Starting phenix.real_space_refine on Sat Jun 14 07:35:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byt_45044/06_2025/9byt_45044_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byt_45044/06_2025/9byt_45044.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9byt_45044/06_2025/9byt_45044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byt_45044/06_2025/9byt_45044.map" model { file = "/net/cci-nas-00/data/ceres_data/9byt_45044/06_2025/9byt_45044_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byt_45044/06_2025/9byt_45044_neut.cif" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.67, per 1000 atoms: 0.60 Number of scatterers: 16038 At special positions: 0 Unit cell: (94.581, 132.21, 132.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.62 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.104A 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: 3.985A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.953A 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: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.694A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.850A 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: 4.118A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.677A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.878A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.026A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.068A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.669A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.360A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.902A 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: 8.394A 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: 4.050A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.516A 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: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.749A 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: 5.63 Time building geometry restraints manager: 5.40 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: 4852 1.34 - 1.46: 3027 1.46 - 1.58: 8326 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.600 -0.060 1.25e-02 6.40e+03 2.31e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.038 1.20e-02 6.94e+03 1.01e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.032 1.08e-02 8.57e+03 8.86e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.569 -0.032 1.17e-02 7.31e+03 7.65e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.574 -0.033 1.25e-02 6.40e+03 7.18e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21572 2.09 - 4.18: 519 4.18 - 6.26: 37 6.26 - 8.35: 2 8.35 - 10.44: 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 110.54 116.62 -6.08 1.36e+00 5.41e-01 2.00e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.11 -4.40 1.15e+00 7.56e-01 1.46e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.23 -3.95 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 113.50 117.88 -4.38 1.23e+00 6.61e-01 1.27e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.72 -4.01 1.15e+00 7.56e-01 1.22e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 9469 35.80 - 71.59: 338 71.59 - 107.39: 37 107.39 - 143.18: 3 143.18 - 178.98: 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 -58.32 120.66 -178.98 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 301.68 151.13 150.56 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 31.89 148.08 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: 2137 0.093 - 0.185: 189 0.185 - 0.278: 29 0.278 - 0.371: 3 0.371 - 0.463: 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 2.05 0.46 2.00e-01 2.50e+01 5.36e+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 4.69e+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 0.34 2.00e-01 2.50e+01 2.97e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " 0.017 2.00e-02 2.50e+03 1.12e-02 2.19e+00 pdb=" CG PHE D 92 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 179 " -0.017 2.00e-02 2.50e+03 9.85e-03 1.94e+00 pdb=" CG TYR D 179 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR D 179 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 179 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR D 179 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 179 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR D 179 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 179 " -0.005 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 129 2.51 - 3.11: 11548 3.11 - 3.70: 27039 3.70 - 4.30: 41566 4.30 - 4.90: 65461 Nonbonded interactions: 145743 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 1.960 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 2.013 3.040 ... (remaining 145738 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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 38.630 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.070 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 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 10.439 22134 Z= 0.463 Chirality : 0.058 0.463 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.930 178.978 6154 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.28 % Allowed : 15.27 % Favored : 83.45 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.18), residues: 1932 helix: 0.59 (0.14), residues: 1151 sheet: 0.47 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE C 227 TYR 0.021 0.002 TYR D 179 ARG 0.004 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.15418 ( 871) hydrogen bonds : angle 6.51825 ( 2571) covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74001 (22134) *********************** 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 865 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 843 time to evaluate : 1.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 GLN cc_start: 0.8483 (mt0) cc_final: 0.7269 (mt0) REVERT: A 157 LEU cc_start: 0.9043 (tp) cc_final: 0.8828 (tt) REVERT: A 158 ASN cc_start: 0.8905 (m-40) cc_final: 0.8612 (m-40) REVERT: A 179 LEU cc_start: 0.9247 (tp) cc_final: 0.8708 (tp) REVERT: A 194 LYS cc_start: 0.8983 (tttt) cc_final: 0.8757 (tttm) REVERT: A 588 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7338 (mm-40) REVERT: A 598 MET cc_start: 0.7934 (mtm) cc_final: 0.7330 (mtp) REVERT: A 606 TYR cc_start: 0.7291 (m-80) cc_final: 0.7057 (m-80) REVERT: B 355 TYR cc_start: 0.7743 (m-80) cc_final: 0.7490 (m-80) REVERT: B 358 ILE cc_start: 0.9170 (mm) cc_final: 0.8929 (mm) REVERT: B 421 GLU cc_start: 0.7475 (tt0) cc_final: 0.7266 (tt0) REVERT: B 602 GLU cc_start: 0.6377 (pt0) cc_final: 0.6090 (pt0) REVERT: B 615 MET cc_start: 0.8772 (mmp) cc_final: 0.8472 (mmp) REVERT: C 250 VAL cc_start: 0.4562 (m) cc_final: 0.4330 (p) REVERT: D 178 PHE cc_start: 0.6980 (m-80) cc_final: 0.5802 (m-10) outliers start: 22 outliers final: 7 residues processed: 848 average time/residue: 0.3020 time to fit residues: 365.8564 Evaluate side-chains 554 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 547 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain D residue 59 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 112 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 304 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS D 50 ASN D 71 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.146657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.093523 restraints weight = 27373.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.097160 restraints weight = 11617.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.099366 restraints weight = 6839.979| |-----------------------------------------------------------------------------| r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3068 r_free = 0.3068 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3068 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 16386 Z= 0.371 Angle : 0.750 12.094 22134 Z= 0.391 Chirality : 0.049 0.271 2360 Planarity : 0.004 0.054 2818 Dihedral : 11.743 175.663 2253 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 5.07 % Allowed : 17.72 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.18), residues: 1932 helix: 1.18 (0.15), residues: 1148 sheet: -0.10 (0.40), residues: 144 loop : 0.57 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 9 HIS 0.006 0.001 HIS A 438 PHE 0.029 0.002 PHE C 168 TYR 0.024 0.002 TYR A 612 ARG 0.007 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04920 ( 871) hydrogen bonds : angle 5.10983 ( 2571) covalent geometry : bond 0.00826 (16386) covalent geometry : angle 0.75034 (22134) *********************** 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 644 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 557 time to evaluate : 1.721 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 65 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7824 (mt-10) REVERT: A 67 GLU cc_start: 0.8323 (pm20) cc_final: 0.8083 (pm20) REVERT: A 103 ASP cc_start: 0.8717 (m-30) cc_final: 0.8455 (m-30) REVERT: A 118 TYR cc_start: 0.9413 (t80) cc_final: 0.9005 (t80) REVERT: A 144 MET cc_start: 0.9139 (mtm) cc_final: 0.8681 (mtm) REVERT: A 147 GLN cc_start: 0.9269 (mt0) cc_final: 0.8808 (mt0) REVERT: A 148 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8271 (mt-10) REVERT: A 250 TYR cc_start: 0.9123 (m-80) cc_final: 0.8707 (m-80) REVERT: A 259 ASN cc_start: 0.9066 (m-40) cc_final: 0.8507 (m-40) REVERT: A 263 ASP cc_start: 0.8738 (m-30) cc_final: 0.8388 (m-30) REVERT: A 277 THR cc_start: 0.8684 (OUTLIER) cc_final: 0.8331 (t) REVERT: A 321 GLU cc_start: 0.8592 (pt0) cc_final: 0.8317 (pt0) REVERT: A 352 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7424 (mm-30) REVERT: A 379 SER cc_start: 0.9369 (t) cc_final: 0.8913 (t) REVERT: A 381 LEU cc_start: 0.9479 (tp) cc_final: 0.9231 (tp) REVERT: A 384 GLU cc_start: 0.8830 (OUTLIER) cc_final: 0.6843 (pm20) REVERT: A 409 CYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8669 (p) REVERT: A 415 ASN cc_start: 0.9391 (t0) cc_final: 0.9180 (t0) REVERT: A 615 MET cc_start: 0.9134 (OUTLIER) cc_final: 0.8871 (mmm) REVERT: A 628 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8377 (mm-30) REVERT: A 658 LEU cc_start: 0.9672 (mt) cc_final: 0.9449 (mp) REVERT: A 683 TYR cc_start: 0.9128 (t80) cc_final: 0.8509 (t80) REVERT: B 40 TYR cc_start: 0.9217 (t80) cc_final: 0.8992 (t80) REVERT: B 253 ILE cc_start: 0.9583 (tt) cc_final: 0.9247 (tt) REVERT: B 263 ASP cc_start: 0.8950 (m-30) cc_final: 0.8615 (m-30) REVERT: B 274 ARG cc_start: 0.8160 (ttm110) cc_final: 0.7614 (ptp90) REVERT: B 336 LYS cc_start: 0.9434 (OUTLIER) cc_final: 0.9039 (ttmm) REVERT: B 355 TYR cc_start: 0.8600 (m-80) cc_final: 0.7910 (m-80) REVERT: B 384 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: B 515 ASP cc_start: 0.8876 (m-30) cc_final: 0.8368 (m-30) REVERT: B 586 TYR cc_start: 0.8913 (m-80) cc_final: 0.8702 (m-80) REVERT: B 599 GLU cc_start: 0.8253 (pt0) cc_final: 0.8012 (pt0) REVERT: B 615 MET cc_start: 0.9575 (mmp) cc_final: 0.9244 (mmp) REVERT: C 21 PHE cc_start: 0.9034 (m-80) cc_final: 0.8628 (m-80) REVERT: C 92 PHE cc_start: 0.8115 (t80) cc_final: 0.7664 (t80) REVERT: C 154 PHE cc_start: 0.9111 (t80) cc_final: 0.8614 (t80) REVERT: C 157 MET cc_start: 0.9404 (mtp) cc_final: 0.9018 (mtp) REVERT: C 189 GLU cc_start: 0.9109 (tp30) cc_final: 0.8801 (tp30) REVERT: C 193 LEU cc_start: 0.9158 (mt) cc_final: 0.8867 (mt) REVERT: C 196 ARG cc_start: 0.9217 (ptm-80) cc_final: 0.8892 (ptm-80) REVERT: C 241 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8900 (mp0) REVERT: C 243 THR cc_start: 0.8760 (p) cc_final: 0.8536 (t) REVERT: C 259 PHE cc_start: 0.8290 (t80) cc_final: 0.8010 (t80) REVERT: D 30 TRP cc_start: 0.7342 (p-90) cc_final: 0.6775 (p-90) REVERT: D 128 ASN cc_start: 0.8021 (t0) cc_final: 0.7807 (m110) REVERT: D 138 ILE cc_start: 0.9508 (mm) cc_final: 0.9045 (mm) REVERT: D 153 LEU cc_start: 0.6097 (tp) cc_final: 0.5751 (mm) REVERT: D 162 TYR cc_start: 0.7948 (t80) cc_final: 0.7533 (t80) REVERT: D 185 MET cc_start: 0.6047 (mmm) cc_final: 0.5759 (mmm) REVERT: D 197 ASP cc_start: 0.8750 (m-30) cc_final: 0.8505 (m-30) REVERT: D 224 LEU cc_start: 0.8535 (mt) cc_final: 0.8324 (mt) REVERT: D 227 PHE cc_start: 0.9180 (t80) cc_final: 0.8970 (t80) REVERT: D 235 LEU cc_start: 0.9282 (mt) cc_final: 0.9067 (mt) REVERT: D 236 TYR cc_start: 0.7901 (t80) cc_final: 0.7680 (t80) REVERT: D 269 MET cc_start: 0.9143 (tmm) cc_final: 0.8725 (tmm) REVERT: D 286 VAL cc_start: 0.6237 (p) cc_final: 0.6010 (m) REVERT: D 287 LEU cc_start: 0.6602 (mt) cc_final: 0.6367 (mt) outliers start: 87 outliers final: 45 residues processed: 609 average time/residue: 0.2779 time to fit residues: 251.8381 Evaluate side-chains 533 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 482 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 615 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 384 GLU 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 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 252 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 132 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 191 optimal weight: 8.9990 chunk 57 optimal weight: 0.5980 chunk 52 optimal weight: 2.9990 chunk 171 optimal weight: 10.0000 chunk 189 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN D 25 ASN D 85 GLN D 263 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.148210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.096322 restraints weight = 27290.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.100009 restraints weight = 11505.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.102162 restraints weight = 6700.627| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4631 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= 0.197 Angle : 0.641 11.425 22134 Z= 0.335 Chirality : 0.044 0.346 2360 Planarity : 0.004 0.057 2818 Dihedral : 11.241 170.592 2249 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.85 % Allowed : 20.28 % Favored : 75.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.19), residues: 1932 helix: 1.25 (0.15), residues: 1153 sheet: -0.36 (0.40), residues: 148 loop : 0.50 (0.24), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 9 HIS 0.005 0.001 HIS A 438 PHE 0.044 0.002 PHE D 172 TYR 0.027 0.002 TYR D 142 ARG 0.006 0.001 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.04321 ( 871) hydrogen bonds : angle 4.93268 ( 2571) covalent geometry : bond 0.00444 (16386) covalent geometry : angle 0.64115 (22134) *********************** 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 613 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 547 time to evaluate : 1.870 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 31 GLU cc_start: 0.8589 (mp0) cc_final: 0.8245 (mp0) REVERT: A 65 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7876 (mt-10) REVERT: A 103 ASP cc_start: 0.8666 (m-30) cc_final: 0.8389 (m-30) REVERT: A 106 LEU cc_start: 0.9170 (tp) cc_final: 0.8938 (tp) REVERT: A 144 MET cc_start: 0.8964 (mtm) cc_final: 0.8260 (mtm) REVERT: A 147 GLN cc_start: 0.9153 (mt0) cc_final: 0.7413 (mt0) REVERT: A 148 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8301 (mt-10) REVERT: A 250 TYR cc_start: 0.9111 (m-80) cc_final: 0.8752 (m-80) REVERT: A 251 LEU cc_start: 0.9368 (tp) cc_final: 0.9036 (tp) REVERT: A 259 ASN cc_start: 0.9079 (m-40) cc_final: 0.8483 (m-40) REVERT: A 263 ASP cc_start: 0.8671 (m-30) cc_final: 0.8289 (m-30) REVERT: A 276 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8611 (ptpp) REVERT: A 277 THR cc_start: 0.8516 (p) cc_final: 0.8218 (t) REVERT: A 335 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7985 (mm-30) REVERT: A 379 SER cc_start: 0.9296 (t) cc_final: 0.8991 (t) REVERT: A 381 LEU cc_start: 0.9490 (tp) cc_final: 0.9219 (tp) REVERT: A 384 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.6823 (pm20) REVERT: A 390 GLN cc_start: 0.8727 (OUTLIER) cc_final: 0.8523 (mt0) REVERT: A 415 ASN cc_start: 0.9376 (t0) cc_final: 0.9147 (t0) REVERT: A 526 GLU cc_start: 0.8484 (tt0) cc_final: 0.8276 (tt0) REVERT: A 583 SER cc_start: 0.9312 (OUTLIER) cc_final: 0.8913 (t) REVERT: A 588 GLN cc_start: 0.9046 (mm-40) cc_final: 0.7827 (mm-40) REVERT: A 628 GLU cc_start: 0.8643 (mt-10) cc_final: 0.8417 (mm-30) REVERT: B 111 LYS cc_start: 0.9444 (mmtp) cc_final: 0.9058 (mmtt) REVERT: B 263 ASP cc_start: 0.8882 (m-30) cc_final: 0.8489 (m-30) REVERT: B 274 ARG cc_start: 0.8143 (ttm110) cc_final: 0.7351 (ptp-110) REVERT: B 394 TYR cc_start: 0.9238 (m-80) cc_final: 0.8651 (m-80) REVERT: B 515 ASP cc_start: 0.8841 (m-30) cc_final: 0.8313 (m-30) REVERT: B 599 GLU cc_start: 0.8246 (pt0) cc_final: 0.7966 (pt0) REVERT: B 615 MET cc_start: 0.9537 (mmp) cc_final: 0.9257 (mmp) REVERT: B 650 GLN cc_start: 0.8859 (mt0) cc_final: 0.8651 (mt0) REVERT: B 662 MET cc_start: 0.8393 (ptp) cc_final: 0.8190 (ptp) REVERT: C 21 PHE cc_start: 0.9120 (m-80) cc_final: 0.8794 (m-80) REVERT: C 56 MET cc_start: 0.7059 (ptm) cc_final: 0.6503 (ttp) REVERT: C 122 PHE cc_start: 0.8710 (m-80) cc_final: 0.8407 (m-10) REVERT: C 130 TYR cc_start: 0.8983 (m-80) cc_final: 0.8202 (m-80) REVERT: C 154 PHE cc_start: 0.9114 (t80) cc_final: 0.8642 (t80) REVERT: C 162 TYR cc_start: 0.9013 (m-80) cc_final: 0.8799 (m-80) REVERT: C 168 PHE cc_start: 0.8883 (m-80) cc_final: 0.8608 (m-80) REVERT: C 189 GLU cc_start: 0.9113 (tp30) cc_final: 0.8785 (tp30) REVERT: C 193 LEU cc_start: 0.9209 (mt) cc_final: 0.8972 (mt) REVERT: C 241 GLU cc_start: 0.9288 (mt-10) cc_final: 0.8857 (mt-10) REVERT: C 244 GLU cc_start: 0.9581 (pt0) cc_final: 0.9187 (pp20) REVERT: C 245 ASP cc_start: 0.8407 (t0) cc_final: 0.7895 (t0) REVERT: C 259 PHE cc_start: 0.8269 (t80) cc_final: 0.8010 (t80) REVERT: D 30 TRP cc_start: 0.7033 (p-90) cc_final: 0.6781 (p-90) REVERT: D 132 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.8212 (mm110) REVERT: D 138 ILE cc_start: 0.9398 (mm) cc_final: 0.9120 (mm) REVERT: D 153 LEU cc_start: 0.6499 (tp) cc_final: 0.5817 (mm) REVERT: D 154 PHE cc_start: 0.7742 (t80) cc_final: 0.7409 (t80) REVERT: D 162 TYR cc_start: 0.7808 (t80) cc_final: 0.6998 (t80) REVERT: D 197 ASP cc_start: 0.8787 (m-30) cc_final: 0.8560 (m-30) outliers start: 66 outliers final: 44 residues processed: 582 average time/residue: 0.2643 time to fit residues: 231.9225 Evaluate side-chains 541 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 492 time to evaluate : 1.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 390 GLN Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER 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 B residue 33 VAL Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 208 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 85 GLN Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 180 optimal weight: 0.9980 chunk 99 optimal weight: 5.9990 chunk 1 optimal weight: 0.0050 chunk 39 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 69 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 148 optimal weight: 20.0000 chunk 90 optimal weight: 0.6980 chunk 94 optimal weight: 0.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN B 474 GLN B 645 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 ASN D 85 GLN D 132 GLN D 265 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.151899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.099961 restraints weight = 27202.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.103700 restraints weight = 11366.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.105894 restraints weight = 6555.615| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16386 Z= 0.162 Angle : 0.609 12.327 22134 Z= 0.318 Chirality : 0.044 0.363 2360 Planarity : 0.003 0.046 2818 Dihedral : 10.851 161.708 2249 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.90 % Allowed : 21.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.19), residues: 1932 helix: 1.30 (0.15), residues: 1127 sheet: -0.38 (0.41), residues: 148 loop : 0.37 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 44 HIS 0.004 0.001 HIS A 438 PHE 0.033 0.002 PHE D 172 TYR 0.030 0.002 TYR D 142 ARG 0.005 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 871) hydrogen bonds : angle 4.86874 ( 2571) covalent geometry : bond 0.00364 (16386) covalent geometry : angle 0.60869 (22134) *********************** 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 587 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 520 time to evaluate : 1.952 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 103 ASP cc_start: 0.8701 (m-30) cc_final: 0.8416 (m-30) REVERT: A 106 LEU cc_start: 0.9134 (tp) cc_final: 0.8919 (tp) REVERT: A 144 MET cc_start: 0.8935 (mtm) cc_final: 0.8315 (mtm) REVERT: A 147 GLN cc_start: 0.9118 (mt0) cc_final: 0.8767 (mt0) REVERT: A 148 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8325 (mt-10) REVERT: A 157 LEU cc_start: 0.9271 (tp) cc_final: 0.9053 (tt) REVERT: A 158 ASN cc_start: 0.8982 (m-40) cc_final: 0.8587 (m-40) REVERT: A 209 LYS cc_start: 0.8979 (tttm) cc_final: 0.8364 (ttmm) REVERT: A 250 TYR cc_start: 0.9114 (m-80) cc_final: 0.8750 (m-80) REVERT: A 259 ASN cc_start: 0.9078 (m-40) cc_final: 0.8476 (m-40) REVERT: A 263 ASP cc_start: 0.8734 (m-30) cc_final: 0.8321 (m-30) REVERT: A 277 THR cc_start: 0.8427 (OUTLIER) cc_final: 0.8161 (t) REVERT: A 335 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7974 (mm-30) REVERT: A 379 SER cc_start: 0.9263 (t) cc_final: 0.8791 (t) REVERT: A 384 GLU cc_start: 0.8846 (OUTLIER) cc_final: 0.6827 (pm20) REVERT: A 583 SER cc_start: 0.9322 (m) cc_final: 0.8928 (t) REVERT: A 589 SER cc_start: 0.9378 (m) cc_final: 0.9029 (p) REVERT: A 628 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8417 (mm-30) REVERT: A 683 TYR cc_start: 0.9181 (t80) cc_final: 0.8952 (t80) REVERT: B 111 LYS cc_start: 0.9399 (mmtp) cc_final: 0.9033 (mmtt) REVERT: B 263 ASP cc_start: 0.8884 (m-30) cc_final: 0.8441 (m-30) REVERT: B 270 ASP cc_start: 0.8777 (t0) cc_final: 0.8424 (t0) REVERT: B 355 TYR cc_start: 0.8443 (m-80) cc_final: 0.7873 (m-80) REVERT: B 359 MET cc_start: 0.9026 (ttp) cc_final: 0.8780 (tmm) REVERT: B 362 ASP cc_start: 0.8369 (m-30) cc_final: 0.7953 (m-30) REVERT: B 394 TYR cc_start: 0.9226 (m-80) cc_final: 0.8562 (m-80) REVERT: B 515 ASP cc_start: 0.8875 (m-30) cc_final: 0.8304 (m-30) REVERT: B 571 TYR cc_start: 0.8676 (t80) cc_final: 0.7673 (t80) REVERT: B 599 GLU cc_start: 0.8231 (pt0) cc_final: 0.7928 (pt0) REVERT: B 615 MET cc_start: 0.9536 (mmp) cc_final: 0.9271 (mmp) REVERT: B 628 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8480 (mt-10) REVERT: C 21 PHE cc_start: 0.9198 (m-80) cc_final: 0.8756 (m-80) REVERT: C 56 MET cc_start: 0.6826 (ptm) cc_final: 0.6183 (ttp) REVERT: C 130 TYR cc_start: 0.8969 (m-80) cc_final: 0.8178 (m-80) REVERT: C 189 GLU cc_start: 0.9113 (tp30) cc_final: 0.8823 (tp30) REVERT: C 193 LEU cc_start: 0.9291 (mt) cc_final: 0.9033 (mt) REVERT: C 196 ARG cc_start: 0.8957 (ptm160) cc_final: 0.8610 (ptm-80) REVERT: C 241 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8760 (mt-10) REVERT: C 244 GLU cc_start: 0.9537 (pt0) cc_final: 0.9196 (pp20) REVERT: C 259 PHE cc_start: 0.8421 (t80) cc_final: 0.8170 (t80) REVERT: C 270 ASN cc_start: 0.8078 (m110) cc_final: 0.7704 (m110) REVERT: C 273 PHE cc_start: 0.7426 (m-80) cc_final: 0.7220 (m-80) REVERT: D 69 GLN cc_start: 0.8065 (tp40) cc_final: 0.7655 (pt0) REVERT: D 142 TYR cc_start: 0.7526 (m-10) cc_final: 0.7229 (m-10) REVERT: D 154 PHE cc_start: 0.7750 (t80) cc_final: 0.7345 (t80) REVERT: D 197 ASP cc_start: 0.8909 (m-30) cc_final: 0.8619 (m-30) outliers start: 67 outliers final: 47 residues processed: 556 average time/residue: 0.2617 time to fit residues: 218.8625 Evaluate side-chains 539 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 490 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 349 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 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 282 ILE 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 67 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 1.9990 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 11 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN D 265 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.149261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.098003 restraints weight = 27787.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.101691 restraints weight = 11488.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.103837 restraints weight = 6566.725| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.5179 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= 0.199 Angle : 0.642 11.632 22134 Z= 0.335 Chirality : 0.044 0.348 2360 Planarity : 0.003 0.054 2818 Dihedral : 10.822 170.652 2248 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.08 % Allowed : 22.38 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.19), residues: 1932 helix: 1.24 (0.15), residues: 1139 sheet: -0.44 (0.41), residues: 148 loop : 0.39 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 30 HIS 0.004 0.001 HIS A 438 PHE 0.036 0.002 PHE C 168 TYR 0.028 0.001 TYR C 236 ARG 0.006 0.001 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.04125 ( 871) hydrogen bonds : angle 4.90688 ( 2571) covalent geometry : bond 0.00447 (16386) covalent geometry : angle 0.64235 (22134) *********************** 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 571 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 501 time to evaluate : 1.910 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 103 ASP cc_start: 0.8711 (m-30) cc_final: 0.8430 (m-30) REVERT: A 144 MET cc_start: 0.8976 (mtm) cc_final: 0.8403 (mtm) REVERT: A 147 GLN cc_start: 0.9108 (mt0) cc_final: 0.8753 (mt0) REVERT: A 148 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8245 (mt-10) REVERT: A 157 LEU cc_start: 0.9282 (tp) cc_final: 0.9059 (tt) REVERT: A 158 ASN cc_start: 0.9058 (m-40) cc_final: 0.8660 (m-40) REVERT: A 209 LYS cc_start: 0.9000 (tttm) cc_final: 0.8401 (ttmm) REVERT: A 250 TYR cc_start: 0.9126 (m-80) cc_final: 0.8742 (m-80) REVERT: A 251 LEU cc_start: 0.9373 (tp) cc_final: 0.9046 (tp) REVERT: A 259 ASN cc_start: 0.9123 (m-40) cc_final: 0.8541 (m-40) REVERT: A 263 ASP cc_start: 0.8740 (m-30) cc_final: 0.8346 (m-30) REVERT: A 277 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8167 (t) REVERT: A 335 GLU cc_start: 0.8291 (mm-30) cc_final: 0.7996 (mm-30) REVERT: A 379 SER cc_start: 0.9269 (t) cc_final: 0.8792 (t) REVERT: A 384 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.6756 (pm20) REVERT: A 583 SER cc_start: 0.9265 (m) cc_final: 0.8928 (t) REVERT: A 589 SER cc_start: 0.9370 (m) cc_final: 0.9048 (p) REVERT: A 598 MET cc_start: 0.8585 (mtm) cc_final: 0.8053 (mtp) REVERT: A 628 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8450 (mm-30) REVERT: B 111 LYS cc_start: 0.9412 (mmtp) cc_final: 0.9057 (mmtt) REVERT: B 147 GLN cc_start: 0.9012 (mt0) cc_final: 0.8674 (mm-40) REVERT: B 263 ASP cc_start: 0.8878 (m-30) cc_final: 0.8446 (m-30) REVERT: B 274 ARG cc_start: 0.8351 (ttp-110) cc_final: 0.7380 (ptp-110) REVERT: B 355 TYR cc_start: 0.8448 (m-80) cc_final: 0.7886 (m-80) REVERT: B 359 MET cc_start: 0.9022 (ttp) cc_final: 0.8751 (tmm) REVERT: B 362 ASP cc_start: 0.8397 (m-30) cc_final: 0.7982 (m-30) REVERT: B 384 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.7260 (pm20) REVERT: B 515 ASP cc_start: 0.8868 (m-30) cc_final: 0.8293 (m-30) REVERT: B 571 TYR cc_start: 0.8810 (t80) cc_final: 0.7749 (t80) REVERT: B 599 GLU cc_start: 0.8243 (pt0) cc_final: 0.7972 (pt0) REVERT: B 615 MET cc_start: 0.9539 (mmp) cc_final: 0.9274 (mmp) REVERT: C 21 PHE cc_start: 0.9187 (m-80) cc_final: 0.8805 (m-80) REVERT: C 56 MET cc_start: 0.6827 (ptm) cc_final: 0.5734 (ttm) REVERT: C 95 MET cc_start: 0.9060 (tmm) cc_final: 0.8799 (tmm) REVERT: C 107 ASN cc_start: 0.8141 (OUTLIER) cc_final: 0.7627 (p0) REVERT: C 122 PHE cc_start: 0.8790 (m-80) cc_final: 0.8558 (m-80) REVERT: C 154 PHE cc_start: 0.9130 (t80) cc_final: 0.8703 (t80) REVERT: C 189 GLU cc_start: 0.9139 (tp30) cc_final: 0.8594 (tp30) REVERT: C 193 LEU cc_start: 0.9307 (mt) cc_final: 0.8949 (mt) REVERT: C 196 ARG cc_start: 0.9032 (ptm160) cc_final: 0.8709 (ptm-80) REVERT: C 244 GLU cc_start: 0.9494 (pt0) cc_final: 0.9163 (pp20) REVERT: C 270 ASN cc_start: 0.8136 (m110) cc_final: 0.7759 (m110) REVERT: D 132 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8090 (mm110) REVERT: D 154 PHE cc_start: 0.7859 (t80) cc_final: 0.7333 (t80) REVERT: D 197 ASP cc_start: 0.8760 (m-30) cc_final: 0.8537 (m-30) REVERT: D 265 ASN cc_start: 0.8239 (m-40) cc_final: 0.7890 (m-40) outliers start: 70 outliers final: 49 residues processed: 536 average time/residue: 0.2694 time to fit residues: 215.8179 Evaluate side-chains 531 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 477 time to evaluate : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain B residue 384 GLU 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 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 141 LEU Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 282 ILE 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 31 optimal weight: 0.9980 chunk 126 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 113 optimal weight: 0.9980 chunk 177 optimal weight: 8.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 132 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.147616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.096147 restraints weight = 27787.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.099771 restraints weight = 11672.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.101906 restraints weight = 6744.831| |-----------------------------------------------------------------------------| r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 16386 Z= 0.251 Angle : 0.667 11.715 22134 Z= 0.348 Chirality : 0.045 0.340 2360 Planarity : 0.004 0.052 2818 Dihedral : 10.748 167.259 2248 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.60 % Allowed : 22.84 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.19), residues: 1932 helix: 1.17 (0.15), residues: 1136 sheet: -0.50 (0.41), residues: 148 loop : 0.35 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 30 HIS 0.004 0.001 HIS A 438 PHE 0.030 0.002 PHE C 172 TYR 0.019 0.002 TYR C 236 ARG 0.006 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.04176 ( 871) hydrogen bonds : angle 4.94641 ( 2571) covalent geometry : bond 0.00561 (16386) covalent geometry : angle 0.66739 (22134) *********************** 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 564 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 485 time to evaluate : 1.910 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 67 GLU cc_start: 0.8252 (pm20) cc_final: 0.8039 (pm20) REVERT: A 76 ASP cc_start: 0.8769 (m-30) cc_final: 0.8386 (m-30) REVERT: A 103 ASP cc_start: 0.8732 (m-30) cc_final: 0.8474 (m-30) REVERT: A 106 LEU cc_start: 0.9091 (tp) cc_final: 0.8784 (tp) REVERT: A 144 MET cc_start: 0.9012 (mtm) cc_final: 0.8459 (mtm) REVERT: A 147 GLN cc_start: 0.9153 (mt0) cc_final: 0.8751 (mt0) REVERT: A 148 GLU cc_start: 0.8540 (mt-10) cc_final: 0.8237 (mt-10) REVERT: A 209 LYS cc_start: 0.9082 (tttm) cc_final: 0.8483 (ttmm) REVERT: A 250 TYR cc_start: 0.9129 (m-80) cc_final: 0.8769 (m-80) REVERT: A 259 ASN cc_start: 0.9127 (m-40) cc_final: 0.8530 (m-40) REVERT: A 263 ASP cc_start: 0.8741 (m-30) cc_final: 0.8337 (m-30) REVERT: A 277 THR cc_start: 0.8550 (OUTLIER) cc_final: 0.8261 (t) REVERT: A 335 GLU cc_start: 0.8307 (mm-30) cc_final: 0.8087 (mm-30) REVERT: A 379 SER cc_start: 0.9301 (t) cc_final: 0.8884 (t) REVERT: A 384 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.6814 (pm20) REVERT: A 486 ASP cc_start: 0.8526 (t0) cc_final: 0.8260 (t0) REVERT: A 583 SER cc_start: 0.9342 (OUTLIER) cc_final: 0.9010 (t) REVERT: A 589 SER cc_start: 0.9371 (m) cc_final: 0.9071 (p) REVERT: A 628 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8445 (mm-30) REVERT: A 686 ARG cc_start: 0.8338 (ttm-80) cc_final: 0.7792 (mmt-90) REVERT: B 79 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8445 (mm-30) REVERT: B 103 ASP cc_start: 0.9052 (m-30) cc_final: 0.8845 (m-30) REVERT: B 108 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.7178 (p) REVERT: B 111 LYS cc_start: 0.9432 (mmtp) cc_final: 0.8945 (mmtm) REVERT: B 263 ASP cc_start: 0.8878 (m-30) cc_final: 0.8454 (m-30) REVERT: B 272 ASP cc_start: 0.8790 (p0) cc_final: 0.8489 (p0) REVERT: B 336 LYS cc_start: 0.9433 (OUTLIER) cc_final: 0.9021 (ttmm) REVERT: B 355 TYR cc_start: 0.8505 (m-80) cc_final: 0.7940 (m-80) REVERT: B 362 ASP cc_start: 0.8444 (m-30) cc_final: 0.8051 (m-30) REVERT: B 384 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.7253 (pm20) REVERT: B 467 ASN cc_start: 0.9208 (t0) cc_final: 0.8979 (t0) REVERT: B 515 ASP cc_start: 0.8879 (m-30) cc_final: 0.8289 (m-30) REVERT: B 599 GLU cc_start: 0.8326 (pt0) cc_final: 0.8052 (pt0) REVERT: B 615 MET cc_start: 0.9543 (mmp) cc_final: 0.9275 (mmp) REVERT: C 21 PHE cc_start: 0.9244 (m-80) cc_final: 0.8859 (m-80) REVERT: C 56 MET cc_start: 0.6895 (ptm) cc_final: 0.5882 (ttm) REVERT: C 95 MET cc_start: 0.9035 (tmm) cc_final: 0.8813 (tmm) REVERT: C 122 PHE cc_start: 0.8754 (m-80) cc_final: 0.8520 (m-80) REVERT: C 154 PHE cc_start: 0.9200 (t80) cc_final: 0.8741 (t80) REVERT: C 162 TYR cc_start: 0.8877 (m-80) cc_final: 0.7869 (m-80) REVERT: C 189 GLU cc_start: 0.9005 (tp30) cc_final: 0.8655 (tp30) REVERT: C 193 LEU cc_start: 0.9401 (mt) cc_final: 0.9051 (mt) REVERT: C 196 ARG cc_start: 0.9030 (ptm160) cc_final: 0.8691 (ptm-80) REVERT: C 244 GLU cc_start: 0.9489 (pt0) cc_final: 0.9150 (pp20) REVERT: C 259 PHE cc_start: 0.8387 (t80) cc_final: 0.8126 (t80) REVERT: C 270 ASN cc_start: 0.8271 (m110) cc_final: 0.7934 (m110) REVERT: C 273 PHE cc_start: 0.7018 (m-80) cc_final: 0.6801 (m-80) REVERT: D 24 GLN cc_start: 0.8895 (tp40) cc_final: 0.8544 (tp40) REVERT: D 53 ASP cc_start: 0.8123 (m-30) cc_final: 0.7878 (p0) REVERT: D 154 PHE cc_start: 0.7891 (t80) cc_final: 0.7450 (t80) REVERT: D 197 ASP cc_start: 0.8825 (m-30) cc_final: 0.8582 (m-30) REVERT: D 231 LEU cc_start: 0.9049 (tp) cc_final: 0.8813 (pp) REVERT: D 269 MET cc_start: 0.9034 (tmm) cc_final: 0.8766 (tmm) outliers start: 79 outliers final: 54 residues processed: 527 average time/residue: 0.2606 time to fit residues: 206.7326 Evaluate side-chains 520 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 460 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 41 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 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 B residue 33 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 389 SER 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 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 185 MET Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 39 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 161 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 119 optimal weight: 0.9990 chunk 175 optimal weight: 5.9990 chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 132 GLN D 233 ASN D 265 ASN D 270 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.150524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.100000 restraints weight = 27473.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.103608 restraints weight = 11315.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105724 restraints weight = 6480.368| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.5544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16386 Z= 0.146 Angle : 0.650 17.240 22134 Z= 0.334 Chirality : 0.044 0.342 2360 Planarity : 0.003 0.045 2818 Dihedral : 10.255 157.812 2246 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.44 % Allowed : 23.89 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.19), residues: 1932 helix: 1.23 (0.15), residues: 1137 sheet: -0.50 (0.41), residues: 148 loop : 0.33 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 44 HIS 0.003 0.001 HIS B 438 PHE 0.032 0.002 PHE C 154 TYR 0.020 0.001 TYR D 236 ARG 0.005 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.03943 ( 871) hydrogen bonds : angle 4.85841 ( 2571) covalent geometry : bond 0.00328 (16386) covalent geometry : angle 0.64979 (22134) *********************** 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 563 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 504 time to evaluate : 1.966 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: A 31 GLU cc_start: 0.8781 (mp0) cc_final: 0.8299 (mp0) REVERT: A 67 GLU cc_start: 0.8296 (pm20) cc_final: 0.8091 (pm20) REVERT: A 103 ASP cc_start: 0.8710 (m-30) cc_final: 0.8439 (m-30) REVERT: A 106 LEU cc_start: 0.9074 (tp) cc_final: 0.8730 (tp) REVERT: A 144 MET cc_start: 0.8916 (mtm) cc_final: 0.8301 (mtm) REVERT: A 147 GLN cc_start: 0.9041 (mt0) cc_final: 0.8647 (mt0) REVERT: A 148 GLU cc_start: 0.8473 (mt-10) cc_final: 0.8175 (mt-10) REVERT: A 209 LYS cc_start: 0.9063 (tttm) cc_final: 0.8548 (ttmm) REVERT: A 250 TYR cc_start: 0.9087 (m-80) cc_final: 0.8748 (m-80) REVERT: A 259 ASN cc_start: 0.9069 (m-40) cc_final: 0.8483 (m-40) REVERT: A 263 ASP cc_start: 0.8756 (m-30) cc_final: 0.8376 (m-30) REVERT: A 277 THR cc_start: 0.8368 (p) cc_final: 0.8104 (t) REVERT: A 335 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8002 (mm-30) REVERT: A 357 TYR cc_start: 0.9070 (m-10) cc_final: 0.8695 (m-10) REVERT: A 379 SER cc_start: 0.9237 (t) cc_final: 0.8744 (t) REVERT: A 384 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.6758 (pm20) REVERT: A 385 VAL cc_start: 0.9568 (t) cc_final: 0.9350 (t) REVERT: A 486 ASP cc_start: 0.8502 (t0) cc_final: 0.8235 (t0) REVERT: A 583 SER cc_start: 0.9292 (OUTLIER) cc_final: 0.8996 (t) REVERT: A 589 SER cc_start: 0.9334 (m) cc_final: 0.9035 (p) REVERT: A 628 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8452 (mm-30) REVERT: A 686 ARG cc_start: 0.8288 (ttm-80) cc_final: 0.7823 (mmt-90) REVERT: B 79 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8468 (mm-30) REVERT: B 108 THR cc_start: 0.8697 (OUTLIER) cc_final: 0.7168 (p) REVERT: B 111 LYS cc_start: 0.9394 (mmtp) cc_final: 0.8926 (mmtm) REVERT: B 147 GLN cc_start: 0.8904 (mt0) cc_final: 0.8508 (mm-40) REVERT: B 149 TYR cc_start: 0.9251 (t80) cc_final: 0.9029 (t80) REVERT: B 263 ASP cc_start: 0.8847 (m-30) cc_final: 0.8390 (m-30) REVERT: B 274 ARG cc_start: 0.8282 (ttm110) cc_final: 0.7417 (ptp-110) REVERT: B 320 ASN cc_start: 0.8855 (m-40) cc_final: 0.8622 (m110) REVERT: B 355 TYR cc_start: 0.8390 (m-80) cc_final: 0.7891 (m-80) REVERT: B 362 ASP cc_start: 0.8341 (m-30) cc_final: 0.7711 (m-30) REVERT: B 394 TYR cc_start: 0.9210 (m-80) cc_final: 0.8531 (m-80) REVERT: B 447 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.7990 (m-40) REVERT: B 474 GLN cc_start: 0.9007 (mt0) cc_final: 0.8599 (mt0) REVERT: B 515 ASP cc_start: 0.8821 (m-30) cc_final: 0.8261 (m-30) REVERT: B 599 GLU cc_start: 0.8263 (pt0) cc_final: 0.8017 (pt0) REVERT: B 615 MET cc_start: 0.9524 (mmp) cc_final: 0.9318 (mmp) REVERT: C 21 PHE cc_start: 0.9268 (m-80) cc_final: 0.8861 (m-80) REVERT: C 95 MET cc_start: 0.9020 (tmm) cc_final: 0.8772 (tmm) REVERT: C 110 MET cc_start: 0.8316 (mpp) cc_final: 0.8104 (mpp) REVERT: C 122 PHE cc_start: 0.8761 (m-80) cc_final: 0.8534 (m-80) REVERT: C 154 PHE cc_start: 0.9175 (t80) cc_final: 0.8797 (t80) REVERT: C 162 TYR cc_start: 0.8968 (m-80) cc_final: 0.7831 (m-80) REVERT: C 189 GLU cc_start: 0.8928 (tp30) cc_final: 0.8594 (tp30) REVERT: C 193 LEU cc_start: 0.9423 (mt) cc_final: 0.9164 (mt) REVERT: C 244 GLU cc_start: 0.9478 (pt0) cc_final: 0.9150 (pp20) REVERT: C 259 PHE cc_start: 0.8386 (t80) cc_final: 0.8159 (t80) REVERT: C 270 ASN cc_start: 0.8356 (m110) cc_final: 0.7990 (m110) REVERT: D 24 GLN cc_start: 0.8787 (tp40) cc_final: 0.8508 (tp40) REVERT: D 28 GLN cc_start: 0.8177 (mt0) cc_final: 0.7880 (mt0) REVERT: D 133 LYS cc_start: 0.9424 (tppt) cc_final: 0.8934 (mtmt) REVERT: D 137 MET cc_start: 0.8555 (mtm) cc_final: 0.8343 (mtm) REVERT: D 154 PHE cc_start: 0.7875 (t80) cc_final: 0.7443 (t80) REVERT: D 197 ASP cc_start: 0.8824 (m-30) cc_final: 0.8567 (m-30) outliers start: 59 outliers final: 47 residues processed: 538 average time/residue: 0.2648 time to fit residues: 214.0958 Evaluate side-chains 534 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 483 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 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 B residue 33 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 277 THR 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 435 SER Chi-restraints excluded: chain B residue 447 ASN Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 34 GLU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 282 ILE 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 96 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 159 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 183 optimal weight: 20.0000 chunk 52 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 132 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.150681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.100198 restraints weight = 27381.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.103773 restraints weight = 11326.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105881 restraints weight = 6549.112| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.5675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16386 Z= 0.156 Angle : 0.650 14.435 22134 Z= 0.336 Chirality : 0.044 0.337 2360 Planarity : 0.003 0.041 2818 Dihedral : 9.873 155.748 2246 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.67 % Allowed : 24.65 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.19), residues: 1932 helix: 1.20 (0.15), residues: 1133 sheet: -0.59 (0.41), residues: 152 loop : 0.32 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 44 HIS 0.004 0.001 HIS A 438 PHE 0.031 0.002 PHE C 172 TYR 0.027 0.001 TYR C 169 ARG 0.007 0.000 ARG B 686 Details of bonding type rmsd hydrogen bonds : bond 0.03979 ( 871) hydrogen bonds : angle 4.86068 ( 2571) covalent geometry : bond 0.00351 (16386) covalent geometry : angle 0.64966 (22134) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 507 time to evaluate : 2.306 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: A 31 GLU cc_start: 0.8794 (mp0) cc_final: 0.8303 (mp0) REVERT: A 103 ASP cc_start: 0.8716 (m-30) cc_final: 0.8455 (m-30) REVERT: A 106 LEU cc_start: 0.9065 (tp) cc_final: 0.8700 (tp) REVERT: A 144 MET cc_start: 0.8896 (mtm) cc_final: 0.8284 (mtm) REVERT: A 147 GLN cc_start: 0.9066 (mt0) cc_final: 0.8751 (mt0) REVERT: A 148 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8176 (mt-10) REVERT: A 209 LYS cc_start: 0.9059 (tttm) cc_final: 0.8652 (ttmm) REVERT: A 250 TYR cc_start: 0.9107 (m-80) cc_final: 0.8774 (m-80) REVERT: A 259 ASN cc_start: 0.9044 (m-40) cc_final: 0.8444 (m-40) REVERT: A 263 ASP cc_start: 0.8731 (m-30) cc_final: 0.8367 (m-30) REVERT: A 277 THR cc_start: 0.8342 (OUTLIER) cc_final: 0.8079 (t) REVERT: A 335 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7986 (mm-30) REVERT: A 379 SER cc_start: 0.9251 (t) cc_final: 0.8742 (t) REVERT: A 384 GLU cc_start: 0.8811 (OUTLIER) cc_final: 0.6836 (pm20) REVERT: A 385 VAL cc_start: 0.9584 (t) cc_final: 0.9349 (t) REVERT: A 486 ASP cc_start: 0.8500 (t0) cc_final: 0.8221 (t0) REVERT: A 493 MET cc_start: 0.9115 (tmm) cc_final: 0.8871 (tmm) REVERT: A 583 SER cc_start: 0.9281 (OUTLIER) cc_final: 0.8973 (t) REVERT: A 589 SER cc_start: 0.9334 (m) cc_final: 0.9049 (p) REVERT: A 628 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8453 (mm-30) REVERT: A 686 ARG cc_start: 0.8235 (ttm-80) cc_final: 0.7763 (mmt-90) REVERT: B 108 THR cc_start: 0.8704 (OUTLIER) cc_final: 0.8163 (p) REVERT: B 111 LYS cc_start: 0.9391 (mmtp) cc_final: 0.9150 (mptt) REVERT: B 147 GLN cc_start: 0.8921 (mt0) cc_final: 0.8516 (mm-40) REVERT: B 263 ASP cc_start: 0.8833 (m-30) cc_final: 0.8393 (m-30) REVERT: B 274 ARG cc_start: 0.8303 (ttm110) cc_final: 0.7443 (ptp-110) REVERT: B 320 ASN cc_start: 0.8842 (m-40) cc_final: 0.8603 (m110) REVERT: B 336 LYS cc_start: 0.9435 (OUTLIER) cc_final: 0.9004 (ttmm) REVERT: B 355 TYR cc_start: 0.8379 (m-80) cc_final: 0.7890 (m-80) REVERT: B 359 MET cc_start: 0.8962 (ttp) cc_final: 0.8710 (tmm) REVERT: B 362 ASP cc_start: 0.8339 (m-30) cc_final: 0.7694 (m-30) REVERT: B 394 TYR cc_start: 0.9231 (m-80) cc_final: 0.8388 (m-80) REVERT: B 447 ASN cc_start: 0.8355 (m-40) cc_final: 0.7577 (m-40) REVERT: B 474 GLN cc_start: 0.9019 (mt0) cc_final: 0.8646 (mt0) REVERT: B 515 ASP cc_start: 0.8814 (m-30) cc_final: 0.8255 (m-30) REVERT: B 571 TYR cc_start: 0.8741 (t80) cc_final: 0.7650 (t80) REVERT: B 599 GLU cc_start: 0.8288 (pt0) cc_final: 0.8031 (pt0) REVERT: C 17 PHE cc_start: 0.8570 (p90) cc_final: 0.8144 (p90) REVERT: C 21 PHE cc_start: 0.9276 (m-80) cc_final: 0.8798 (m-80) REVERT: C 56 MET cc_start: 0.6930 (ptt) cc_final: 0.6589 (ttp) REVERT: C 92 PHE cc_start: 0.7850 (t80) cc_final: 0.7502 (t80) REVERT: C 95 MET cc_start: 0.9018 (tmm) cc_final: 0.8759 (tmm) REVERT: C 121 VAL cc_start: 0.8162 (p) cc_final: 0.7895 (p) REVERT: C 122 PHE cc_start: 0.8809 (m-80) cc_final: 0.8564 (m-80) REVERT: C 154 PHE cc_start: 0.9125 (t80) cc_final: 0.8798 (t80) REVERT: C 162 TYR cc_start: 0.8942 (m-80) cc_final: 0.7642 (m-80) REVERT: C 189 GLU cc_start: 0.8932 (tp30) cc_final: 0.8598 (tp30) REVERT: C 193 LEU cc_start: 0.9450 (mt) cc_final: 0.9133 (mt) REVERT: C 196 ARG cc_start: 0.9071 (ptm160) cc_final: 0.8787 (ptt90) REVERT: C 244 GLU cc_start: 0.9478 (pt0) cc_final: 0.9155 (pp20) REVERT: C 252 LEU cc_start: 0.6271 (tp) cc_final: 0.6067 (mt) REVERT: C 259 PHE cc_start: 0.8548 (t80) cc_final: 0.8278 (t80) REVERT: D 24 GLN cc_start: 0.8771 (tp40) cc_final: 0.8423 (tp40) REVERT: D 28 GLN cc_start: 0.8082 (mt0) cc_final: 0.7835 (mt0) REVERT: D 31 LEU cc_start: 0.8448 (mt) cc_final: 0.8115 (mt) REVERT: D 44 TRP cc_start: 0.8358 (t-100) cc_final: 0.8085 (t-100) REVERT: D 56 MET cc_start: 0.8073 (ptp) cc_final: 0.7674 (mmp) REVERT: D 69 GLN cc_start: 0.8278 (tp40) cc_final: 0.7858 (pt0) REVERT: D 132 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7933 (mm110) REVERT: D 133 LYS cc_start: 0.9497 (tppt) cc_final: 0.9061 (mtpt) REVERT: D 154 PHE cc_start: 0.7834 (t80) cc_final: 0.7396 (t80) REVERT: D 197 ASP cc_start: 0.8912 (m-30) cc_final: 0.8564 (m-30) REVERT: D 231 LEU cc_start: 0.9091 (tp) cc_final: 0.8884 (pp) outliers start: 63 outliers final: 43 residues processed: 540 average time/residue: 0.3079 time to fit residues: 250.1518 Evaluate side-chains 527 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 478 time to evaluate : 3.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 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 B residue 33 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 336 LYS 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 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 282 ILE 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 111 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 182 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 96 optimal weight: 0.5980 chunk 115 optimal weight: 3.9990 chunk 127 optimal weight: 5.9990 chunk 188 optimal weight: 20.0000 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 0.0970 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 132 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.151111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.100761 restraints weight = 27312.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.104323 restraints weight = 11272.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.106411 restraints weight = 6500.202| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3182 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3182 r_free = 0.3182 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3182 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.5827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16386 Z= 0.167 Angle : 0.690 13.049 22134 Z= 0.357 Chirality : 0.045 0.333 2360 Planarity : 0.004 0.046 2818 Dihedral : 9.476 149.329 2244 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.67 % Allowed : 25.82 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.19), residues: 1932 helix: 1.13 (0.15), residues: 1127 sheet: -0.62 (0.41), residues: 152 loop : 0.37 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 44 HIS 0.005 0.001 HIS D 201 PHE 0.038 0.002 PHE C 172 TYR 0.019 0.001 TYR D 236 ARG 0.007 0.001 ARG B 686 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 871) hydrogen bonds : angle 4.93760 ( 2571) covalent geometry : bond 0.00378 (16386) covalent geometry : angle 0.69040 (22134) *********************** 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 552 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 489 time to evaluate : 1.746 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: A 31 GLU cc_start: 0.8810 (mp0) cc_final: 0.8310 (mp0) REVERT: A 67 GLU cc_start: 0.8446 (pm20) cc_final: 0.7615 (pm20) REVERT: A 76 ASP cc_start: 0.8757 (m-30) cc_final: 0.8382 (m-30) REVERT: A 103 ASP cc_start: 0.8736 (m-30) cc_final: 0.8489 (m-30) REVERT: A 106 LEU cc_start: 0.9050 (tp) cc_final: 0.8694 (tp) REVERT: A 144 MET cc_start: 0.8885 (mtm) cc_final: 0.8296 (mtm) REVERT: A 147 GLN cc_start: 0.9064 (mt0) cc_final: 0.8756 (mt0) REVERT: A 148 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8168 (mt-10) REVERT: A 209 LYS cc_start: 0.9050 (tttm) cc_final: 0.8643 (ttmm) REVERT: A 250 TYR cc_start: 0.9095 (m-80) cc_final: 0.8728 (m-80) REVERT: A 259 ASN cc_start: 0.9047 (m-40) cc_final: 0.8448 (m-40) REVERT: A 263 ASP cc_start: 0.8710 (m-30) cc_final: 0.8356 (m-30) REVERT: A 277 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.8072 (t) REVERT: A 335 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7981 (mm-30) REVERT: A 357 TYR cc_start: 0.9060 (m-10) cc_final: 0.8617 (m-10) REVERT: A 379 SER cc_start: 0.9240 (t) cc_final: 0.8695 (t) REVERT: A 384 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.6819 (pm20) REVERT: A 385 VAL cc_start: 0.9584 (t) cc_final: 0.9341 (t) REVERT: A 486 ASP cc_start: 0.8491 (t0) cc_final: 0.8265 (t0) REVERT: A 493 MET cc_start: 0.9121 (tmm) cc_final: 0.8861 (tmm) REVERT: A 583 SER cc_start: 0.9298 (OUTLIER) cc_final: 0.8987 (t) REVERT: A 589 SER cc_start: 0.9257 (m) cc_final: 0.9050 (p) REVERT: A 598 MET cc_start: 0.8345 (mtp) cc_final: 0.8005 (mtt) REVERT: A 628 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8419 (mm-30) REVERT: A 686 ARG cc_start: 0.8204 (ttm-80) cc_final: 0.7825 (mmm-85) REVERT: B 65 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7846 (mm-30) REVERT: B 108 THR cc_start: 0.8741 (OUTLIER) cc_final: 0.8224 (p) REVERT: B 111 LYS cc_start: 0.9391 (mmtp) cc_final: 0.9154 (mptt) REVERT: B 150 GLN cc_start: 0.9120 (tp-100) cc_final: 0.8914 (tp-100) REVERT: B 263 ASP cc_start: 0.8833 (m-30) cc_final: 0.8384 (m-30) REVERT: B 274 ARG cc_start: 0.8325 (ttm110) cc_final: 0.7399 (ptp-110) REVERT: B 320 ASN cc_start: 0.8855 (m-40) cc_final: 0.8642 (m110) REVERT: B 336 LYS cc_start: 0.9439 (OUTLIER) cc_final: 0.9014 (ttmm) REVERT: B 355 TYR cc_start: 0.8397 (m-80) cc_final: 0.7916 (m-80) REVERT: B 359 MET cc_start: 0.8962 (ttp) cc_final: 0.8716 (tmm) REVERT: B 362 ASP cc_start: 0.8342 (m-30) cc_final: 0.7693 (m-30) REVERT: B 474 GLN cc_start: 0.9034 (mt0) cc_final: 0.8667 (mt0) REVERT: B 515 ASP cc_start: 0.8840 (m-30) cc_final: 0.8298 (m-30) REVERT: B 571 TYR cc_start: 0.8756 (t80) cc_final: 0.7682 (t80) REVERT: B 586 TYR cc_start: 0.8859 (m-80) cc_final: 0.8531 (m-80) REVERT: B 599 GLU cc_start: 0.8293 (pt0) cc_final: 0.8069 (pt0) REVERT: B 602 GLU cc_start: 0.8082 (pt0) cc_final: 0.7840 (pt0) REVERT: C 17 PHE cc_start: 0.8616 (p90) cc_final: 0.8128 (p90) REVERT: C 21 PHE cc_start: 0.9283 (m-80) cc_final: 0.8764 (m-80) REVERT: C 56 MET cc_start: 0.6853 (ptt) cc_final: 0.6629 (ttp) REVERT: C 92 PHE cc_start: 0.7678 (t80) cc_final: 0.7321 (t80) REVERT: C 95 MET cc_start: 0.8895 (tmm) cc_final: 0.8632 (tmm) REVERT: C 122 PHE cc_start: 0.8872 (m-80) cc_final: 0.8637 (m-80) REVERT: C 154 PHE cc_start: 0.9111 (t80) cc_final: 0.8798 (t80) REVERT: C 162 TYR cc_start: 0.8894 (m-80) cc_final: 0.8518 (m-80) REVERT: C 189 GLU cc_start: 0.8926 (tp30) cc_final: 0.8603 (tp30) REVERT: C 193 LEU cc_start: 0.9427 (mt) cc_final: 0.9100 (mt) REVERT: C 196 ARG cc_start: 0.9094 (ptm160) cc_final: 0.8814 (ptt90) REVERT: C 259 PHE cc_start: 0.8568 (t80) cc_final: 0.8301 (t80) REVERT: D 24 GLN cc_start: 0.8635 (tp40) cc_final: 0.8124 (tp40) REVERT: D 28 GLN cc_start: 0.8148 (mt0) cc_final: 0.7613 (mt0) REVERT: D 56 MET cc_start: 0.8025 (ptp) cc_final: 0.7674 (mmp) REVERT: D 69 GLN cc_start: 0.8263 (tp40) cc_final: 0.7801 (pt0) REVERT: D 133 LYS cc_start: 0.9577 (tppt) cc_final: 0.9169 (mtpt) REVERT: D 154 PHE cc_start: 0.7921 (t80) cc_final: 0.7490 (t80) REVERT: D 196 ARG cc_start: 0.8914 (ttt180) cc_final: 0.8410 (ptm160) REVERT: D 231 LEU cc_start: 0.9118 (tp) cc_final: 0.8790 (pp) outliers start: 63 outliers final: 49 residues processed: 524 average time/residue: 0.2634 time to fit residues: 207.0475 Evaluate side-chains 533 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 479 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 386 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 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 B residue 33 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 336 LYS 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 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 282 ILE 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 137 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 160 optimal weight: 20.0000 chunk 106 optimal weight: 0.8980 chunk 120 optimal weight: 0.6980 chunk 135 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.149497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.099334 restraints weight = 27464.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.102907 restraints weight = 11451.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.105011 restraints weight = 6546.045| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.5932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 16386 Z= 0.201 Angle : 0.729 14.945 22134 Z= 0.373 Chirality : 0.046 0.343 2360 Planarity : 0.004 0.056 2818 Dihedral : 9.357 144.849 2244 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.55 % Allowed : 26.34 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.19), residues: 1932 helix: 1.07 (0.15), residues: 1128 sheet: -0.64 (0.42), residues: 152 loop : 0.37 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 44 HIS 0.005 0.001 HIS A 438 PHE 0.042 0.002 PHE C 172 TYR 0.020 0.002 TYR D 236 ARG 0.007 0.000 ARG B 686 Details of bonding type rmsd hydrogen bonds : bond 0.04071 ( 871) hydrogen bonds : angle 4.98662 ( 2571) covalent geometry : bond 0.00459 (16386) covalent geometry : angle 0.72887 (22134) ********************** 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 529 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 468 time to evaluate : 1.870 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: A 31 GLU cc_start: 0.8818 (mp0) cc_final: 0.8314 (mp0) REVERT: A 67 GLU cc_start: 0.8062 (pm20) cc_final: 0.7831 (pm20) REVERT: A 76 ASP cc_start: 0.8770 (m-30) cc_final: 0.8393 (m-30) REVERT: A 103 ASP cc_start: 0.8725 (m-30) cc_final: 0.8472 (m-30) REVERT: A 106 LEU cc_start: 0.9067 (tp) cc_final: 0.8712 (tp) REVERT: A 144 MET cc_start: 0.8939 (mtm) cc_final: 0.8364 (mtm) REVERT: A 147 GLN cc_start: 0.9129 (mt0) cc_final: 0.8408 (mt0) REVERT: A 148 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8189 (mt-10) REVERT: A 209 LYS cc_start: 0.9064 (tttm) cc_final: 0.8556 (ttmm) REVERT: A 250 TYR cc_start: 0.9106 (m-80) cc_final: 0.8782 (m-80) REVERT: A 259 ASN cc_start: 0.9053 (m-40) cc_final: 0.8433 (m110) REVERT: A 263 ASP cc_start: 0.8724 (m-30) cc_final: 0.8393 (m-30) REVERT: A 277 THR cc_start: 0.8409 (p) cc_final: 0.8126 (t) REVERT: A 286 ASP cc_start: 0.8582 (t70) cc_final: 0.8327 (t0) REVERT: A 335 GLU cc_start: 0.8294 (mm-30) cc_final: 0.8015 (mm-30) REVERT: A 350 ARG cc_start: 0.9296 (mtp85) cc_final: 0.8285 (mtp85) REVERT: A 379 SER cc_start: 0.9260 (t) cc_final: 0.8802 (t) REVERT: A 384 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.6790 (pm20) REVERT: A 385 VAL cc_start: 0.9581 (t) cc_final: 0.9333 (t) REVERT: A 486 ASP cc_start: 0.8504 (t0) cc_final: 0.8277 (t0) REVERT: A 583 SER cc_start: 0.9306 (OUTLIER) cc_final: 0.9021 (t) REVERT: A 588 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8507 (mm110) REVERT: A 589 SER cc_start: 0.9274 (m) cc_final: 0.9054 (p) REVERT: A 628 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8420 (mm-30) REVERT: B 65 GLU cc_start: 0.8295 (mm-30) cc_final: 0.7875 (mm-30) REVERT: B 108 THR cc_start: 0.8770 (OUTLIER) cc_final: 0.7293 (p) REVERT: B 111 LYS cc_start: 0.9397 (mmtp) cc_final: 0.8938 (mmtm) REVERT: B 263 ASP cc_start: 0.8843 (m-30) cc_final: 0.8407 (m-30) REVERT: B 274 ARG cc_start: 0.8327 (ttm110) cc_final: 0.7478 (ptp-110) REVERT: B 320 ASN cc_start: 0.8873 (m-40) cc_final: 0.8644 (m110) REVERT: B 355 TYR cc_start: 0.8432 (m-80) cc_final: 0.7926 (m-80) REVERT: B 362 ASP cc_start: 0.8363 (m-30) cc_final: 0.7724 (m-30) REVERT: B 384 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.7126 (pm20) REVERT: B 474 GLN cc_start: 0.9036 (mt0) cc_final: 0.8764 (mt0) REVERT: B 515 ASP cc_start: 0.8848 (m-30) cc_final: 0.8294 (m-30) REVERT: B 571 TYR cc_start: 0.8799 (t80) cc_final: 0.7719 (t80) REVERT: B 586 TYR cc_start: 0.8880 (m-80) cc_final: 0.8571 (m-80) REVERT: B 599 GLU cc_start: 0.8356 (pt0) cc_final: 0.8099 (pt0) REVERT: B 602 GLU cc_start: 0.8022 (pt0) cc_final: 0.7717 (pt0) REVERT: C 17 PHE cc_start: 0.8506 (p90) cc_final: 0.8263 (p90) REVERT: C 21 PHE cc_start: 0.9283 (m-80) cc_final: 0.8627 (m-80) REVERT: C 56 MET cc_start: 0.6875 (ptt) cc_final: 0.6622 (ttp) REVERT: C 92 PHE cc_start: 0.7797 (t80) cc_final: 0.7453 (t80) REVERT: C 95 MET cc_start: 0.8870 (tmm) cc_final: 0.8650 (tmm) REVERT: C 122 PHE cc_start: 0.8848 (m-80) cc_final: 0.8615 (m-80) REVERT: C 154 PHE cc_start: 0.9052 (t80) cc_final: 0.8764 (t80) REVERT: C 162 TYR cc_start: 0.8860 (m-80) cc_final: 0.8430 (m-80) REVERT: C 189 GLU cc_start: 0.8965 (tp30) cc_final: 0.8641 (tp30) REVERT: C 193 LEU cc_start: 0.9419 (mt) cc_final: 0.9085 (mt) REVERT: C 196 ARG cc_start: 0.9108 (ptm160) cc_final: 0.8813 (ptt90) REVERT: C 259 PHE cc_start: 0.8642 (t80) cc_final: 0.8337 (t80) REVERT: D 44 TRP cc_start: 0.8366 (t-100) cc_final: 0.8109 (t-100) REVERT: D 56 MET cc_start: 0.8000 (ptp) cc_final: 0.7682 (mmp) REVERT: D 69 GLN cc_start: 0.8361 (tp40) cc_final: 0.7845 (pt0) REVERT: D 133 LYS cc_start: 0.9606 (tppt) cc_final: 0.9268 (pttt) REVERT: D 137 MET cc_start: 0.8579 (mtt) cc_final: 0.8162 (ptp) REVERT: D 154 PHE cc_start: 0.7992 (t80) cc_final: 0.7532 (t80) REVERT: D 196 ARG cc_start: 0.8939 (ttt180) cc_final: 0.8598 (ptm160) REVERT: D 231 LEU cc_start: 0.9065 (tp) cc_final: 0.8753 (pp) outliers start: 61 outliers final: 49 residues processed: 502 average time/residue: 0.2743 time to fit residues: 207.7492 Evaluate side-chains 517 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 463 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 588 GLN 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 B residue 33 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 145 ILE Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 384 GLU 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 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 189 GLU Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 282 ILE 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 81 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 97 optimal weight: 0.6980 chunk 105 optimal weight: 0.5980 chunk 179 optimal weight: 9.9990 chunk 190 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 108 optimal weight: 0.0770 chunk 43 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 132 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.152483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.102200 restraints weight = 27254.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.105826 restraints weight = 11374.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.107971 restraints weight = 6523.981| |-----------------------------------------------------------------------------| r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.6073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 16386 Z= 0.151 Angle : 0.736 15.760 22134 Z= 0.374 Chirality : 0.046 0.335 2360 Planarity : 0.004 0.055 2818 Dihedral : 9.151 139.004 2244 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.86 % Allowed : 27.04 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.19), residues: 1932 helix: 1.07 (0.15), residues: 1127 sheet: -0.67 (0.42), residues: 152 loop : 0.25 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 44 HIS 0.008 0.001 HIS D 201 PHE 0.042 0.002 PHE C 172 TYR 0.039 0.001 TYR D 204 ARG 0.008 0.001 ARG B 686 Details of bonding type rmsd hydrogen bonds : bond 0.04029 ( 871) hydrogen bonds : angle 4.94464 ( 2571) covalent geometry : bond 0.00343 (16386) covalent geometry : angle 0.73601 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6567.65 seconds wall clock time: 115 minutes 8.10 seconds (6908.10 seconds total)