAL cc_start: 0.9342 (OUTLIER) cc_final: 0.9138 (t) REVERT: B 109 ASN cc_start: 0.8024 (m-40) cc_final: 0.7577 (p0) REVERT: B 121 ARG cc_start: 0.8401 (tpm170) cc_final: 0.7984 (tpp-160) REVERT: B 187 ASP cc_start: 0.6443 (t70) cc_final: 0.6238 (t0) REVERT: B 286 ASP cc_start: 0.6756 (OUTLIER) cc_final: 0.6118 (m-30) REVERT: B 295 ASP cc_start: 0.8038 (t0) cc_final: 0.7783 (t0) REVERT: B 348 MET cc_start: 0.6874 (tmm) cc_final: 0.6617 (ttp) REVERT: B 350 ARG cc_start: 0.7566 (mtp85) cc_final: 0.7299 (mtp85) REVERT: B 362 ASP cc_start: 0.6613 (m-30) cc_final: 0.6351 (m-30) REVERT: B 366 LYS cc_start: 0.8398 (ptpp) cc_final: 0.8183 (ttmt) REVERT: B 381 LEU cc_start: 0.8713 (tp) cc_final: 0.8398 (tp) REVERT: B 458 MET cc_start: 0.8485 (mmm) cc_final: 0.8224 (mmm) REVERT: B 460 SER cc_start: 0.8996 (t) cc_final: 0.8648 (p) REVERT: B 471 TYR cc_start: 0.8414 (t80) cc_final: 0.7955 (t80) REVERT: B 485 ARG cc_start: 0.7856 (mtm-85) cc_final: 0.7314 (mtm-85) REVERT: B 493 MET cc_start: 0.8356 (tmm) cc_final: 0.8147 (tmm) REVERT: B 496 ASN cc_start: 0.8372 (t0) cc_final: 0.8076 (t0) REVERT: B 500 ILE cc_start: 0.8730 (mt) cc_final: 0.8327 (mt) REVERT: B 546 LEU cc_start: 0.9032 (mt) cc_final: 0.8740 (mt) REVERT: B 550 MET cc_start: 0.7893 (mtm) cc_final: 0.7345 (mtm) REVERT: B 601 ILE cc_start: 0.8458 (mt) cc_final: 0.8138 (mt) REVERT: B 604 ARG cc_start: 0.7109 (mmp80) cc_final: 0.6767 (tpp80) REVERT: B 612 TYR cc_start: 0.7795 (m-80) cc_final: 0.7493 (m-80) REVERT: B 664 THR cc_start: 0.8952 (p) cc_final: 0.8745 (p) REVERT: C 106 SER cc_start: 0.7759 (m) cc_final: 0.6432 (m) REVERT: C 212 ILE cc_start: 0.6000 (mt) cc_final: 0.5753 (mt) REVERT: D 178 PHE cc_start: 0.5471 (m-80) cc_final: 0.5088 (m-80) REVERT: D 193 LEU cc_start: 0.7895 (mt) cc_final: 0.7624 (mt) REVERT: D 260 ILE cc_start: 0.7126 (mt) cc_final: 0.6763 (mt) REVERT: D 315 LEU cc_start: 0.7098 (mt) cc_final: 0.6817 (mt) outliers start: 23 outliers final: 7 residues processed: 1082 average time/residue: 0.1464 time to fit residues: 227.5293 Evaluate side-chains 725 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 716 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.0370 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 25 GLN B 320 ASN B 329 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN B 467 ASN B 474 GLN B 501 GLN B 676 HIS C 24 GLN C 28 GLN C 80 HIS C 85 GLN C 107 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN C 270 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 80 HIS D 91 ASN D 128 ASN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.132053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.097667 restraints weight = 33293.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.101071 restraints weight = 15965.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.103450 restraints weight = 9742.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.104772 restraints weight = 6878.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.105834 restraints weight = 5310.277| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3230 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3230 r_free = 0.3230 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16386 Z= 0.159 Angle : 0.720 15.022 22134 Z= 0.373 Chirality : 0.046 0.190 2360 Planarity : 0.004 0.039 2818 Dihedral : 11.495 179.488 2257 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.67 % Allowed : 21.62 % Favored : 74.71 % 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: 1.34 (0.18), residues: 1932 helix: 1.33 (0.15), residues: 1129 sheet: 1.07 (0.48), residues: 100 loop : 0.29 (0.23), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 243 TYR 0.021 0.002 TYR B 72 PHE 0.032 0.002 PHE D 172 TRP 0.025 0.003 TRP D 30 HIS 0.009 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00352 (16386) covalent geometry : angle 0.71995 (22134) hydrogen bonds : bond 0.04871 ( 871) hydrogen bonds : angle 5.15087 ( 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 852 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 789 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8480 (mm-30) cc_final: 0.8219 (mm-30) REVERT: A 66 GLU cc_start: 0.8509 (tp30) cc_final: 0.8306 (tp30) REVERT: A 144 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.8781 (mtm) REVERT: A 181 ASP cc_start: 0.8722 (m-30) cc_final: 0.8385 (m-30) REVERT: A 218 ASN cc_start: 0.9018 (t0) cc_final: 0.8754 (t0) REVERT: A 221 LYS cc_start: 0.8855 (mmtp) cc_final: 0.8624 (mttp) REVERT: A 243 ARG cc_start: 0.7620 (ttp80) cc_final: 0.7322 (tmm-80) REVERT: A 274 ARG cc_start: 0.8184 (ttp80) cc_final: 0.7386 (mtm-85) REVERT: A 322 MET cc_start: 0.8762 (mmm) cc_final: 0.8303 (mmm) REVERT: A 335 GLU cc_start: 0.8787 (mm-30) cc_final: 0.8543 (mm-30) REVERT: A 348 MET cc_start: 0.8073 (OUTLIER) cc_final: 0.7217 (tmm) REVERT: A 352 GLU cc_start: 0.7855 (mt-10) cc_final: 0.6911 (mt-10) REVERT: A 384 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7818 (pm20) REVERT: A 415 ASN cc_start: 0.9407 (t0) cc_final: 0.9130 (t0) REVERT: A 420 MET cc_start: 0.9308 (mmm) cc_final: 0.8934 (mmm) REVERT: A 444 ASP cc_start: 0.8614 (t70) cc_final: 0.8387 (t70) REVERT: A 492 PHE cc_start: 0.9159 (m-80) cc_final: 0.8934 (m-10) REVERT: A 493 MET cc_start: 0.8980 (tmm) cc_final: 0.8591 (tmm) REVERT: A 505 GLU cc_start: 0.9111 (mt-10) cc_final: 0.8577 (mt-10) REVERT: A 528 PHE cc_start: 0.8962 (m-80) cc_final: 0.8647 (m-80) REVERT: A 586 TYR cc_start: 0.8607 (m-80) cc_final: 0.8389 (m-10) REVERT: A 598 MET cc_start: 0.8676 (mtm) cc_final: 0.8271 (mtp) REVERT: A 602 GLU cc_start: 0.7754 (pt0) cc_final: 0.7422 (pt0) REVERT: A 640 MET cc_start: 0.9476 (tpp) cc_final: 0.9230 (tpp) REVERT: A 686 ARG cc_start: 0.8446 (mmm-85) cc_final: 0.8052 (mmm-85) REVERT: B 18 ILE cc_start: 0.9520 (mm) cc_final: 0.9291 (pt) REVERT: B 20 LYS cc_start: 0.9518 (OUTLIER) cc_final: 0.9165 (mmmm) REVERT: B 41 ILE cc_start: 0.9528 (mm) cc_final: 0.9282 (mm) REVERT: B 65 GLU cc_start: 0.8718 (mm-30) cc_final: 0.8046 (mp0) REVERT: B 99 LYS cc_start: 0.9530 (mmmm) cc_final: 0.9289 (mmmm) REVERT: B 106 LEU cc_start: 0.9201 (tp) cc_final: 0.8788 (tt) REVERT: B 109 ASN cc_start: 0.9042 (m-40) cc_final: 0.8355 (p0) REVERT: B 147 GLN cc_start: 0.8752 (mt0) cc_final: 0.8275 (mm110) REVERT: B 184 ARG cc_start: 0.9222 (mmm-85) cc_final: 0.8946 (tpp80) REVERT: B 246 SER cc_start: 0.7669 (m) cc_final: 0.7433 (p) REVERT: B 257 ASP cc_start: 0.8779 (m-30) cc_final: 0.8400 (m-30) REVERT: B 286 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7296 (m-30) REVERT: B 288 PHE cc_start: 0.9387 (t80) cc_final: 0.9132 (t80) REVERT: B 290 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8443 (tm-30) REVERT: B 312 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8588 (pm20) REVERT: B 317 MET cc_start: 0.8486 (ptp) cc_final: 0.8021 (pmm) REVERT: B 321 GLU cc_start: 0.8604 (tm-30) cc_final: 0.8313 (tm-30) REVERT: B 322 MET cc_start: 0.9280 (mmm) cc_final: 0.8905 (mmm) REVERT: B 348 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8141 (tmm) REVERT: B 362 ASP cc_start: 0.8545 (m-30) cc_final: 0.7360 (m-30) REVERT: B 374 SER cc_start: 0.8890 (t) cc_final: 0.8496 (t) REVERT: B 408 SER cc_start: 0.9385 (OUTLIER) cc_final: 0.9170 (p) REVERT: B 447 ASN cc_start: 0.8507 (m-40) cc_final: 0.7890 (t0) REVERT: B 471 TYR cc_start: 0.9423 (t80) cc_final: 0.9192 (t80) REVERT: B 477 ILE cc_start: 0.9321 (mp) cc_final: 0.9088 (pt) REVERT: B 492 PHE cc_start: 0.9492 (m-80) cc_final: 0.9044 (m-10) REVERT: B 493 MET cc_start: 0.9675 (tmm) cc_final: 0.9077 (tmm) REVERT: B 515 ASP cc_start: 0.9130 (m-30) cc_final: 0.8684 (m-30) REVERT: B 610 LYS cc_start: 0.8727 (mmmt) cc_final: 0.8452 (mmmt) REVERT: B 612 TYR cc_start: 0.8788 (m-80) cc_final: 0.8323 (m-80) REVERT: B 640 MET cc_start: 0.9311 (tpp) cc_final: 0.9041 (tpp) REVERT: B 664 THR cc_start: 0.9336 (p) cc_final: 0.9030 (p) REVERT: B 668 ASN cc_start: 0.9222 (m-40) cc_final: 0.8863 (m110) REVERT: C 41 LEU cc_start: 0.8450 (mm) cc_final: 0.8211 (mm) REVERT: C 47 LEU cc_start: 0.8088 (mt) cc_final: 0.7697 (tp) REVERT: C 55 TYR cc_start: 0.8199 (t80) cc_final: 0.7377 (t80) REVERT: C 56 MET cc_start: 0.5838 (ttt) cc_final: 0.5633 (ttt) REVERT: C 96 MET cc_start: 0.8905 (mmt) cc_final: 0.8460 (mmm) REVERT: C 97 GLU cc_start: 0.6732 (mm-30) cc_final: 0.5588 (mm-30) REVERT: C 111 THR cc_start: 0.7990 (m) cc_final: 0.7777 (p) REVERT: C 164 GLU cc_start: 0.9220 (mm-30) cc_final: 0.8711 (mm-30) REVERT: C 178 PHE cc_start: 0.8947 (m-80) cc_final: 0.7675 (m-80) REVERT: C 185 MET cc_start: 0.8214 (pmm) cc_final: 0.6843 (pmm) REVERT: C 186 GLN cc_start: 0.9441 (mm110) cc_final: 0.8959 (mp10) REVERT: C 198 GLU cc_start: 0.9305 (mm-30) cc_final: 0.8977 (mm-30) REVERT: C 259 PHE cc_start: 0.8922 (t80) cc_final: 0.8677 (t80) REVERT: C 261 ARG cc_start: 0.8868 (mtm-85) cc_final: 0.8524 (ptt180) REVERT: C 270 ASN cc_start: 0.7895 (m110) cc_final: 0.7518 (m110) REVERT: C 320 PHE cc_start: 0.8830 (m-80) cc_final: 0.8624 (m-10) REVERT: D 21 PHE cc_start: 0.9447 (m-80) cc_final: 0.9230 (m-80) REVERT: D 30 TRP cc_start: 0.8629 (p-90) cc_final: 0.7556 (p-90) REVERT: D 46 TYR cc_start: 0.9144 (m-80) cc_final: 0.8821 (m-80) REVERT: D 96 MET cc_start: 0.8425 (mmt) cc_final: 0.8108 (mmt) REVERT: D 178 PHE cc_start: 0.8941 (m-10) cc_final: 0.8079 (m-80) REVERT: D 186 GLN cc_start: 0.8955 (mm-40) cc_final: 0.8587 (mp10) REVERT: D 200 ILE cc_start: 0.8032 (tt) cc_final: 0.7577 (tt) REVERT: D 207 LEU cc_start: 0.9274 (mp) cc_final: 0.9059 (mp) REVERT: D 212 ILE cc_start: 0.9094 (mt) cc_final: 0.8745 (mt) REVERT: D 227 PHE cc_start: 0.8263 (t80) cc_final: 0.7951 (m-80) outliers start: 63 outliers final: 29 residues processed: 814 average time/residue: 0.1222 time to fit residues: 150.0442 Evaluate side-chains 744 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 707 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 6.9990 chunk 131 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 182 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 158 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 19 GLN B 232 ASN B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN B 410 ASN B 467 ASN B 668 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.122038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.085826 restraints weight = 36516.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.089311 restraints weight = 17150.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.091666 restraints weight = 10161.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.093173 restraints weight = 6949.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.094120 restraints weight = 5303.506| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16386 Z= 0.213 Angle : 0.708 14.539 22134 Z= 0.368 Chirality : 0.046 0.240 2360 Planarity : 0.004 0.045 2818 Dihedral : 11.172 171.545 2249 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.25 % Allowed : 25.52 % Favored : 70.22 % 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: 1.18 (0.19), residues: 1932 helix: 1.24 (0.15), residues: 1139 sheet: 0.05 (0.42), residues: 136 loop : 0.33 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 243 TYR 0.026 0.002 TYR A 612 PHE 0.048 0.002 PHE C 168 TRP 0.015 0.002 TRP B 558 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00471 (16386) covalent geometry : angle 0.70782 (22134) hydrogen bonds : bond 0.04447 ( 871) hydrogen bonds : angle 5.12212 ( 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 811 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 738 time to evaluate : 0.645 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 64 TYR cc_start: 0.9128 (m-10) cc_final: 0.8433 (m-10) REVERT: A 65 GLU cc_start: 0.8592 (mm-30) cc_final: 0.7858 (mp0) REVERT: A 66 GLU cc_start: 0.8535 (tp30) cc_final: 0.8274 (tp30) REVERT: A 82 LYS cc_start: 0.9653 (mmmm) cc_final: 0.9337 (mmmm) REVERT: A 127 LEU cc_start: 0.9405 (mt) cc_final: 0.9181 (mm) REVERT: A 144 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8736 (mtm) REVERT: A 163 ARG cc_start: 0.8397 (mmp80) cc_final: 0.8154 (mmm-85) REVERT: A 181 ASP cc_start: 0.8794 (m-30) cc_final: 0.8439 (m-30) REVERT: A 187 ASP cc_start: 0.9045 (t70) cc_final: 0.8720 (t70) REVERT: A 243 ARG cc_start: 0.7752 (ttp80) cc_final: 0.7548 (tmm-80) REVERT: A 257 ASP cc_start: 0.9378 (m-30) cc_final: 0.8867 (m-30) REVERT: A 321 GLU cc_start: 0.8721 (tp30) cc_final: 0.8340 (tp30) REVERT: A 348 MET cc_start: 0.8234 (OUTLIER) cc_final: 0.7559 (tmm) REVERT: A 352 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7372 (mt-10) REVERT: A 359 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8117 (ttp) REVERT: A 370 ASN cc_start: 0.9177 (m-40) cc_final: 0.8826 (m-40) REVERT: A 384 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.7286 (pm20) REVERT: A 415 ASN cc_start: 0.9295 (t0) cc_final: 0.9021 (t0) REVERT: A 420 MET cc_start: 0.9394 (mmm) cc_final: 0.9145 (mmm) REVERT: A 444 ASP cc_start: 0.8581 (t70) cc_final: 0.8378 (t70) REVERT: A 466 MET cc_start: 0.9174 (ptt) cc_final: 0.8860 (ptt) REVERT: A 493 MET cc_start: 0.9054 (tmm) cc_final: 0.8602 (tmm) REVERT: A 505 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8553 (mt-10) REVERT: A 510 LYS cc_start: 0.9146 (mtpt) cc_final: 0.8674 (mtpt) REVERT: A 512 GLU cc_start: 0.8512 (pt0) cc_final: 0.8158 (pm20) REVERT: A 527 TYR cc_start: 0.8856 (t80) cc_final: 0.8650 (t80) REVERT: A 571 TYR cc_start: 0.8520 (t80) cc_final: 0.8186 (t80) REVERT: A 602 GLU cc_start: 0.7613 (pt0) cc_final: 0.6880 (pt0) REVERT: A 604 ARG cc_start: 0.8865 (mmp80) cc_final: 0.8225 (mmt90) REVERT: A 612 TYR cc_start: 0.9156 (m-10) cc_final: 0.8545 (m-10) REVERT: A 632 MET cc_start: 0.8780 (mtm) cc_final: 0.7979 (mtp) REVERT: A 634 MET cc_start: 0.8966 (mmm) cc_final: 0.8590 (mmt) REVERT: A 640 MET cc_start: 0.9524 (tpp) cc_final: 0.9011 (tpp) REVERT: A 659 LYS cc_start: 0.8884 (mmmt) cc_final: 0.8416 (mmmt) REVERT: B 27 ASP cc_start: 0.9063 (p0) cc_final: 0.8645 (p0) REVERT: B 65 GLU cc_start: 0.8712 (mm-30) cc_final: 0.7972 (mp0) REVERT: B 89 PHE cc_start: 0.8914 (t80) cc_final: 0.8651 (t80) REVERT: B 99 LYS cc_start: 0.9601 (mmmm) cc_final: 0.9357 (mmmm) REVERT: B 106 LEU cc_start: 0.9207 (tp) cc_final: 0.8916 (tt) REVERT: B 109 ASN cc_start: 0.9120 (m-40) cc_final: 0.8601 (p0) REVERT: B 147 GLN cc_start: 0.8959 (mt0) cc_final: 0.8743 (mm-40) REVERT: B 184 ARG cc_start: 0.9273 (mmm-85) cc_final: 0.8984 (tpp80) REVERT: B 202 ASN cc_start: 0.9295 (t0) cc_final: 0.8155 (t0) REVERT: B 257 ASP cc_start: 0.9098 (m-30) cc_final: 0.8722 (m-30) REVERT: B 286 ASP cc_start: 0.8376 (OUTLIER) cc_final: 0.7510 (m-30) REVERT: B 290 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8524 (tm-30) REVERT: B 312 GLN cc_start: 0.8974 (OUTLIER) cc_final: 0.8718 (pm20) REVERT: B 317 MET cc_start: 0.8716 (ptp) cc_final: 0.8126 (pmm) REVERT: B 362 ASP cc_start: 0.8635 (m-30) cc_final: 0.7511 (m-30) REVERT: B 374 SER cc_start: 0.9152 (t) cc_final: 0.8772 (t) REVERT: B 399 GLU cc_start: 0.8270 (mp0) cc_final: 0.7989 (mp0) REVERT: B 403 ILE cc_start: 0.9487 (mm) cc_final: 0.9264 (tp) REVERT: B 434 ASP cc_start: 0.9021 (m-30) cc_final: 0.8514 (m-30) REVERT: B 447 ASN cc_start: 0.8580 (m-40) cc_final: 0.8050 (t0) REVERT: B 471 TYR cc_start: 0.9423 (t80) cc_final: 0.9186 (t80) REVERT: B 477 ILE cc_start: 0.9316 (mp) cc_final: 0.9094 (pt) REVERT: B 493 MET cc_start: 0.9701 (tmm) cc_final: 0.9003 (tmm) REVERT: B 515 ASP cc_start: 0.9143 (m-30) cc_final: 0.8792 (m-30) REVERT: B 558 TRP cc_start: 0.9597 (m100) cc_final: 0.8826 (m100) REVERT: B 610 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8444 (mmmt) REVERT: B 612 TYR cc_start: 0.8722 (m-80) cc_final: 0.8117 (m-80) REVERT: B 640 MET cc_start: 0.9287 (tpp) cc_final: 0.8944 (tpp) REVERT: C 19 GLN cc_start: 0.7821 (mp10) cc_final: 0.7427 (pm20) REVERT: C 55 TYR cc_start: 0.8364 (t80) cc_final: 0.7965 (t80) REVERT: C 56 MET cc_start: 0.5797 (ttt) cc_final: 0.5282 (ttt) REVERT: C 95 MET cc_start: 0.9078 (tmm) cc_final: 0.8856 (tmm) REVERT: C 164 GLU cc_start: 0.9480 (mm-30) cc_final: 0.8958 (mm-30) REVERT: C 166 PHE cc_start: 0.7885 (t80) cc_final: 0.7665 (t80) REVERT: C 169 TYR cc_start: 0.8027 (m-80) cc_final: 0.7798 (m-80) REVERT: C 178 PHE cc_start: 0.9220 (m-80) cc_final: 0.8293 (m-80) REVERT: C 185 MET cc_start: 0.8477 (pmm) cc_final: 0.7616 (pmm) REVERT: C 186 GLN cc_start: 0.9412 (mm110) cc_final: 0.9017 (mp10) REVERT: C 189 GLU cc_start: 0.8698 (tp30) cc_final: 0.8458 (mm-30) REVERT: C 223 GLU cc_start: 0.8899 (tm-30) cc_final: 0.7930 (pt0) REVERT: C 259 PHE cc_start: 0.8907 (t80) cc_final: 0.8534 (t80) REVERT: C 268 LEU cc_start: 0.9034 (tp) cc_final: 0.8487 (pp) REVERT: C 270 ASN cc_start: 0.7970 (m110) cc_final: 0.7691 (m110) REVERT: C 274 ASP cc_start: 0.7530 (p0) cc_final: 0.7295 (p0) REVERT: D 30 TRP cc_start: 0.8769 (p-90) cc_final: 0.8277 (p-90) REVERT: D 46 TYR cc_start: 0.9264 (m-80) cc_final: 0.8817 (m-80) REVERT: D 96 MET cc_start: 0.8508 (mmt) cc_final: 0.8305 (mmt) REVERT: D 178 PHE cc_start: 0.9128 (m-10) cc_final: 0.8253 (m-80) REVERT: D 186 GLN cc_start: 0.9140 (mm-40) cc_final: 0.8721 (mp10) REVERT: D 212 ILE cc_start: 0.9348 (mt) cc_final: 0.9045 (mm) REVERT: D 287 LEU cc_start: 0.7079 (mt) cc_final: 0.6803 (mt) outliers start: 73 outliers final: 50 residues processed: 763 average time/residue: 0.1199 time to fit residues: 139.1020 Evaluate side-chains 737 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 681 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 281 ASP 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: 2.9990 chunk 168 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 127 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 185 optimal weight: 8.9990 chunk 191 optimal weight: 8.9990 chunk 159 optimal weight: 2.9990 chunk 182 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 GLN B 467 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN D 91 ASN ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 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 = 0.3613 r_free = 0.3613 target = 0.122853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.087467 restraints weight = 36066.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.090789 restraints weight = 16735.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.093028 restraints weight = 10032.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.094472 restraints weight = 6829.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.095347 restraints weight = 5171.423| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.5874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16386 Z= 0.188 Angle : 0.699 15.226 22134 Z= 0.357 Chirality : 0.045 0.202 2360 Planarity : 0.004 0.048 2818 Dihedral : 10.964 170.843 2247 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.02 % Allowed : 27.10 % Favored : 68.88 % 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: 1.03 (0.19), residues: 1932 helix: 1.14 (0.15), residues: 1135 sheet: 0.60 (0.47), residues: 110 loop : 0.11 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 235 TYR 0.022 0.001 TYR C 242 PHE 0.037 0.002 PHE D 172 TRP 0.017 0.002 TRP D 44 HIS 0.010 0.001 HIS A 647 Details of bonding type rmsd covalent geometry : bond 0.00416 (16386) covalent geometry : angle 0.69921 (22134) hydrogen bonds : bond 0.04270 ( 871) hydrogen bonds : angle 5.09665 ( 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 788 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 719 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.9147 (m-10) cc_final: 0.8571 (m-10) REVERT: A 65 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8034 (mp0) REVERT: A 66 GLU cc_start: 0.8443 (tp30) cc_final: 0.8166 (tp30) REVERT: A 82 LYS cc_start: 0.9641 (mmmm) cc_final: 0.9352 (mmmm) REVERT: A 144 MET cc_start: 0.9177 (OUTLIER) cc_final: 0.8690 (mtm) REVERT: A 181 ASP cc_start: 0.8789 (m-30) cc_final: 0.8480 (m-30) REVERT: A 187 ASP cc_start: 0.9051 (t70) cc_final: 0.8694 (t70) REVERT: A 202 ASN cc_start: 0.9535 (t0) cc_final: 0.9241 (t0) REVERT: A 218 ASN cc_start: 0.9081 (t0) cc_final: 0.8810 (t0) REVERT: A 257 ASP cc_start: 0.9405 (m-30) cc_final: 0.9025 (m-30) REVERT: A 279 SER cc_start: 0.9114 (m) cc_final: 0.8819 (p) REVERT: A 286 ASP cc_start: 0.8456 (m-30) cc_final: 0.8146 (m-30) REVERT: A 321 GLU cc_start: 0.8728 (tp30) cc_final: 0.8355 (tp30) REVERT: A 348 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7641 (tmm) REVERT: A 352 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7528 (mt-10) REVERT: A 359 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8242 (ttp) REVERT: A 362 ASP cc_start: 0.8589 (m-30) cc_final: 0.8052 (m-30) REVERT: A 370 ASN cc_start: 0.9206 (m-40) cc_final: 0.8919 (m110) REVERT: A 384 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.7465 (pm20) REVERT: A 415 ASN cc_start: 0.9219 (t0) cc_final: 0.8945 (t0) REVERT: A 420 MET cc_start: 0.9328 (mmm) cc_final: 0.9028 (mmm) REVERT: A 447 ASN cc_start: 0.8819 (m-40) cc_final: 0.8446 (m-40) REVERT: A 466 MET cc_start: 0.9173 (ptt) cc_final: 0.8951 (ptt) REVERT: A 493 MET cc_start: 0.9124 (tmm) cc_final: 0.8407 (tmm) REVERT: A 496 ASN cc_start: 0.9528 (t0) cc_final: 0.9313 (t0) REVERT: A 505 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8788 (mt-10) REVERT: A 550 MET cc_start: 0.7538 (mtm) cc_final: 0.7030 (mtm) REVERT: A 604 ARG cc_start: 0.8853 (mmp80) cc_final: 0.8402 (mmt-90) REVERT: A 632 MET cc_start: 0.8794 (mtm) cc_final: 0.8024 (mtp) REVERT: A 634 MET cc_start: 0.8961 (mmm) cc_final: 0.8697 (mmt) REVERT: A 640 MET cc_start: 0.9622 (tpp) cc_final: 0.8761 (tpp) REVERT: A 647 HIS cc_start: 0.9021 (m-70) cc_final: 0.8660 (m170) REVERT: A 686 ARG cc_start: 0.8657 (mmm-85) cc_final: 0.8380 (ttm-80) REVERT: B 8 LYS cc_start: 0.9057 (tppt) cc_final: 0.8780 (tppt) REVERT: B 15 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8637 (tm-30) REVERT: B 27 ASP cc_start: 0.8961 (p0) cc_final: 0.8615 (p0) REVERT: B 89 PHE cc_start: 0.8987 (t80) cc_final: 0.8615 (t80) REVERT: B 99 LYS cc_start: 0.9574 (mmmm) cc_final: 0.9320 (mmmm) REVERT: B 106 LEU cc_start: 0.9256 (tp) cc_final: 0.8969 (tt) REVERT: B 109 ASN cc_start: 0.9120 (m-40) cc_final: 0.8684 (p0) REVERT: B 174 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8400 (mm-30) REVERT: B 181 ASP cc_start: 0.8981 (m-30) cc_final: 0.8769 (t0) REVERT: B 202 ASN cc_start: 0.9458 (t0) cc_final: 0.8986 (t0) REVERT: B 257 ASP cc_start: 0.8959 (m-30) cc_final: 0.8437 (m-30) REVERT: B 286 ASP cc_start: 0.8406 (OUTLIER) cc_final: 0.7568 (m-30) REVERT: B 317 MET cc_start: 0.8658 (ptp) cc_final: 0.8050 (pmm) REVERT: B 362 ASP cc_start: 0.8673 (m-30) cc_final: 0.7453 (m-30) REVERT: B 374 SER cc_start: 0.9202 (t) cc_final: 0.8827 (t) REVERT: B 403 ILE cc_start: 0.9530 (mm) cc_final: 0.9282 (tp) REVERT: B 434 ASP cc_start: 0.9043 (m-30) cc_final: 0.8818 (m-30) REVERT: B 447 ASN cc_start: 0.8618 (m-40) cc_final: 0.8118 (t0) REVERT: B 471 TYR cc_start: 0.9452 (t80) cc_final: 0.9236 (t80) REVERT: B 483 GLU cc_start: 0.9473 (mp0) cc_final: 0.9262 (mp0) REVERT: B 493 MET cc_start: 0.9698 (tmm) cc_final: 0.8874 (tmm) REVERT: B 515 ASP cc_start: 0.9067 (m-30) cc_final: 0.8762 (m-30) REVERT: B 610 LYS cc_start: 0.8764 (mmmt) cc_final: 0.8437 (mmmt) REVERT: B 612 TYR cc_start: 0.8656 (m-80) cc_final: 0.8063 (m-80) REVERT: B 628 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8058 (mm-30) REVERT: C 19 GLN cc_start: 0.7738 (mp10) cc_final: 0.7399 (pm20) REVERT: C 55 TYR cc_start: 0.8392 (t80) cc_final: 0.7938 (t80) REVERT: C 56 MET cc_start: 0.5965 (ttt) cc_final: 0.5495 (ttt) REVERT: C 80 HIS cc_start: 0.8884 (m90) cc_final: 0.8414 (m90) REVERT: C 86 ARG cc_start: 0.6839 (mpt180) cc_final: 0.6597 (mmt180) REVERT: C 96 MET cc_start: 0.8553 (mmt) cc_final: 0.8316 (mmm) REVERT: C 164 GLU cc_start: 0.9395 (mm-30) cc_final: 0.8869 (mm-30) REVERT: C 178 PHE cc_start: 0.9348 (m-80) cc_final: 0.8535 (m-10) REVERT: C 185 MET cc_start: 0.8539 (pmm) cc_final: 0.7532 (pmm) REVERT: C 186 GLN cc_start: 0.9371 (mm110) cc_final: 0.8890 (mp10) REVERT: C 189 GLU cc_start: 0.8711 (tp30) cc_final: 0.8423 (mm-30) REVERT: C 223 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8060 (pt0) REVERT: C 259 PHE cc_start: 0.8829 (t80) cc_final: 0.8384 (t80) REVERT: C 270 ASN cc_start: 0.8081 (m110) cc_final: 0.7790 (m110) REVERT: D 30 TRP cc_start: 0.8648 (p-90) cc_final: 0.8045 (p-90) REVERT: D 34 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8366 (mm-30) REVERT: D 46 TYR cc_start: 0.9238 (m-80) cc_final: 0.8837 (m-80) REVERT: D 136 GLN cc_start: 0.8562 (OUTLIER) cc_final: 0.8245 (mt0) REVERT: D 178 PHE cc_start: 0.9212 (m-10) cc_final: 0.8440 (m-80) REVERT: D 186 GLN cc_start: 0.9157 (mm-40) cc_final: 0.8712 (mp10) REVERT: D 210 GLN cc_start: 0.9378 (tm-30) cc_final: 0.9109 (pt0) REVERT: D 231 LEU cc_start: 0.7972 (mt) cc_final: 0.7736 (mt) outliers start: 69 outliers final: 49 residues processed: 745 average time/residue: 0.1200 time to fit residues: 134.7748 Evaluate side-chains 738 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 683 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 0.9990 chunk 46 optimal weight: 4.9990 chunk 120 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 467 ASN B 668 ASN C 84 HIS C 107 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN D 23 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.122068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.085973 restraints weight = 35949.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.089390 restraints weight = 17068.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.091579 restraints weight = 10328.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.093104 restraints weight = 7195.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.094038 restraints weight = 5554.571| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3071 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.6250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16386 Z= 0.169 Angle : 0.715 15.494 22134 Z= 0.358 Chirality : 0.045 0.196 2360 Planarity : 0.004 0.048 2818 Dihedral : 10.787 169.231 2247 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.60 % Allowed : 28.90 % Favored : 66.49 % 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: 0.98 (0.19), residues: 1932 helix: 1.15 (0.15), residues: 1134 sheet: -0.22 (0.42), residues: 148 loop : 0.17 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 196 TYR 0.022 0.001 TYR C 242 PHE 0.032 0.002 PHE D 172 TRP 0.014 0.001 TRP D 44 HIS 0.007 0.001 HIS A 647 Details of bonding type rmsd covalent geometry : bond 0.00379 (16386) covalent geometry : angle 0.71519 (22134) hydrogen bonds : bond 0.04116 ( 871) hydrogen bonds : angle 5.07694 ( 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 780 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 701 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.9134 (m-10) cc_final: 0.8589 (m-10) REVERT: A 65 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8100 (mp0) REVERT: A 66 GLU cc_start: 0.8431 (tp30) cc_final: 0.8140 (tp30) REVERT: A 82 LYS cc_start: 0.9643 (mmmm) cc_final: 0.9349 (mmmm) REVERT: A 144 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8660 (mtm) REVERT: A 181 ASP cc_start: 0.8790 (m-30) cc_final: 0.8519 (m-30) REVERT: A 202 ASN cc_start: 0.9550 (t0) cc_final: 0.9240 (t0) REVERT: A 218 ASN cc_start: 0.9141 (t0) cc_final: 0.8846 (t0) REVERT: A 243 ARG cc_start: 0.7297 (ttp80) cc_final: 0.7016 (ttp80) REVERT: A 257 ASP cc_start: 0.9311 (m-30) cc_final: 0.9082 (m-30) REVERT: A 279 SER cc_start: 0.9257 (m) cc_final: 0.8823 (p) REVERT: A 286 ASP cc_start: 0.8473 (m-30) cc_final: 0.8150 (m-30) REVERT: A 296 LYS cc_start: 0.8179 (mmmt) cc_final: 0.7867 (mtmm) REVERT: A 321 GLU cc_start: 0.8774 (tp30) cc_final: 0.8287 (tp30) REVERT: A 359 MET cc_start: 0.9088 (OUTLIER) cc_final: 0.8210 (ttp) REVERT: A 362 ASP cc_start: 0.8586 (m-30) cc_final: 0.7894 (m-30) REVERT: A 370 ASN cc_start: 0.9214 (m-40) cc_final: 0.8940 (m110) REVERT: A 384 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.7496 (pm20) REVERT: A 389 SER cc_start: 0.9411 (OUTLIER) cc_final: 0.9116 (p) REVERT: A 415 ASN cc_start: 0.9252 (t0) cc_final: 0.8988 (t0) REVERT: A 420 MET cc_start: 0.9351 (mmm) cc_final: 0.9046 (mmm) REVERT: A 447 ASN cc_start: 0.8777 (m-40) cc_final: 0.8400 (m-40) REVERT: A 466 MET cc_start: 0.9183 (ptt) cc_final: 0.8962 (ptt) REVERT: A 493 MET cc_start: 0.9097 (tmm) cc_final: 0.8339 (tmm) REVERT: A 505 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8761 (mt-10) REVERT: A 512 GLU cc_start: 0.8597 (pt0) cc_final: 0.8141 (pt0) REVERT: A 602 GLU cc_start: 0.7864 (pt0) cc_final: 0.7074 (pt0) REVERT: A 604 ARG cc_start: 0.8804 (mmp80) cc_final: 0.8557 (mmt-90) REVERT: A 632 MET cc_start: 0.8713 (mtm) cc_final: 0.7904 (mtp) REVERT: A 634 MET cc_start: 0.8929 (mmm) cc_final: 0.8708 (mmt) REVERT: A 640 MET cc_start: 0.9587 (tpp) cc_final: 0.8843 (tpp) REVERT: A 647 HIS cc_start: 0.8985 (m-70) cc_final: 0.8706 (m170) REVERT: B 8 LYS cc_start: 0.9049 (tppt) cc_final: 0.8778 (tppt) REVERT: B 17 MET cc_start: 0.8689 (mmm) cc_final: 0.8275 (mmm) REVERT: B 27 ASP cc_start: 0.8917 (p0) cc_final: 0.8558 (p0) REVERT: B 31 GLU cc_start: 0.8414 (mt-10) cc_final: 0.7858 (mt-10) REVERT: B 65 GLU cc_start: 0.8808 (mm-30) cc_final: 0.8279 (mp0) REVERT: B 99 LYS cc_start: 0.9568 (mmmm) cc_final: 0.9295 (mmmm) REVERT: B 108 THR cc_start: 0.8364 (OUTLIER) cc_final: 0.8094 (p) REVERT: B 109 ASN cc_start: 0.9226 (m-40) cc_final: 0.8641 (p0) REVERT: B 147 GLN cc_start: 0.9153 (mt0) cc_final: 0.8435 (mm-40) REVERT: B 161 ARG cc_start: 0.8902 (ttm170) cc_final: 0.8612 (ttm170) REVERT: B 174 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8356 (mm-30) REVERT: B 181 ASP cc_start: 0.8996 (m-30) cc_final: 0.8637 (t0) REVERT: B 202 ASN cc_start: 0.9468 (t0) cc_final: 0.8878 (t0) REVERT: B 257 ASP cc_start: 0.8911 (m-30) cc_final: 0.8400 (m-30) REVERT: B 263 ASP cc_start: 0.9128 (m-30) cc_final: 0.8757 (p0) REVERT: B 286 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.7590 (m-30) REVERT: B 290 GLU cc_start: 0.8574 (tm-30) cc_final: 0.8209 (tm-30) REVERT: B 317 MET cc_start: 0.8524 (ptp) cc_final: 0.7997 (pmm) REVERT: B 362 ASP cc_start: 0.8641 (m-30) cc_final: 0.7397 (m-30) REVERT: B 374 SER cc_start: 0.9237 (t) cc_final: 0.8880 (t) REVERT: B 393 SER cc_start: 0.9373 (m) cc_final: 0.9072 (p) REVERT: B 394 TYR cc_start: 0.9142 (m-80) cc_final: 0.8620 (m-80) REVERT: B 434 ASP cc_start: 0.9056 (m-30) cc_final: 0.8842 (m-30) REVERT: B 447 ASN cc_start: 0.8606 (m-40) cc_final: 0.8149 (t0) REVERT: B 471 TYR cc_start: 0.9471 (t80) cc_final: 0.9269 (t80) REVERT: B 477 ILE cc_start: 0.9337 (mp) cc_final: 0.9114 (pt) REVERT: B 483 GLU cc_start: 0.9463 (mp0) cc_final: 0.9235 (mp0) REVERT: B 493 MET cc_start: 0.9682 (tmm) cc_final: 0.8896 (tmm) REVERT: B 515 ASP cc_start: 0.9066 (m-30) cc_final: 0.8775 (m-30) REVERT: B 610 LYS cc_start: 0.8811 (mmmt) cc_final: 0.8462 (mmmt) REVERT: B 612 TYR cc_start: 0.8623 (m-80) cc_final: 0.8138 (m-80) REVERT: B 628 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8084 (mm-30) REVERT: C 19 GLN cc_start: 0.7712 (mp10) cc_final: 0.7286 (pm20) REVERT: C 20 MET cc_start: 0.9017 (tpp) cc_final: 0.8714 (tmm) REVERT: C 55 TYR cc_start: 0.8384 (t80) cc_final: 0.7922 (t80) REVERT: C 56 MET cc_start: 0.5887 (ttt) cc_final: 0.5403 (ttt) REVERT: C 80 HIS cc_start: 0.8911 (m90) cc_final: 0.8438 (m90) REVERT: C 164 GLU cc_start: 0.9408 (mm-30) cc_final: 0.9076 (mm-30) REVERT: C 178 PHE cc_start: 0.9324 (m-80) cc_final: 0.8474 (m-10) REVERT: C 185 MET cc_start: 0.8587 (pmm) cc_final: 0.7502 (pmm) REVERT: C 186 GLN cc_start: 0.9382 (mm110) cc_final: 0.8874 (mp10) REVERT: C 216 GLN cc_start: 0.6937 (OUTLIER) cc_final: 0.6706 (mp10) REVERT: C 242 TYR cc_start: 0.9348 (t80) cc_final: 0.9055 (t80) REVERT: C 259 PHE cc_start: 0.8778 (t80) cc_final: 0.8277 (t80) REVERT: C 269 MET cc_start: 0.9285 (ppp) cc_final: 0.9085 (ppp) REVERT: C 270 ASN cc_start: 0.8140 (m110) cc_final: 0.7747 (m110) REVERT: C 313 GLU cc_start: 0.8974 (tt0) cc_final: 0.8739 (tt0) REVERT: D 17 PHE cc_start: 0.7077 (m-80) cc_final: 0.6784 (t80) REVERT: D 30 TRP cc_start: 0.8535 (p-90) cc_final: 0.7981 (p-90) REVERT: D 34 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8263 (mm-30) REVERT: D 46 TYR cc_start: 0.9235 (m-80) cc_final: 0.8895 (m-10) REVERT: D 56 MET cc_start: 0.7534 (mmm) cc_final: 0.6435 (ptp) REVERT: D 130 TYR cc_start: 0.6054 (m-80) cc_final: 0.5796 (m-10) REVERT: D 136 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.8268 (mt0) REVERT: D 178 PHE cc_start: 0.9256 (m-10) cc_final: 0.8481 (m-80) REVERT: D 186 GLN cc_start: 0.9155 (mm-40) cc_final: 0.8686 (mp10) REVERT: D 210 GLN cc_start: 0.9390 (tm-30) cc_final: 0.9136 (pt0) REVERT: D 240 LEU cc_start: 0.8744 (mt) cc_final: 0.7966 (pp) REVERT: D 244 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: D 246 LEU cc_start: 0.8196 (mm) cc_final: 0.7975 (mt) outliers start: 79 outliers final: 47 residues processed: 733 average time/residue: 0.1093 time to fit residues: 121.4545 Evaluate side-chains 724 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 668 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 21 PHE Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 2.9990 chunk 183 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 chunk 172 optimal weight: 0.0040 chunk 52 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN B 467 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN C 98 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN D 24 GLN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN D 128 ASN ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.120536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.085806 restraints weight = 36067.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.089216 restraints weight = 16872.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.091413 restraints weight = 10080.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.092884 restraints weight = 6971.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.093806 restraints weight = 5324.099| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.6569 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= 0.167 Angle : 0.728 15.736 22134 Z= 0.362 Chirality : 0.045 0.196 2360 Planarity : 0.004 0.049 2818 Dihedral : 10.712 168.227 2247 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.37 % Allowed : 30.48 % Favored : 65.15 % 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: 0.87 (0.19), residues: 1932 helix: 1.09 (0.15), residues: 1139 sheet: -0.40 (0.42), residues: 148 loop : 0.09 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 196 TYR 0.019 0.001 TYR C 242 PHE 0.030 0.002 PHE C 172 TRP 0.017 0.002 TRP D 44 HIS 0.007 0.001 HIS A 647 Details of bonding type rmsd covalent geometry : bond 0.00381 (16386) covalent geometry : angle 0.72847 (22134) hydrogen bonds : bond 0.04062 ( 871) hydrogen bonds : angle 5.08013 ( 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 756 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 681 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.9175 (m-10) cc_final: 0.8673 (m-10) REVERT: A 65 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8104 (mp0) REVERT: A 66 GLU cc_start: 0.8480 (tp30) cc_final: 0.8174 (tp30) REVERT: A 82 LYS cc_start: 0.9652 (mmmm) cc_final: 0.9344 (mmmm) REVERT: A 144 MET cc_start: 0.9167 (OUTLIER) cc_final: 0.8609 (mtm) REVERT: A 149 TYR cc_start: 0.9266 (t80) cc_final: 0.8679 (t80) REVERT: A 163 ARG cc_start: 0.8341 (mmm-85) cc_final: 0.8060 (mmm160) REVERT: A 181 ASP cc_start: 0.8799 (m-30) cc_final: 0.8545 (m-30) REVERT: A 187 ASP cc_start: 0.9049 (OUTLIER) cc_final: 0.8649 (t70) REVERT: A 202 ASN cc_start: 0.9587 (t0) cc_final: 0.9265 (t0) REVERT: A 218 ASN cc_start: 0.9253 (t0) cc_final: 0.9049 (t0) REVERT: A 228 LYS cc_start: 0.9498 (mmmm) cc_final: 0.9083 (mmtm) REVERT: A 232 ASN cc_start: 0.9353 (OUTLIER) cc_final: 0.9032 (m-40) REVERT: A 321 GLU cc_start: 0.8841 (tp30) cc_final: 0.8462 (tp30) REVERT: A 348 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8055 (tmm) REVERT: A 359 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8194 (ttp) REVERT: A 370 ASN cc_start: 0.9266 (m-40) cc_final: 0.8907 (m110) REVERT: A 384 GLU cc_start: 0.9023 (OUTLIER) cc_final: 0.7713 (pm20) REVERT: A 389 SER cc_start: 0.9459 (OUTLIER) cc_final: 0.9153 (p) REVERT: A 415 ASN cc_start: 0.9289 (t0) cc_final: 0.8992 (t0) REVERT: A 447 ASN cc_start: 0.8740 (m-40) cc_final: 0.8398 (m-40) REVERT: A 453 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.8999 (ttp80) REVERT: A 493 MET cc_start: 0.9034 (tmm) cc_final: 0.8281 (tmm) REVERT: A 494 MET cc_start: 0.9251 (mtm) cc_final: 0.8886 (mtt) REVERT: A 505 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8743 (mt-10) REVERT: A 512 GLU cc_start: 0.8657 (pt0) cc_final: 0.8316 (pt0) REVERT: A 583 SER cc_start: 0.9412 (m) cc_final: 0.8831 (t) REVERT: A 602 GLU cc_start: 0.8034 (pt0) cc_final: 0.7032 (pt0) REVERT: A 604 ARG cc_start: 0.8860 (mmp80) cc_final: 0.8574 (mmt-90) REVERT: A 606 TYR cc_start: 0.8299 (m-80) cc_final: 0.8081 (m-80) REVERT: A 632 MET cc_start: 0.8734 (mtm) cc_final: 0.7920 (mtp) REVERT: A 634 MET cc_start: 0.8985 (mmm) cc_final: 0.8771 (mmt) REVERT: A 640 MET cc_start: 0.9611 (tpp) cc_final: 0.8791 (tpp) REVERT: A 686 ARG cc_start: 0.8800 (mmm-85) cc_final: 0.8588 (mmm-85) REVERT: B 8 LYS cc_start: 0.9055 (tppt) cc_final: 0.8807 (tppt) REVERT: B 17 MET cc_start: 0.8819 (mmm) cc_final: 0.8456 (mmm) REVERT: B 31 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8122 (mt-10) REVERT: B 65 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8265 (mp0) REVERT: B 99 LYS cc_start: 0.9538 (mmmm) cc_final: 0.9260 (mmmm) REVERT: B 109 ASN cc_start: 0.9281 (m-40) cc_final: 0.8799 (p0) REVERT: B 161 ARG cc_start: 0.8828 (ttm170) cc_final: 0.8528 (ttm170) REVERT: B 202 ASN cc_start: 0.9401 (t0) cc_final: 0.8988 (t0) REVERT: B 232 ASN cc_start: 0.9356 (m-40) cc_final: 0.9020 (m-40) REVERT: B 243 ARG cc_start: 0.7155 (tmm-80) cc_final: 0.6882 (ttp80) REVERT: B 257 ASP cc_start: 0.8919 (m-30) cc_final: 0.8436 (m-30) REVERT: B 286 ASP cc_start: 0.8409 (OUTLIER) cc_final: 0.7622 (m-30) REVERT: B 290 GLU cc_start: 0.8600 (tm-30) cc_final: 0.8194 (tm-30) REVERT: B 317 MET cc_start: 0.8405 (ptp) cc_final: 0.8007 (pmm) REVERT: B 344 GLU cc_start: 0.9113 (mt-10) cc_final: 0.8798 (mt-10) REVERT: B 362 ASP cc_start: 0.8669 (m-30) cc_final: 0.7412 (m-30) REVERT: B 374 SER cc_start: 0.9233 (t) cc_final: 0.8973 (t) REVERT: B 393 SER cc_start: 0.9344 (m) cc_final: 0.9062 (p) REVERT: B 394 TYR cc_start: 0.9219 (m-80) cc_final: 0.8993 (m-80) REVERT: B 434 ASP cc_start: 0.9125 (m-30) cc_final: 0.8919 (m-30) REVERT: B 483 GLU cc_start: 0.9480 (mp0) cc_final: 0.9226 (mp0) REVERT: B 493 MET cc_start: 0.9689 (tmm) cc_final: 0.8887 (tmm) REVERT: B 515 ASP cc_start: 0.9084 (m-30) cc_final: 0.8815 (m-30) REVERT: B 604 ARG cc_start: 0.9316 (tpp80) cc_final: 0.9016 (ttm-80) REVERT: B 610 LYS cc_start: 0.8850 (mmmt) cc_final: 0.8486 (mmmt) REVERT: B 612 TYR cc_start: 0.8598 (m-80) cc_final: 0.8113 (m-80) REVERT: B 628 GLU cc_start: 0.8565 (mm-30) cc_final: 0.7956 (mm-30) REVERT: B 632 MET cc_start: 0.8813 (mtp) cc_final: 0.8301 (mpp) REVERT: C 19 GLN cc_start: 0.7707 (mp10) cc_final: 0.7288 (pm20) REVERT: C 20 MET cc_start: 0.9039 (tpp) cc_final: 0.8722 (tmm) REVERT: C 29 PHE cc_start: 0.8500 (t80) cc_final: 0.8175 (t80) REVERT: C 55 TYR cc_start: 0.8345 (t80) cc_final: 0.7646 (t80) REVERT: C 56 MET cc_start: 0.5892 (ttt) cc_final: 0.5441 (ttt) REVERT: C 68 GLU cc_start: 0.9340 (tm-30) cc_final: 0.9105 (tm-30) REVERT: C 80 HIS cc_start: 0.8914 (m90) cc_final: 0.8522 (m90) REVERT: C 96 MET cc_start: 0.8706 (mmt) cc_final: 0.8173 (mmm) REVERT: C 150 GLU cc_start: 0.9263 (OUTLIER) cc_final: 0.8957 (tp30) REVERT: C 164 GLU cc_start: 0.9314 (mm-30) cc_final: 0.9082 (mm-30) REVERT: C 178 PHE cc_start: 0.9362 (m-80) cc_final: 0.8445 (m-10) REVERT: C 185 MET cc_start: 0.8651 (pmm) cc_final: 0.7763 (pmm) REVERT: C 186 GLN cc_start: 0.9354 (mm110) cc_final: 0.8891 (mp10) REVERT: C 189 GLU cc_start: 0.8700 (tp30) cc_final: 0.8444 (mm-30) REVERT: C 242 TYR cc_start: 0.9364 (t80) cc_final: 0.9082 (t80) REVERT: C 247 TYR cc_start: 0.8626 (m-80) cc_final: 0.8344 (m-10) REVERT: C 259 PHE cc_start: 0.8748 (t80) cc_final: 0.8207 (t80) REVERT: C 270 ASN cc_start: 0.8221 (m110) cc_final: 0.7844 (m110) REVERT: C 274 ASP cc_start: 0.7406 (p0) cc_final: 0.7020 (p0) REVERT: D 21 PHE cc_start: 0.9428 (m-80) cc_final: 0.9152 (m-80) REVERT: D 30 TRP cc_start: 0.8514 (p-90) cc_final: 0.8189 (p-90) REVERT: D 34 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8325 (mm-30) REVERT: D 41 LEU cc_start: 0.8876 (pp) cc_final: 0.8456 (mm) REVERT: D 46 TYR cc_start: 0.9228 (m-80) cc_final: 0.8935 (m-10) REVERT: D 47 LEU cc_start: 0.9062 (tp) cc_final: 0.8833 (mt) REVERT: D 136 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8397 (mt0) REVERT: D 186 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8788 (mp10) REVERT: D 210 GLN cc_start: 0.9391 (tm-30) cc_final: 0.9107 (pt0) REVERT: D 240 LEU cc_start: 0.8813 (mt) cc_final: 0.8043 (pp) REVERT: D 244 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: D 246 LEU cc_start: 0.8186 (mm) cc_final: 0.7844 (mt) REVERT: D 269 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8260 (ppp) outliers start: 75 outliers final: 51 residues processed: 706 average time/residue: 0.1085 time to fit residues: 115.1496 Evaluate side-chains 721 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 657 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 105 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 186 optimal weight: 20.0000 chunk 140 optimal weight: 7.9990 chunk 115 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN C 98 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.122885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.087518 restraints weight = 35475.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.090965 restraints weight = 16849.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.093205 restraints weight = 10077.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.094668 restraints weight = 7010.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.095666 restraints weight = 5384.356| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.6858 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= 0.187 Angle : 0.752 15.509 22134 Z= 0.371 Chirality : 0.047 0.393 2360 Planarity : 0.004 0.045 2818 Dihedral : 10.649 167.909 2246 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.42 % Allowed : 30.19 % Favored : 64.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.19), residues: 1932 helix: 1.03 (0.15), residues: 1149 sheet: -0.49 (0.42), residues: 148 loop : 0.02 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 243 TYR 0.016 0.001 TYR C 242 PHE 0.029 0.002 PHE C 172 TRP 0.016 0.002 TRP D 44 HIS 0.006 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00420 (16386) covalent geometry : angle 0.75247 (22134) hydrogen bonds : bond 0.04040 ( 871) hydrogen bonds : angle 5.12380 ( 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 761 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 668 time to evaluate : 0.634 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 64 TYR cc_start: 0.9206 (m-10) cc_final: 0.8711 (m-10) REVERT: A 65 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8144 (mp0) REVERT: A 66 GLU cc_start: 0.8443 (tp30) cc_final: 0.8136 (tp30) REVERT: A 82 LYS cc_start: 0.9636 (mmmm) cc_final: 0.9318 (mmmm) REVERT: A 144 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8633 (mtm) REVERT: A 149 TYR cc_start: 0.9265 (t80) cc_final: 0.8825 (t80) REVERT: A 181 ASP cc_start: 0.8749 (m-30) cc_final: 0.8533 (m-30) REVERT: A 202 ASN cc_start: 0.9606 (t0) cc_final: 0.9296 (t0) REVERT: A 232 ASN cc_start: 0.9403 (OUTLIER) cc_final: 0.9067 (m-40) REVERT: A 286 ASP cc_start: 0.8618 (m-30) cc_final: 0.8194 (m-30) REVERT: A 321 GLU cc_start: 0.8887 (tp30) cc_final: 0.8493 (tp30) REVERT: A 322 MET cc_start: 0.9279 (mmm) cc_final: 0.8932 (mmm) REVERT: A 348 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8068 (tmm) REVERT: A 359 MET cc_start: 0.9112 (OUTLIER) cc_final: 0.8233 (ttp) REVERT: A 362 ASP cc_start: 0.8576 (m-30) cc_final: 0.8118 (m-30) REVERT: A 370 ASN cc_start: 0.9283 (m-40) cc_final: 0.8914 (m110) REVERT: A 384 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.7716 (pm20) REVERT: A 389 SER cc_start: 0.9422 (OUTLIER) cc_final: 0.9105 (p) REVERT: A 447 ASN cc_start: 0.8743 (m-40) cc_final: 0.8393 (m-40) REVERT: A 453 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.9008 (ttp80) REVERT: A 493 MET cc_start: 0.8991 (tmm) cc_final: 0.8176 (tmm) REVERT: A 505 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8699 (mt-10) REVERT: A 512 GLU cc_start: 0.8655 (pt0) cc_final: 0.8326 (pt0) REVERT: A 526 GLU cc_start: 0.8246 (mm-30) cc_final: 0.8036 (mp0) REVERT: A 583 SER cc_start: 0.9427 (m) cc_final: 0.8853 (t) REVERT: A 602 GLU cc_start: 0.7670 (pt0) cc_final: 0.5827 (pt0) REVERT: A 604 ARG cc_start: 0.8951 (mmp80) cc_final: 0.8408 (mmt-90) REVERT: A 632 MET cc_start: 0.8803 (mtm) cc_final: 0.8044 (mtp) REVERT: A 640 MET cc_start: 0.9603 (tpp) cc_final: 0.8799 (tpp) REVERT: A 686 ARG cc_start: 0.8791 (mmm-85) cc_final: 0.8532 (mmm-85) REVERT: B 8 LYS cc_start: 0.9064 (tppt) cc_final: 0.8859 (tppt) REVERT: B 17 MET cc_start: 0.8903 (mmm) cc_final: 0.8512 (mmm) REVERT: B 31 GLU cc_start: 0.8357 (mt-10) cc_final: 0.8097 (mt-10) REVERT: B 65 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8227 (mp0) REVERT: B 99 LYS cc_start: 0.9547 (mmmm) cc_final: 0.9302 (mmmm) REVERT: B 108 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8365 (p) REVERT: B 109 ASN cc_start: 0.9269 (m-40) cc_final: 0.8809 (p0) REVERT: B 181 ASP cc_start: 0.9003 (m-30) cc_final: 0.8470 (t0) REVERT: B 232 ASN cc_start: 0.9397 (m-40) cc_final: 0.9019 (m-40) REVERT: B 243 ARG cc_start: 0.7208 (tmm-80) cc_final: 0.7007 (tmm-80) REVERT: B 257 ASP cc_start: 0.8851 (m-30) cc_final: 0.8362 (m-30) REVERT: B 263 ASP cc_start: 0.9149 (m-30) cc_final: 0.8743 (p0) REVERT: B 286 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.7663 (m-30) REVERT: B 290 GLU cc_start: 0.8608 (tm-30) cc_final: 0.8059 (tm-30) REVERT: B 317 MET cc_start: 0.8532 (ptp) cc_final: 0.8210 (pmm) REVERT: B 362 ASP cc_start: 0.8692 (m-30) cc_final: 0.7393 (m-30) REVERT: B 378 PHE cc_start: 0.9351 (p90) cc_final: 0.8992 (p90) REVERT: B 393 SER cc_start: 0.9369 (m) cc_final: 0.8972 (p) REVERT: B 394 TYR cc_start: 0.9167 (m-80) cc_final: 0.8663 (m-80) REVERT: B 447 ASN cc_start: 0.8240 (m-40) cc_final: 0.7846 (t0) REVERT: B 483 GLU cc_start: 0.9470 (mp0) cc_final: 0.9226 (mp0) REVERT: B 493 MET cc_start: 0.9691 (tmm) cc_final: 0.8876 (tmm) REVERT: B 515 ASP cc_start: 0.9066 (m-30) cc_final: 0.8829 (m-30) REVERT: B 610 LYS cc_start: 0.8882 (mmmt) cc_final: 0.8518 (mmmt) REVERT: B 612 TYR cc_start: 0.8586 (m-80) cc_final: 0.8088 (m-80) REVERT: B 628 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8080 (mm-30) REVERT: B 632 MET cc_start: 0.8850 (mtp) cc_final: 0.8303 (mpp) REVERT: C 19 GLN cc_start: 0.7661 (mp10) cc_final: 0.7236 (pm20) REVERT: C 20 MET cc_start: 0.8998 (tpp) cc_final: 0.8685 (tmm) REVERT: C 29 PHE cc_start: 0.8513 (t80) cc_final: 0.8139 (t80) REVERT: C 55 TYR cc_start: 0.8352 (t80) cc_final: 0.7805 (t80) REVERT: C 56 MET cc_start: 0.5872 (ttt) cc_final: 0.5368 (ttt) REVERT: C 64 LEU cc_start: 0.4475 (OUTLIER) cc_final: 0.4274 (mm) REVERT: C 68 GLU cc_start: 0.9371 (tm-30) cc_final: 0.9131 (tm-30) REVERT: C 69 GLN cc_start: 0.9169 (tp-100) cc_final: 0.8946 (tp-100) REVERT: C 80 HIS cc_start: 0.8883 (m90) cc_final: 0.8615 (m90) REVERT: C 96 MET cc_start: 0.8739 (mmt) cc_final: 0.8052 (mmm) REVERT: C 145 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7858 (tp) REVERT: C 150 GLU cc_start: 0.9237 (OUTLIER) cc_final: 0.8978 (tp30) REVERT: C 164 GLU cc_start: 0.9303 (mm-30) cc_final: 0.8754 (tp30) REVERT: C 169 TYR cc_start: 0.8349 (m-80) cc_final: 0.8015 (m-80) REVERT: C 174 TYR cc_start: 0.9346 (OUTLIER) cc_final: 0.8732 (t80) REVERT: C 185 MET cc_start: 0.8604 (pmm) cc_final: 0.7657 (pmm) REVERT: C 186 GLN cc_start: 0.9318 (mm110) cc_final: 0.8858 (mp10) REVERT: C 189 GLU cc_start: 0.8702 (tp30) cc_final: 0.8401 (mm-30) REVERT: C 259 PHE cc_start: 0.8809 (t80) cc_final: 0.8336 (t80) REVERT: D 17 PHE cc_start: 0.7324 (m-10) cc_final: 0.6639 (m-80) REVERT: D 30 TRP cc_start: 0.8721 (p-90) cc_final: 0.7734 (p-90) REVERT: D 46 TYR cc_start: 0.9184 (m-80) cc_final: 0.8878 (m-10) REVERT: D 96 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8368 (mmt) REVERT: D 130 TYR cc_start: 0.6220 (m-10) cc_final: 0.5823 (m-10) REVERT: D 136 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8487 (mt0) REVERT: D 153 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8777 (mt) REVERT: D 186 GLN cc_start: 0.9136 (mm-40) cc_final: 0.8627 (mp10) REVERT: D 207 LEU cc_start: 0.9253 (mm) cc_final: 0.8804 (mm) REVERT: D 210 GLN cc_start: 0.9375 (tm-30) cc_final: 0.9121 (pt0) REVERT: D 240 LEU cc_start: 0.8753 (mt) cc_final: 0.7897 (pp) REVERT: D 244 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7628 (mp0) REVERT: D 246 LEU cc_start: 0.8236 (mm) cc_final: 0.7940 (mt) REVERT: D 252 LEU cc_start: 0.6584 (mp) cc_final: 0.6299 (mt) REVERT: D 269 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8254 (ppp) outliers start: 93 outliers final: 63 residues processed: 702 average time/residue: 0.1076 time to fit residues: 115.0994 Evaluate side-chains 722 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 641 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 530 LYS Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 134 optimal weight: 0.9990 chunk 153 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 158 optimal weight: 8.9990 chunk 97 optimal weight: 0.8980 chunk 151 optimal weight: 20.0000 chunk 81 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.120955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.086224 restraints weight = 36022.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.089686 restraints weight = 17077.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.091893 restraints weight = 10199.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.093338 restraints weight = 7038.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.094273 restraints weight = 5363.109| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.7084 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= 0.168 Angle : 0.776 15.557 22134 Z= 0.378 Chirality : 0.047 0.387 2360 Planarity : 0.004 0.045 2818 Dihedral : 10.558 165.937 2246 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.90 % Allowed : 31.41 % Favored : 63.69 % 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: 0.71 (0.19), residues: 1932 helix: 0.99 (0.15), residues: 1131 sheet: -0.60 (0.42), residues: 152 loop : 0.02 (0.23), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 261 TYR 0.018 0.001 TYR C 242 PHE 0.028 0.002 PHE C 172 TRP 0.015 0.001 TRP C 44 HIS 0.006 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00381 (16386) covalent geometry : angle 0.77583 (22134) hydrogen bonds : bond 0.04084 ( 871) hydrogen bonds : angle 5.12858 ( 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 746 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 662 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.9657 (tttt) cc_final: 0.9449 (ttmm) REVERT: A 64 TYR cc_start: 0.9203 (m-10) cc_final: 0.8787 (m-10) REVERT: A 65 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8208 (mp0) REVERT: A 66 GLU cc_start: 0.8428 (tp30) cc_final: 0.8113 (tp30) REVERT: A 82 LYS cc_start: 0.9629 (mmmm) cc_final: 0.9292 (mmmm) REVERT: A 144 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8695 (mtm) REVERT: A 149 TYR cc_start: 0.9286 (t80) cc_final: 0.8874 (t80) REVERT: A 181 ASP cc_start: 0.8784 (m-30) cc_final: 0.8529 (m-30) REVERT: A 202 ASN cc_start: 0.9591 (t0) cc_final: 0.9275 (t0) REVERT: A 228 LYS cc_start: 0.9466 (mmmm) cc_final: 0.8944 (mmtt) REVERT: A 232 ASN cc_start: 0.9405 (OUTLIER) cc_final: 0.9090 (m-40) REVERT: A 286 ASP cc_start: 0.8600 (m-30) cc_final: 0.8273 (m-30) REVERT: A 321 GLU cc_start: 0.8870 (tp30) cc_final: 0.8439 (tp30) REVERT: A 359 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.8248 (ttp) REVERT: A 362 ASP cc_start: 0.8580 (m-30) cc_final: 0.8063 (m-30) REVERT: A 370 ASN cc_start: 0.9266 (m-40) cc_final: 0.8892 (m110) REVERT: A 384 GLU cc_start: 0.9004 (OUTLIER) cc_final: 0.7658 (pm20) REVERT: A 389 SER cc_start: 0.9384 (OUTLIER) cc_final: 0.9086 (p) REVERT: A 435 SER cc_start: 0.9512 (OUTLIER) cc_final: 0.9271 (t) REVERT: A 447 ASN cc_start: 0.8714 (m-40) cc_final: 0.7932 (m-40) REVERT: A 453 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.9003 (ttp80) REVERT: A 493 MET cc_start: 0.8894 (tmm) cc_final: 0.8135 (tmm) REVERT: A 505 GLU cc_start: 0.8996 (mt-10) cc_final: 0.8694 (mt-10) REVERT: A 512 GLU cc_start: 0.8655 (pt0) cc_final: 0.8333 (pt0) REVERT: A 583 SER cc_start: 0.9412 (m) cc_final: 0.8843 (t) REVERT: A 588 GLN cc_start: 0.9476 (tp40) cc_final: 0.9235 (tp-100) REVERT: A 602 GLU cc_start: 0.7820 (pt0) cc_final: 0.6006 (pt0) REVERT: A 604 ARG cc_start: 0.8950 (mmp80) cc_final: 0.8371 (mmt-90) REVERT: A 632 MET cc_start: 0.8769 (mtm) cc_final: 0.7966 (mtp) REVERT: A 640 MET cc_start: 0.9626 (tpp) cc_final: 0.8807 (tpp) REVERT: A 686 ARG cc_start: 0.8834 (mmm-85) cc_final: 0.8536 (mtp85) REVERT: B 17 MET cc_start: 0.8871 (mmm) cc_final: 0.8536 (mmm) REVERT: B 28 LYS cc_start: 0.9299 (mmtt) cc_final: 0.8986 (mmmm) REVERT: B 31 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8071 (mt-10) REVERT: B 65 GLU cc_start: 0.8747 (mm-30) cc_final: 0.8201 (mp0) REVERT: B 99 LYS cc_start: 0.9528 (mmmm) cc_final: 0.9285 (mmmm) REVERT: B 108 THR cc_start: 0.8627 (OUTLIER) cc_final: 0.8426 (p) REVERT: B 109 ASN cc_start: 0.9266 (m-40) cc_final: 0.8689 (p0) REVERT: B 116 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8329 (mt-10) REVERT: B 232 ASN cc_start: 0.9393 (m-40) cc_final: 0.9024 (m-40) REVERT: B 257 ASP cc_start: 0.8859 (m-30) cc_final: 0.8364 (m-30) REVERT: B 263 ASP cc_start: 0.9139 (m-30) cc_final: 0.8694 (p0) REVERT: B 286 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.7672 (m-30) REVERT: B 290 GLU cc_start: 0.8546 (tm-30) cc_final: 0.7944 (tm-30) REVERT: B 317 MET cc_start: 0.8450 (ptp) cc_final: 0.8174 (pmm) REVERT: B 319 MET cc_start: 0.8779 (tpp) cc_final: 0.8507 (tmm) REVERT: B 362 ASP cc_start: 0.8714 (m-30) cc_final: 0.7478 (m-30) REVERT: B 378 PHE cc_start: 0.9345 (p90) cc_final: 0.8885 (p90) REVERT: B 393 SER cc_start: 0.9349 (m) cc_final: 0.9091 (p) REVERT: B 394 TYR cc_start: 0.9166 (m-80) cc_final: 0.8894 (m-80) REVERT: B 447 ASN cc_start: 0.8239 (m-40) cc_final: 0.7877 (t0) REVERT: B 483 GLU cc_start: 0.9468 (mp0) cc_final: 0.9230 (mp0) REVERT: B 493 MET cc_start: 0.9689 (tmm) cc_final: 0.8873 (tmm) REVERT: B 515 ASP cc_start: 0.9035 (m-30) cc_final: 0.8801 (m-30) REVERT: B 610 LYS cc_start: 0.8927 (mmmt) cc_final: 0.8563 (mmmt) REVERT: B 612 TYR cc_start: 0.8567 (m-80) cc_final: 0.8093 (m-80) REVERT: B 628 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8170 (mm-30) REVERT: B 632 MET cc_start: 0.8906 (mtp) cc_final: 0.8406 (mpp) REVERT: C 19 GLN cc_start: 0.7546 (mp10) cc_final: 0.7127 (pm20) REVERT: C 20 MET cc_start: 0.9009 (tpp) cc_final: 0.8679 (tmm) REVERT: C 29 PHE cc_start: 0.8522 (t80) cc_final: 0.8160 (t80) REVERT: C 55 TYR cc_start: 0.8236 (t80) cc_final: 0.7401 (t80) REVERT: C 56 MET cc_start: 0.5842 (ttt) cc_final: 0.5334 (ttt) REVERT: C 69 GLN cc_start: 0.9254 (tp-100) cc_final: 0.9030 (tp-100) REVERT: C 80 HIS cc_start: 0.8882 (m90) cc_final: 0.8591 (m90) REVERT: C 96 MET cc_start: 0.8731 (mmt) cc_final: 0.8079 (mmm) REVERT: C 131 LEU cc_start: 0.9360 (mt) cc_final: 0.9111 (mt) REVERT: C 134 LYS cc_start: 0.9591 (pttm) cc_final: 0.9175 (pttm) REVERT: C 145 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7941 (tp) REVERT: C 150 GLU cc_start: 0.9254 (OUTLIER) cc_final: 0.8990 (tp30) REVERT: C 164 GLU cc_start: 0.9260 (mm-30) cc_final: 0.8674 (tp30) REVERT: C 169 TYR cc_start: 0.8463 (m-80) cc_final: 0.8216 (m-80) REVERT: C 178 PHE cc_start: 0.9345 (m-80) cc_final: 0.8385 (m-10) REVERT: C 185 MET cc_start: 0.8607 (pmm) cc_final: 0.7564 (pmm) REVERT: C 186 GLN cc_start: 0.9323 (mm110) cc_final: 0.8867 (mp10) REVERT: C 242 TYR cc_start: 0.9357 (t80) cc_final: 0.9116 (t80) REVERT: C 259 PHE cc_start: 0.8813 (t80) cc_final: 0.8331 (t80) REVERT: C 269 MET cc_start: 0.9145 (ppp) cc_final: 0.8941 (ppp) REVERT: C 313 GLU cc_start: 0.9030 (tt0) cc_final: 0.8827 (tm-30) REVERT: D 17 PHE cc_start: 0.7504 (m-10) cc_final: 0.7179 (m-80) REVERT: D 21 PHE cc_start: 0.9439 (m-80) cc_final: 0.8963 (m-80) REVERT: D 30 TRP cc_start: 0.8805 (p-90) cc_final: 0.7939 (p-90) REVERT: D 34 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8187 (mm-30) REVERT: D 42 LEU cc_start: 0.9390 (mp) cc_final: 0.9133 (mm) REVERT: D 46 TYR cc_start: 0.9057 (m-80) cc_final: 0.8769 (m-10) REVERT: D 136 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.8504 (mt0) REVERT: D 153 LEU cc_start: 0.9143 (tp) cc_final: 0.8777 (mt) REVERT: D 186 GLN cc_start: 0.9112 (mm-40) cc_final: 0.8581 (mp10) REVERT: D 207 LEU cc_start: 0.9233 (mm) cc_final: 0.8745 (mm) REVERT: D 210 GLN cc_start: 0.9349 (tm-30) cc_final: 0.9079 (pt0) REVERT: D 240 LEU cc_start: 0.8774 (mt) cc_final: 0.7921 (pp) REVERT: D 244 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7684 (mp0) REVERT: D 246 LEU cc_start: 0.8135 (mm) cc_final: 0.7701 (mt) REVERT: D 269 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.8089 (ppp) REVERT: D 287 LEU cc_start: 0.6549 (mt) cc_final: 0.6267 (mt) outliers start: 84 outliers final: 61 residues processed: 696 average time/residue: 0.1072 time to fit residues: 113.6755 Evaluate side-chains 723 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 648 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 87 LYS Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 7.9990 chunk 133 optimal weight: 1.9990 chunk 149 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 86 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 88 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN C 98 ASN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.124450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.088740 restraints weight = 35891.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.092254 restraints weight = 16985.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.094604 restraints weight = 10139.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.096081 restraints weight = 7016.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.097119 restraints weight = 5433.371| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.7316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16386 Z= 0.153 Angle : 0.801 15.691 22134 Z= 0.389 Chirality : 0.047 0.316 2360 Planarity : 0.004 0.045 2818 Dihedral : 10.380 161.766 2246 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 4.25 % Allowed : 32.34 % Favored : 63.40 % 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: 0.61 (0.19), residues: 1932 helix: 0.91 (0.15), residues: 1132 sheet: -0.52 (0.42), residues: 152 loop : -0.04 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 502 TYR 0.017 0.001 TYR A 355 PHE 0.040 0.002 PHE C 227 TRP 0.023 0.002 TRP D 124 HIS 0.006 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00349 (16386) covalent geometry : angle 0.80097 (22134) hydrogen bonds : bond 0.04108 ( 871) hydrogen bonds : angle 5.16272 ( 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 743 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 670 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.9672 (tttt) cc_final: 0.9462 (ttmm) REVERT: A 64 TYR cc_start: 0.9214 (m-10) cc_final: 0.8874 (m-10) REVERT: A 65 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8226 (mp0) REVERT: A 66 GLU cc_start: 0.8436 (tp30) cc_final: 0.8100 (tp30) REVERT: A 82 LYS cc_start: 0.9624 (mmmm) cc_final: 0.9290 (mmmm) REVERT: A 102 ASN cc_start: 0.9298 (m110) cc_final: 0.8875 (m110) REVERT: A 144 MET cc_start: 0.9131 (OUTLIER) cc_final: 0.8627 (mtm) REVERT: A 181 ASP cc_start: 0.8757 (m-30) cc_final: 0.8511 (m-30) REVERT: A 187 ASP cc_start: 0.9061 (OUTLIER) cc_final: 0.8612 (t70) REVERT: A 202 ASN cc_start: 0.9561 (t0) cc_final: 0.9233 (t0) REVERT: A 227 MET cc_start: 0.9089 (mtp) cc_final: 0.8861 (mtp) REVERT: A 228 LYS cc_start: 0.9444 (mmmm) cc_final: 0.8938 (mmtt) REVERT: A 232 ASN cc_start: 0.9399 (OUTLIER) cc_final: 0.9094 (m-40) REVERT: A 270 ASP cc_start: 0.9281 (p0) cc_final: 0.8937 (p0) REVERT: A 286 ASP cc_start: 0.8471 (m-30) cc_final: 0.8204 (m-30) REVERT: A 321 GLU cc_start: 0.8866 (tp30) cc_final: 0.8442 (tp30) REVERT: A 350 ARG cc_start: 0.9283 (mtp85) cc_final: 0.8936 (mtp180) REVERT: A 357 TYR cc_start: 0.8950 (m-10) cc_final: 0.8312 (m-10) REVERT: A 359 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8200 (ttp) REVERT: A 362 ASP cc_start: 0.8546 (m-30) cc_final: 0.8066 (m-30) REVERT: A 370 ASN cc_start: 0.9238 (m-40) cc_final: 0.8867 (m110) REVERT: A 384 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.7651 (pm20) REVERT: A 389 SER cc_start: 0.9372 (OUTLIER) cc_final: 0.9064 (p) REVERT: A 435 SER cc_start: 0.9510 (OUTLIER) cc_final: 0.9242 (t) REVERT: A 447 ASN cc_start: 0.8167 (m-40) cc_final: 0.7725 (t0) REVERT: A 453 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.9011 (ttp80) REVERT: A 493 MET cc_start: 0.8930 (tmm) cc_final: 0.8151 (tmm) REVERT: A 505 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8709 (mt-10) REVERT: A 512 GLU cc_start: 0.8617 (pt0) cc_final: 0.8387 (pt0) REVERT: A 583 SER cc_start: 0.9402 (m) cc_final: 0.8823 (t) REVERT: A 598 MET cc_start: 0.8550 (mmm) cc_final: 0.8129 (mmt) REVERT: A 602 GLU cc_start: 0.7901 (pt0) cc_final: 0.5907 (pt0) REVERT: A 604 ARG cc_start: 0.8954 (mmp80) cc_final: 0.8375 (mmt-90) REVERT: A 632 MET cc_start: 0.8676 (mtm) cc_final: 0.7901 (mtp) REVERT: A 640 MET cc_start: 0.9646 (tpp) cc_final: 0.8788 (tpp) REVERT: B 28 LYS cc_start: 0.9275 (mmtt) cc_final: 0.8683 (mmmm) REVERT: B 31 GLU cc_start: 0.8385 (mt-10) cc_final: 0.7894 (mt-10) REVERT: B 65 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8239 (mp0) REVERT: B 99 LYS cc_start: 0.9488 (mmmm) cc_final: 0.9256 (mmmm) REVERT: B 108 THR cc_start: 0.8838 (OUTLIER) cc_final: 0.8589 (p) REVERT: B 109 ASN cc_start: 0.9249 (m-40) cc_final: 0.8727 (p0) REVERT: B 232 ASN cc_start: 0.9379 (m-40) cc_final: 0.9045 (m-40) REVERT: B 257 ASP cc_start: 0.8852 (m-30) cc_final: 0.8356 (m-30) REVERT: B 263 ASP cc_start: 0.9133 (m-30) cc_final: 0.8672 (p0) REVERT: B 286 ASP cc_start: 0.8484 (OUTLIER) cc_final: 0.7806 (m-30) REVERT: B 290 GLU cc_start: 0.8502 (tm-30) cc_final: 0.7946 (tm-30) REVERT: B 319 MET cc_start: 0.8740 (tpp) cc_final: 0.8510 (tmm) REVERT: B 335 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7945 (mt-10) REVERT: B 344 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8481 (mt-10) REVERT: B 362 ASP cc_start: 0.8636 (m-30) cc_final: 0.7409 (m-30) REVERT: B 378 PHE cc_start: 0.9294 (p90) cc_final: 0.9091 (p90) REVERT: B 393 SER cc_start: 0.9293 (m) cc_final: 0.9076 (p) REVERT: B 394 TYR cc_start: 0.9092 (m-80) cc_final: 0.8698 (m-80) REVERT: B 413 SER cc_start: 0.9391 (OUTLIER) cc_final: 0.8518 (t) REVERT: B 447 ASN cc_start: 0.8137 (m-40) cc_final: 0.7848 (t0) REVERT: B 483 GLU cc_start: 0.9470 (mp0) cc_final: 0.9219 (mp0) REVERT: B 493 MET cc_start: 0.9664 (tmm) cc_final: 0.8845 (tmm) REVERT: B 515 ASP cc_start: 0.9015 (m-30) cc_final: 0.8787 (m-30) REVERT: B 610 LYS cc_start: 0.9017 (mmmt) cc_final: 0.8701 (mmmt) REVERT: B 628 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8336 (mm-30) REVERT: B 688 LYS cc_start: 0.8228 (tppt) cc_final: 0.7974 (ttpp) REVERT: C 19 GLN cc_start: 0.7502 (mp10) cc_final: 0.7076 (pm20) REVERT: C 20 MET cc_start: 0.8996 (tpp) cc_final: 0.8683 (tmm) REVERT: C 29 PHE cc_start: 0.8500 (t80) cc_final: 0.8223 (t80) REVERT: C 55 TYR cc_start: 0.8213 (t80) cc_final: 0.7339 (t80) REVERT: C 56 MET cc_start: 0.5726 (ttt) cc_final: 0.5205 (ttt) REVERT: C 80 HIS cc_start: 0.8884 (m90) cc_final: 0.8565 (m170) REVERT: C 96 MET cc_start: 0.8621 (mmt) cc_final: 0.8127 (mmm) REVERT: C 145 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7825 (tp) REVERT: C 150 GLU cc_start: 0.9239 (OUTLIER) cc_final: 0.8943 (mm-30) REVERT: C 164 GLU cc_start: 0.9288 (mm-30) cc_final: 0.8593 (tp30) REVERT: C 169 TYR cc_start: 0.8444 (m-80) cc_final: 0.8194 (m-80) REVERT: C 178 PHE cc_start: 0.9334 (m-80) cc_final: 0.8378 (m-80) REVERT: C 185 MET cc_start: 0.8705 (pmm) cc_final: 0.8480 (pmm) REVERT: C 186 GLN cc_start: 0.9352 (mm110) cc_final: 0.9066 (mp10) REVERT: C 189 GLU cc_start: 0.8444 (tp30) cc_final: 0.7734 (mp0) REVERT: C 229 ILE cc_start: 0.8539 (mm) cc_final: 0.8262 (mm) REVERT: C 259 PHE cc_start: 0.8867 (t80) cc_final: 0.8368 (t80) REVERT: C 274 ASP cc_start: 0.7275 (p0) cc_final: 0.6858 (p0) REVERT: D 17 PHE cc_start: 0.7595 (m-10) cc_final: 0.7255 (m-80) REVERT: D 21 PHE cc_start: 0.9370 (m-80) cc_final: 0.8875 (m-80) REVERT: D 30 TRP cc_start: 0.8862 (p-90) cc_final: 0.7840 (p-90) REVERT: D 42 LEU cc_start: 0.9388 (mp) cc_final: 0.9143 (mm) REVERT: D 46 TYR cc_start: 0.9017 (m-80) cc_final: 0.8737 (m-10) REVERT: D 136 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8542 (mt0) REVERT: D 186 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8525 (mp10) REVERT: D 207 LEU cc_start: 0.9211 (mm) cc_final: 0.8727 (mm) REVERT: D 210 GLN cc_start: 0.9341 (tm-30) cc_final: 0.9070 (pt0) REVERT: D 240 LEU cc_start: 0.8730 (mt) cc_final: 0.8173 (pp) REVERT: D 269 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.7956 (ppp) outliers start: 73 outliers final: 55 residues processed: 703 average time/residue: 0.1017 time to fit residues: 108.0511 Evaluate side-chains 718 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 648 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 189 optimal weight: 10.0000 chunk 181 optimal weight: 0.9980 chunk 165 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 54 optimal weight: 0.7980 chunk 132 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.125166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.089632 restraints weight = 36075.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.093134 restraints weight = 17254.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.095440 restraints weight = 10308.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.096983 restraints weight = 7160.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.097948 restraints weight = 5505.789| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.7519 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= 0.164 Angle : 0.856 15.716 22134 Z= 0.415 Chirality : 0.049 0.308 2360 Planarity : 0.004 0.058 2818 Dihedral : 10.314 156.882 2246 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 4.02 % Allowed : 33.74 % Favored : 62.24 % 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: 0.46 (0.19), residues: 1932 helix: 0.77 (0.15), residues: 1144 sheet: -0.45 (0.43), residues: 152 loop : -0.14 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG C 261 TYR 0.044 0.001 TYR B 571 PHE 0.030 0.002 PHE B 89 TRP 0.028 0.002 TRP D 124 HIS 0.006 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00377 (16386) covalent geometry : angle 0.85557 (22134) hydrogen bonds : bond 0.04226 ( 871) hydrogen bonds : angle 5.23411 ( 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 742 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 673 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9231 (mmmm) cc_final: 0.9020 (ttmm) REVERT: A 27 ASP cc_start: 0.9085 (p0) cc_final: 0.8812 (p0) REVERT: A 54 LYS cc_start: 0.9670 (tttt) cc_final: 0.9468 (ttmm) REVERT: A 64 TYR cc_start: 0.9217 (m-10) cc_final: 0.8889 (m-10) REVERT: A 65 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8355 (mp0) REVERT: A 66 GLU cc_start: 0.8496 (tp30) cc_final: 0.8230 (tp30) REVERT: A 82 LYS cc_start: 0.9607 (mmmm) cc_final: 0.9256 (mmmm) REVERT: A 102 ASN cc_start: 0.9278 (m110) cc_final: 0.8880 (m110) REVERT: A 149 TYR cc_start: 0.9316 (t80) cc_final: 0.8831 (t80) REVERT: A 181 ASP cc_start: 0.8726 (m-30) cc_final: 0.8518 (m-30) REVERT: A 187 ASP cc_start: 0.9041 (OUTLIER) cc_final: 0.8742 (t70) REVERT: A 191 GLN cc_start: 0.8446 (mm-40) cc_final: 0.7944 (mt0) REVERT: A 202 ASN cc_start: 0.9525 (t0) cc_final: 0.9192 (t0) REVERT: A 227 MET cc_start: 0.9095 (mtp) cc_final: 0.8849 (mtp) REVERT: A 228 LYS cc_start: 0.9438 (mmmm) cc_final: 0.8940 (mmtt) REVERT: A 232 ASN cc_start: 0.9403 (OUTLIER) cc_final: 0.9068 (m-40) REVERT: A 270 ASP cc_start: 0.9278 (p0) cc_final: 0.8991 (p0) REVERT: A 321 GLU cc_start: 0.8846 (tp30) cc_final: 0.8417 (tp30) REVERT: A 350 ARG cc_start: 0.9273 (mtp85) cc_final: 0.8980 (mtp180) REVERT: A 357 TYR cc_start: 0.8949 (m-10) cc_final: 0.8242 (m-10) REVERT: A 359 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8213 (ttp) REVERT: A 362 ASP cc_start: 0.8533 (m-30) cc_final: 0.8128 (m-30) REVERT: A 370 ASN cc_start: 0.9236 (m-40) cc_final: 0.8879 (m110) REVERT: A 384 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.7664 (pm20) REVERT: A 389 SER cc_start: 0.9377 (OUTLIER) cc_final: 0.9071 (p) REVERT: A 435 SER cc_start: 0.9521 (OUTLIER) cc_final: 0.9270 (t) REVERT: A 447 ASN cc_start: 0.8064 (m-40) cc_final: 0.6676 (m-40) REVERT: A 453 ARG cc_start: 0.9225 (OUTLIER) cc_final: 0.9000 (ttp80) REVERT: A 493 MET cc_start: 0.8910 (tmm) cc_final: 0.8097 (tmm) REVERT: A 505 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8717 (mt-10) REVERT: A 512 GLU cc_start: 0.8607 (pt0) cc_final: 0.8392 (pt0) REVERT: A 583 SER cc_start: 0.9376 (m) cc_final: 0.8810 (t) REVERT: A 598 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8229 (mmt) REVERT: A 602 GLU cc_start: 0.7834 (pt0) cc_final: 0.6232 (pt0) REVERT: A 604 ARG cc_start: 0.8933 (mmp80) cc_final: 0.8230 (mmt-90) REVERT: A 632 MET cc_start: 0.8681 (mtm) cc_final: 0.7919 (mtp) REVERT: A 640 MET cc_start: 0.9626 (tpp) cc_final: 0.8793 (tpp) REVERT: B 28 LYS cc_start: 0.9250 (mmtt) cc_final: 0.8633 (mmmm) REVERT: B 31 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7860 (mt-10) REVERT: B 65 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8172 (mp0) REVERT: B 99 LYS cc_start: 0.9481 (mmmm) cc_final: 0.9253 (mmmm) REVERT: B 161 ARG cc_start: 0.8867 (ttm110) cc_final: 0.8314 (ttm-80) REVERT: B 232 ASN cc_start: 0.9387 (m-40) cc_final: 0.9058 (m-40) REVERT: B 257 ASP cc_start: 0.8830 (m-30) cc_final: 0.8369 (m-30) REVERT: B 263 ASP cc_start: 0.9128 (m-30) cc_final: 0.8661 (p0) REVERT: B 271 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8601 (tp30) REVERT: B 286 ASP cc_start: 0.8496 (OUTLIER) cc_final: 0.7802 (m-30) REVERT: B 290 GLU cc_start: 0.8447 (tm-30) cc_final: 0.7898 (tm-30) REVERT: B 319 MET cc_start: 0.8842 (tpp) cc_final: 0.8642 (tmm) REVERT: B 335 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7976 (mt-10) REVERT: B 344 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8413 (mt-10) REVERT: B 362 ASP cc_start: 0.8656 (m-30) cc_final: 0.7407 (m-30) REVERT: B 393 SER cc_start: 0.9238 (m) cc_final: 0.9021 (p) REVERT: B 394 TYR cc_start: 0.9007 (m-80) cc_final: 0.8683 (m-80) REVERT: B 413 SER cc_start: 0.9399 (OUTLIER) cc_final: 0.8581 (t) REVERT: B 447 ASN cc_start: 0.8162 (m-40) cc_final: 0.7876 (t0) REVERT: B 483 GLU cc_start: 0.9456 (mp0) cc_final: 0.9217 (mp0) REVERT: B 493 MET cc_start: 0.9670 (tmm) cc_final: 0.8847 (tmm) REVERT: B 515 ASP cc_start: 0.9009 (m-30) cc_final: 0.8774 (m-30) REVERT: B 610 LYS cc_start: 0.8996 (mmmt) cc_final: 0.8716 (mmmt) REVERT: B 628 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8358 (mm-30) REVERT: B 688 LYS cc_start: 0.8277 (tppt) cc_final: 0.8019 (ttpp) REVERT: C 19 GLN cc_start: 0.7311 (mp10) cc_final: 0.6897 (pm20) REVERT: C 20 MET cc_start: 0.8899 (tpp) cc_final: 0.8518 (tmm) REVERT: C 29 PHE cc_start: 0.8471 (t80) cc_final: 0.8189 (t80) REVERT: C 56 MET cc_start: 0.5696 (ttt) cc_final: 0.5266 (ttt) REVERT: C 80 HIS cc_start: 0.8753 (m90) cc_final: 0.8529 (m90) REVERT: C 96 MET cc_start: 0.8710 (mmt) cc_final: 0.8230 (mmm) REVERT: C 145 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7829 (tp) REVERT: C 164 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8932 (tp30) REVERT: C 178 PHE cc_start: 0.9342 (m-80) cc_final: 0.8804 (m-10) REVERT: C 185 MET cc_start: 0.8745 (pmm) cc_final: 0.7732 (pmm) REVERT: C 186 GLN cc_start: 0.9347 (mm110) cc_final: 0.8939 (mp10) REVERT: C 229 ILE cc_start: 0.8594 (mm) cc_final: 0.8252 (mm) REVERT: C 259 PHE cc_start: 0.8892 (t80) cc_final: 0.8394 (t80) REVERT: D 17 PHE cc_start: 0.7566 (m-10) cc_final: 0.7227 (m-80) REVERT: D 21 PHE cc_start: 0.9322 (m-80) cc_final: 0.8818 (m-80) REVERT: D 28 GLN cc_start: 0.9141 (tt0) cc_final: 0.8740 (tm-30) REVERT: D 30 TRP cc_start: 0.8680 (p-90) cc_final: 0.7840 (p-90) REVERT: D 42 LEU cc_start: 0.9369 (mp) cc_final: 0.9153 (mm) REVERT: D 46 TYR cc_start: 0.8981 (m-80) cc_final: 0.8693 (m-10) REVERT: D 96 MET cc_start: 0.8671 (mmt) cc_final: 0.8292 (mmm) REVERT: D 129 LYS cc_start: 0.9407 (tmtt) cc_final: 0.9077 (tppt) REVERT: D 130 TYR cc_start: 0.6671 (m-10) cc_final: 0.6346 (m-10) REVERT: D 137 MET cc_start: 0.7797 (mtt) cc_final: 0.7400 (ptp) REVERT: D 153 LEU cc_start: 0.9313 (tp) cc_final: 0.8965 (mt) REVERT: D 154 PHE cc_start: 0.9013 (m-80) cc_final: 0.8812 (m-80) REVERT: D 186 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8482 (mp10) REVERT: D 207 LEU cc_start: 0.9164 (mm) cc_final: 0.8787 (mm) REVERT: D 210 GLN cc_start: 0.9262 (tm-30) cc_final: 0.8978 (pt0) REVERT: D 240 LEU cc_start: 0.8709 (mt) cc_final: 0.7917 (pp) REVERT: D 244 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7642 (mp0) REVERT: D 269 MET cc_start: 0.8317 (OUTLIER) cc_final: 0.7916 (ppp) outliers start: 69 outliers final: 50 residues processed: 704 average time/residue: 0.1070 time to fit residues: 114.6632 Evaluate side-chains 716 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 653 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain A residue 687 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 599 GLU Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 41 LEU Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 0.8980 chunk 1 optimal weight: 0.0050 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 148 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN D 249 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.127472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.091973 restraints weight = 35667.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.095494 restraints weight = 16817.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.097811 restraints weight = 10084.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.099339 restraints weight = 6984.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.100371 restraints weight = 5392.209| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.7744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16386 Z= 0.154 Angle : 0.850 15.265 22134 Z= 0.415 Chirality : 0.048 0.354 2360 Planarity : 0.004 0.048 2818 Dihedral : 9.958 143.786 2246 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.44 % Allowed : 34.38 % Favored : 62.18 % 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: 0.40 (0.19), residues: 1932 helix: 0.76 (0.15), residues: 1132 sheet: -0.37 (0.44), residues: 152 loop : -0.26 (0.23), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG C 261 TYR 0.023 0.001 TYR D 242 PHE 0.038 0.002 PHE B 378 TRP 0.029 0.002 TRP D 124 HIS 0.006 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00349 (16386) covalent geometry : angle 0.85026 (22134) hydrogen bonds : bond 0.04217 ( 871) hydrogen bonds : angle 5.25268 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3201.60 seconds wall clock time: 56 minutes 10.62 seconds (3370.62 seconds total)