Starting phenix.real_space_refine on Sat May 17 16:54:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byt_45044/05_2025/9byt_45044_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byt_45044/05_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_45044/05_2025/9byt_45044.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byt_45044/05_2025/9byt_45044.map" model { file = "/net/cci-nas-00/data/ceres_data/9byt_45044/05_2025/9byt_45044_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byt_45044/05_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-5687/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: 9.20, per 1000 atoms: 0.57 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: 3.94 Conformation dependent library (CDL) restraints added in 2.0 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: 1.66 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: 5.06 Time building geometry restraints manager: 4.61 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: 0.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 35.890 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.060 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:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.200 ------------------------------------------------------------------------------- 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 : 2.015 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: 0.3038 time to fit residues: 369.2432 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 : 1.697 ------------------------------------------------------------------------------- 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 = 0.146652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.093613 restraints weight = 27371.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.097218 restraints weight = 11690.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.099440 restraints weight = 6910.493| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3071 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3071 r_free = 0.3071 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 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 : 1.714 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: 0.8195 (mt-10) cc_final: 0.7792 (mt-10) REVERT: A 67 GLU cc_start: 0.8295 (pm20) cc_final: 0.8058 (pm20) REVERT: A 103 ASP cc_start: 0.8691 (m-30) cc_final: 0.8436 (m-30) REVERT: A 118 TYR cc_start: 0.9402 (t80) cc_final: 0.9000 (t80) REVERT: A 144 MET cc_start: 0.9110 (mtm) cc_final: 0.8665 (mtm) REVERT: A 147 GLN cc_start: 0.9262 (mt0) cc_final: 0.8822 (mt0) REVERT: A 148 GLU cc_start: 0.8517 (mt-10) cc_final: 0.8240 (mt-10) REVERT: A 250 TYR cc_start: 0.9125 (m-80) cc_final: 0.8732 (m-80) REVERT: A 259 ASN cc_start: 0.9061 (m-40) cc_final: 0.8502 (m-40) REVERT: A 263 ASP cc_start: 0.8727 (m-30) cc_final: 0.8381 (m-30) REVERT: A 277 THR cc_start: 0.8662 (OUTLIER) cc_final: 0.8309 (t) REVERT: A 321 GLU cc_start: 0.8550 (pt0) cc_final: 0.8289 (pt0) REVERT: A 352 GLU cc_start: 0.7903 (mm-30) cc_final: 0.7410 (mm-30) REVERT: A 379 SER cc_start: 0.9372 (t) cc_final: 0.8931 (t) REVERT: A 381 LEU cc_start: 0.9479 (tp) cc_final: 0.9239 (tp) REVERT: A 384 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.6880 (pm20) REVERT: A 409 CYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8666 (p) REVERT: A 415 ASN cc_start: 0.9393 (t0) cc_final: 0.9192 (t0) REVERT: A 615 MET cc_start: 0.9111 (OUTLIER) cc_final: 0.8866 (mmm) REVERT: A 628 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8393 (mm-30) REVERT: A 658 LEU cc_start: 0.9659 (mt) cc_final: 0.9440 (mp) REVERT: A 683 TYR cc_start: 0.9146 (t80) cc_final: 0.8524 (t80) REVERT: B 40 TYR cc_start: 0.9194 (t80) cc_final: 0.8971 (t80) REVERT: B 253 ILE cc_start: 0.9585 (tt) cc_final: 0.9254 (tt) REVERT: B 263 ASP cc_start: 0.8923 (m-30) cc_final: 0.8597 (m-30) REVERT: B 274 ARG cc_start: 0.8158 (ttm110) cc_final: 0.7632 (ptp90) REVERT: B 336 LYS cc_start: 0.9417 (OUTLIER) cc_final: 0.9038 (ttmm) REVERT: B 355 TYR cc_start: 0.8593 (m-80) cc_final: 0.7918 (m-80) REVERT: B 384 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.7662 (pm20) REVERT: B 515 ASP cc_start: 0.8838 (m-30) cc_final: 0.8351 (m-30) REVERT: B 586 TYR cc_start: 0.8898 (m-80) cc_final: 0.8690 (m-80) REVERT: B 599 GLU cc_start: 0.8222 (pt0) cc_final: 0.8011 (pt0) REVERT: B 615 MET cc_start: 0.9563 (mmp) cc_final: 0.9220 (mmp) REVERT: C 21 PHE cc_start: 0.9033 (m-80) cc_final: 0.8625 (m-80) REVERT: C 92 PHE cc_start: 0.8123 (t80) cc_final: 0.7674 (t80) REVERT: C 154 PHE cc_start: 0.9103 (t80) cc_final: 0.8610 (t80) REVERT: C 157 MET cc_start: 0.9399 (mtp) cc_final: 0.9011 (mtp) REVERT: C 189 GLU cc_start: 0.9108 (tp30) cc_final: 0.8796 (tp30) REVERT: C 193 LEU cc_start: 0.9158 (mt) cc_final: 0.8867 (mt) REVERT: C 196 ARG cc_start: 0.9220 (ptm-80) cc_final: 0.8892 (ptm-80) REVERT: C 241 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8892 (mp0) REVERT: C 243 THR cc_start: 0.8761 (p) cc_final: 0.8538 (t) REVERT: C 259 PHE cc_start: 0.8291 (t80) cc_final: 0.8010 (t80) REVERT: D 30 TRP cc_start: 0.7356 (p-90) cc_final: 0.6786 (p-90) REVERT: D 128 ASN cc_start: 0.8013 (t0) cc_final: 0.7802 (m110) REVERT: D 138 ILE cc_start: 0.9506 (mm) cc_final: 0.9042 (mm) REVERT: D 153 LEU cc_start: 0.6105 (tp) cc_final: 0.5757 (mm) REVERT: D 162 TYR cc_start: 0.7953 (t80) cc_final: 0.7539 (t80) REVERT: D 185 MET cc_start: 0.6058 (mmm) cc_final: 0.5771 (mmm) REVERT: D 197 ASP cc_start: 0.8756 (m-30) cc_final: 0.8507 (m-30) REVERT: D 224 LEU cc_start: 0.8528 (mt) cc_final: 0.8317 (mt) REVERT: D 227 PHE cc_start: 0.9177 (t80) cc_final: 0.8970 (t80) REVERT: D 235 LEU cc_start: 0.9278 (mt) cc_final: 0.9063 (mt) REVERT: D 236 TYR cc_start: 0.7900 (t80) cc_final: 0.7682 (t80) REVERT: D 269 MET cc_start: 0.9139 (tmm) cc_final: 0.8718 (tmm) REVERT: D 286 VAL cc_start: 0.6247 (p) cc_final: 0.6019 (m) REVERT: D 287 LEU cc_start: 0.6596 (mt) cc_final: 0.6362 (mt) outliers start: 87 outliers final: 45 residues processed: 609 average time/residue: 0.2686 time to fit residues: 243.5022 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 : 1.758 ------------------------------------------------------------------------------- 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: 0.8980 chunk 168 optimal weight: 6.9990 chunk 175 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 191 optimal weight: 0.3980 chunk 57 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 171 optimal weight: 10.0000 chunk 189 optimal weight: 8.9990 chunk 141 optimal weight: 5.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.150260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.098262 restraints weight = 27195.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.102022 restraints weight = 11502.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.104226 restraints weight = 6644.479| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.4578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16386 Z= 0.161 Angle : 0.628 11.458 22134 Z= 0.328 Chirality : 0.044 0.346 2360 Planarity : 0.003 0.055 2818 Dihedral : 11.173 169.676 2249 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.44 % Allowed : 20.40 % Favored : 76.17 % 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: 1.23 (0.19), residues: 1932 helix: 1.26 (0.15), residues: 1154 sheet: -0.33 (0.40), residues: 148 loop : 0.51 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 9 HIS 0.004 0.001 HIS A 438 PHE 0.044 0.002 PHE D 172 TYR 0.026 0.002 TYR D 142 ARG 0.006 0.001 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.04285 ( 871) hydrogen bonds : angle 4.89617 ( 2571) covalent geometry : bond 0.00355 (16386) covalent geometry : angle 0.62843 (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 622 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 563 time to evaluate : 1.803 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: 0.8577 (mp0) cc_final: 0.8253 (mp0) REVERT: A 65 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7739 (mt-10) REVERT: A 67 GLU cc_start: 0.8236 (pm20) cc_final: 0.8028 (pm20) REVERT: A 103 ASP cc_start: 0.8654 (m-30) cc_final: 0.8370 (m-30) REVERT: A 106 LEU cc_start: 0.9144 (tp) cc_final: 0.8911 (tp) REVERT: A 119 GLU cc_start: 0.8143 (mp0) cc_final: 0.7942 (mp0) REVERT: A 144 MET cc_start: 0.8914 (mtm) cc_final: 0.8269 (mtm) REVERT: A 147 GLN cc_start: 0.9103 (mt0) cc_final: 0.7430 (mt0) REVERT: A 148 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8263 (mt-10) REVERT: A 158 ASN cc_start: 0.9134 (m-40) cc_final: 0.8903 (m-40) REVERT: A 250 TYR cc_start: 0.9083 (m-80) cc_final: 0.8740 (m-80) REVERT: A 251 LEU cc_start: 0.9317 (tp) cc_final: 0.9009 (tp) REVERT: A 259 ASN cc_start: 0.9050 (m-40) cc_final: 0.8445 (m-40) REVERT: A 263 ASP cc_start: 0.8721 (m-30) cc_final: 0.8292 (m-30) REVERT: A 276 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8589 (ptpp) REVERT: A 277 THR cc_start: 0.8466 (p) cc_final: 0.8181 (t) REVERT: A 357 TYR cc_start: 0.9064 (m-10) cc_final: 0.8802 (m-10) REVERT: A 379 SER cc_start: 0.9292 (t) cc_final: 0.8911 (t) REVERT: A 381 LEU cc_start: 0.9473 (tp) cc_final: 0.9206 (tp) REVERT: A 384 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.6933 (pm20) REVERT: A 415 ASN cc_start: 0.9382 (t0) cc_final: 0.9148 (t0) REVERT: A 583 SER cc_start: 0.9278 (m) cc_final: 0.8869 (t) REVERT: A 588 GLN cc_start: 0.9004 (mm-40) cc_final: 0.7870 (mm-40) REVERT: A 598 MET cc_start: 0.8695 (mtm) cc_final: 0.7803 (mtm) REVERT: A 628 GLU cc_start: 0.8652 (mt-10) cc_final: 0.8309 (mm-30) REVERT: B 111 LYS cc_start: 0.9424 (mmtp) cc_final: 0.9049 (mmtt) REVERT: B 263 ASP cc_start: 0.8863 (m-30) cc_final: 0.8459 (m-30) REVERT: B 274 ARG cc_start: 0.8067 (ttm110) cc_final: 0.7327 (ptp-110) REVERT: B 359 MET cc_start: 0.9012 (ttp) cc_final: 0.8784 (tmm) REVERT: B 394 TYR cc_start: 0.9196 (m-80) cc_final: 0.8696 (m-80) REVERT: B 515 ASP cc_start: 0.8833 (m-30) cc_final: 0.8284 (m-30) REVERT: B 599 GLU cc_start: 0.8218 (pt0) cc_final: 0.7949 (pt0) REVERT: B 610 LYS cc_start: 0.8919 (ptpt) cc_final: 0.8589 (ptmm) REVERT: B 615 MET cc_start: 0.9519 (mmp) cc_final: 0.9253 (mmp) REVERT: C 21 PHE cc_start: 0.9115 (m-80) cc_final: 0.8781 (m-80) REVERT: C 56 MET cc_start: 0.7074 (ptm) cc_final: 0.6486 (ttp) REVERT: C 130 TYR cc_start: 0.8968 (m-80) cc_final: 0.8198 (m-80) REVERT: C 154 PHE cc_start: 0.9097 (t80) cc_final: 0.8630 (t80) REVERT: C 162 TYR cc_start: 0.9010 (m-80) cc_final: 0.8799 (m-80) REVERT: C 168 PHE cc_start: 0.8858 (m-80) cc_final: 0.8611 (m-80) REVERT: C 189 GLU cc_start: 0.9115 (tp30) cc_final: 0.8780 (tp30) REVERT: C 193 LEU cc_start: 0.9216 (mt) cc_final: 0.8972 (mt) REVERT: C 241 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8853 (mt-10) REVERT: C 244 GLU cc_start: 0.9574 (pt0) cc_final: 0.9191 (pp20) REVERT: C 245 ASP cc_start: 0.8401 (t0) cc_final: 0.7892 (t0) REVERT: C 259 PHE cc_start: 0.8250 (t80) cc_final: 0.8001 (t80) REVERT: D 132 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8216 (mm110) REVERT: D 138 ILE cc_start: 0.9389 (mm) cc_final: 0.9140 (mm) REVERT: D 153 LEU cc_start: 0.6511 (tp) cc_final: 0.5816 (mm) REVERT: D 154 PHE cc_start: 0.7738 (t80) cc_final: 0.7413 (t80) REVERT: D 162 TYR cc_start: 0.7737 (t80) cc_final: 0.6939 (t80) REVERT: D 196 ARG cc_start: 0.8754 (ttt180) cc_final: 0.8512 (ttt180) REVERT: D 197 ASP cc_start: 0.8769 (m-30) cc_final: 0.8548 (m-30) outliers start: 59 outliers final: 37 residues processed: 595 average time/residue: 0.2658 time to fit residues: 237.6315 Evaluate side-chains 545 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 505 time to evaluate : 1.887 ------------------------------------------------------------------------------- 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 276 LYS Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 384 GLU 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 145 ILE 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 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 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 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: 0.0020 chunk 39 optimal weight: 6.9990 chunk 50 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 148 optimal weight: 20.0000 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 overall best weight: 0.9590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN A 645 GLN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** 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 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 ASN D 25 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 = 0.3836 r_free = 0.3836 target = 0.152030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.100497 restraints weight = 27119.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.104245 restraints weight = 11258.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.106441 restraints weight = 6476.409| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16386 Z= 0.151 Angle : 0.607 12.343 22134 Z= 0.317 Chirality : 0.043 0.367 2360 Planarity : 0.003 0.050 2818 Dihedral : 10.799 155.801 2249 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.61 % Allowed : 21.74 % Favored : 74.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.19 (0.19), residues: 1932 helix: 1.36 (0.15), residues: 1117 sheet: -0.39 (0.40), residues: 148 loop : 0.28 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 30 HIS 0.005 0.001 HIS C 201 PHE 0.035 0.002 PHE D 172 TYR 0.032 0.002 TYR D 142 ARG 0.007 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 871) hydrogen bonds : angle 4.84801 ( 2571) covalent geometry : bond 0.00341 (16386) covalent geometry : angle 0.60660 (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 591 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 529 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8651 (mp0) cc_final: 0.8266 (mp0) REVERT: A 65 GLU cc_start: 0.8078 (mt-10) cc_final: 0.7748 (mt-10) REVERT: A 67 GLU cc_start: 0.8339 (pm20) cc_final: 0.8112 (pm20) REVERT: A 103 ASP cc_start: 0.8708 (m-30) cc_final: 0.8415 (m-30) REVERT: A 106 LEU cc_start: 0.9114 (tp) cc_final: 0.8872 (tp) REVERT: A 144 MET cc_start: 0.8912 (mtm) cc_final: 0.8315 (mtm) REVERT: A 147 GLN cc_start: 0.9091 (mt0) cc_final: 0.8754 (mt0) REVERT: A 148 GLU cc_start: 0.8562 (mt-10) cc_final: 0.8335 (mt-10) REVERT: A 157 LEU cc_start: 0.9268 (tp) cc_final: 0.9056 (tt) REVERT: A 158 ASN cc_start: 0.8968 (m-40) cc_final: 0.8576 (m-40) REVERT: A 209 LYS cc_start: 0.8952 (tttm) cc_final: 0.8330 (ttmm) REVERT: A 250 TYR cc_start: 0.9112 (m-80) cc_final: 0.8711 (m-80) REVERT: A 259 ASN cc_start: 0.9083 (m-40) cc_final: 0.8466 (m-40) REVERT: A 263 ASP cc_start: 0.8712 (m-30) cc_final: 0.8293 (m-30) REVERT: A 277 THR cc_start: 0.8415 (p) cc_final: 0.8152 (t) REVERT: A 379 SER cc_start: 0.9253 (t) cc_final: 0.8777 (t) REVERT: A 381 LEU cc_start: 0.9470 (tp) cc_final: 0.9181 (tp) REVERT: A 384 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.6802 (pm20) REVERT: A 583 SER cc_start: 0.9296 (m) cc_final: 0.8908 (t) REVERT: A 628 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8407 (mm-30) REVERT: B 111 LYS cc_start: 0.9393 (mmtp) cc_final: 0.9030 (mmtt) REVERT: B 218 ASN cc_start: 0.8911 (OUTLIER) cc_final: 0.8407 (t0) REVERT: B 263 ASP cc_start: 0.8887 (m-30) cc_final: 0.8435 (m-30) REVERT: B 270 ASP cc_start: 0.8770 (t0) cc_final: 0.8358 (t0) REVERT: B 355 TYR cc_start: 0.8429 (m-80) cc_final: 0.7861 (m-80) REVERT: B 359 MET cc_start: 0.8965 (ttp) cc_final: 0.8677 (tmm) REVERT: B 362 ASP cc_start: 0.8263 (m-30) cc_final: 0.7962 (m-30) REVERT: B 394 TYR cc_start: 0.9207 (m-80) cc_final: 0.8622 (m-80) REVERT: B 447 ASN cc_start: 0.8544 (OUTLIER) cc_final: 0.7828 (m-40) REVERT: B 515 ASP cc_start: 0.8859 (m-30) cc_final: 0.8303 (m-30) REVERT: B 599 GLU cc_start: 0.8214 (pt0) cc_final: 0.7915 (pt0) REVERT: B 610 LYS cc_start: 0.8935 (ptpt) cc_final: 0.8649 (ptmm) REVERT: B 615 MET cc_start: 0.9534 (mmp) cc_final: 0.9326 (mmp) REVERT: B 628 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8486 (mt-10) REVERT: C 21 PHE cc_start: 0.9181 (m-80) cc_final: 0.8739 (m-80) REVERT: C 56 MET cc_start: 0.6817 (ptm) cc_final: 0.6170 (ttp) REVERT: C 124 TRP cc_start: 0.8678 (t60) cc_final: 0.8456 (t60) REVERT: C 130 TYR cc_start: 0.8967 (m-80) cc_final: 0.8195 (m-80) REVERT: C 154 PHE cc_start: 0.9180 (t80) cc_final: 0.8934 (t80) REVERT: C 189 GLU cc_start: 0.9101 (tp30) cc_final: 0.8812 (tp30) REVERT: C 193 LEU cc_start: 0.9290 (mt) cc_final: 0.9057 (mt) REVERT: C 241 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8798 (mt-10) REVERT: C 244 GLU cc_start: 0.9535 (pt0) cc_final: 0.9193 (pp20) REVERT: C 259 PHE cc_start: 0.8288 (t80) cc_final: 0.8074 (t80) REVERT: C 270 ASN cc_start: 0.7995 (m110) cc_final: 0.7616 (m110) REVERT: D 69 GLN cc_start: 0.8166 (tp40) cc_final: 0.7958 (pt0) REVERT: D 154 PHE cc_start: 0.7770 (t80) cc_final: 0.7397 (t80) REVERT: D 196 ARG cc_start: 0.8755 (ttt180) cc_final: 0.8547 (ttt180) REVERT: D 197 ASP cc_start: 0.8776 (m-30) cc_final: 0.8456 (m-30) outliers start: 62 outliers final: 46 residues processed: 562 average time/residue: 0.2532 time to fit residues: 214.4576 Evaluate side-chains 544 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 495 time to evaluate : 1.697 ------------------------------------------------------------------------------- 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 267 ILE Chi-restraints excluded: chain A residue 296 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 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 218 ASN Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN 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 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 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 208 LEU 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 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 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: 1.9990 chunk 41 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 175 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 668 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN D 119 ASN D 265 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.150573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.098650 restraints weight = 27666.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.102334 restraints weight = 11551.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.104628 restraints weight = 6672.081| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16386 Z= 0.216 Angle : 0.647 11.098 22134 Z= 0.339 Chirality : 0.045 0.366 2360 Planarity : 0.003 0.055 2818 Dihedral : 10.797 166.124 2248 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.14 % Allowed : 22.44 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.13 (0.19), residues: 1932 helix: 1.24 (0.15), residues: 1139 sheet: -0.49 (0.41), residues: 148 loop : 0.39 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 44 HIS 0.004 0.001 HIS A 438 PHE 0.037 0.002 PHE D 172 TYR 0.027 0.002 TYR C 236 ARG 0.008 0.000 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04133 ( 871) hydrogen bonds : angle 4.91088 ( 2571) covalent geometry : bond 0.00486 (16386) covalent geometry : angle 0.64660 (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 573 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 502 time to evaluate : 1.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7770 (mt-10) REVERT: A 67 GLU cc_start: 0.8309 (pm20) cc_final: 0.8092 (pm20) REVERT: A 103 ASP cc_start: 0.8710 (m-30) cc_final: 0.8449 (m-30) REVERT: A 106 LEU cc_start: 0.9132 (tp) cc_final: 0.8905 (tp) REVERT: A 144 MET cc_start: 0.8990 (mtm) cc_final: 0.8441 (mtm) REVERT: A 147 GLN cc_start: 0.9112 (mt0) cc_final: 0.8758 (mt0) REVERT: A 148 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8241 (mt-10) REVERT: A 209 LYS cc_start: 0.8982 (tttm) cc_final: 0.8382 (ttmm) REVERT: A 250 TYR cc_start: 0.9137 (m-80) cc_final: 0.8795 (m-80) REVERT: A 259 ASN cc_start: 0.9125 (m-40) cc_final: 0.8519 (m-40) REVERT: A 263 ASP cc_start: 0.8783 (m-30) cc_final: 0.8344 (m-30) REVERT: A 277 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8158 (t) REVERT: A 379 SER cc_start: 0.9324 (t) cc_final: 0.8910 (t) REVERT: A 384 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.6763 (pm20) REVERT: A 561 LEU cc_start: 0.9329 (tp) cc_final: 0.9118 (tp) REVERT: A 583 SER cc_start: 0.9287 (OUTLIER) cc_final: 0.8945 (t) REVERT: A 589 SER cc_start: 0.9368 (m) cc_final: 0.9051 (p) REVERT: A 628 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8430 (mm-30) REVERT: B 111 LYS cc_start: 0.9407 (mmtp) cc_final: 0.9043 (mmtt) REVERT: B 147 GLN cc_start: 0.9047 (mt0) cc_final: 0.8692 (mm-40) REVERT: B 263 ASP cc_start: 0.8870 (m-30) cc_final: 0.8450 (m-30) REVERT: B 318 ASP cc_start: 0.8455 (t0) cc_final: 0.8233 (t70) REVERT: B 355 TYR cc_start: 0.8479 (m-80) cc_final: 0.7904 (m-80) REVERT: B 362 ASP cc_start: 0.8336 (m-30) cc_final: 0.8055 (m-30) REVERT: B 515 ASP cc_start: 0.8900 (m-30) cc_final: 0.8326 (m-30) REVERT: B 599 GLU cc_start: 0.8238 (pt0) cc_final: 0.7976 (pt0) REVERT: B 615 MET cc_start: 0.9558 (mmp) cc_final: 0.9346 (mmp) REVERT: C 21 PHE cc_start: 0.9216 (m-80) cc_final: 0.8844 (m-80) REVERT: C 56 MET cc_start: 0.6836 (ptm) cc_final: 0.5733 (ttm) REVERT: C 95 MET cc_start: 0.9061 (tmm) cc_final: 0.8853 (tmm) REVERT: C 122 PHE cc_start: 0.8783 (m-80) cc_final: 0.8557 (m-80) REVERT: C 189 GLU cc_start: 0.9147 (tp30) cc_final: 0.8610 (tp30) REVERT: C 193 LEU cc_start: 0.9299 (mt) cc_final: 0.8919 (mt) REVERT: C 196 ARG cc_start: 0.9020 (ptm160) cc_final: 0.8717 (ptm-80) REVERT: C 244 GLU cc_start: 0.9486 (pt0) cc_final: 0.9165 (pp20) REVERT: D 30 TRP cc_start: 0.7028 (p-90) cc_final: 0.5878 (p-90) REVERT: D 74 MET cc_start: 0.6971 (OUTLIER) cc_final: 0.6669 (tpt) REVERT: D 96 MET cc_start: 0.8215 (mmt) cc_final: 0.7933 (mmt) REVERT: D 132 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8085 (mm-40) REVERT: D 154 PHE cc_start: 0.7785 (t80) cc_final: 0.7285 (t80) REVERT: D 162 TYR cc_start: 0.7491 (t80) cc_final: 0.6941 (t80) REVERT: D 174 TYR cc_start: 0.8008 (t80) cc_final: 0.7152 (t80) REVERT: D 197 ASP cc_start: 0.8755 (m-30) cc_final: 0.8507 (m-30) REVERT: D 265 ASN cc_start: 0.8210 (m-40) cc_final: 0.7897 (m-40) outliers start: 71 outliers final: 51 residues processed: 537 average time/residue: 0.2594 time to fit residues: 209.0854 Evaluate side-chains 534 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 478 time to evaluate : 1.668 ------------------------------------------------------------------------------- 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 179 LEU 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 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 442 THR 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 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 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 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 141 LEU Chi-restraints excluded: chain C residue 147 LYS Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 211 GLU 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 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 161 VAL Chi-restraints excluded: chain D residue 184 LEU 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: 3.9990 chunk 126 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 69 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 177 optimal weight: 0.4980 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 127 GLN D 249 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.149253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.097844 restraints weight = 27676.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.101389 restraints weight = 11565.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.103610 restraints weight = 6737.856| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.5398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 16386 Z= 0.253 Angle : 0.692 14.903 22134 Z= 0.356 Chirality : 0.045 0.393 2360 Planarity : 0.004 0.054 2818 Dihedral : 10.720 164.801 2248 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 4.60 % Allowed : 22.79 % Favored : 72.61 % 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: 1.17 (0.15), residues: 1138 sheet: -0.55 (0.41), residues: 148 loop : 0.37 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 44 HIS 0.005 0.001 HIS A 438 PHE 0.041 0.002 PHE C 154 TYR 0.032 0.002 TYR D 142 ARG 0.009 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 871) hydrogen bonds : angle 4.96013 ( 2571) covalent geometry : bond 0.00565 (16386) covalent geometry : angle 0.69196 (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 579 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 500 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7926 (mt-10) REVERT: A 103 ASP cc_start: 0.8716 (m-30) cc_final: 0.8440 (m-30) REVERT: A 144 MET cc_start: 0.9020 (mtm) cc_final: 0.8478 (mtm) REVERT: A 147 GLN cc_start: 0.9166 (mt0) cc_final: 0.8766 (mt0) REVERT: A 148 GLU cc_start: 0.8497 (mt-10) cc_final: 0.8192 (mt-10) REVERT: A 209 LYS cc_start: 0.9075 (tttm) cc_final: 0.8476 (ttmm) REVERT: A 250 TYR cc_start: 0.9118 (m-80) cc_final: 0.8754 (m-80) REVERT: A 259 ASN cc_start: 0.9140 (m-40) cc_final: 0.8524 (m-40) REVERT: A 263 ASP cc_start: 0.8801 (m-30) cc_final: 0.8368 (m-30) REVERT: A 277 THR cc_start: 0.8546 (OUTLIER) cc_final: 0.8246 (t) REVERT: A 286 ASP cc_start: 0.8832 (t0) cc_final: 0.8562 (t0) REVERT: A 379 SER cc_start: 0.9315 (t) cc_final: 0.8947 (t) REVERT: A 384 GLU cc_start: 0.8826 (OUTLIER) cc_final: 0.6931 (pm20) REVERT: A 486 ASP cc_start: 0.8525 (t0) cc_final: 0.8253 (t0) REVERT: A 583 SER cc_start: 0.9351 (OUTLIER) cc_final: 0.9031 (t) REVERT: A 584 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8929 (pt) REVERT: A 589 SER cc_start: 0.9357 (m) cc_final: 0.9078 (p) REVERT: A 598 MET cc_start: 0.8550 (mtm) cc_final: 0.8045 (mtp) REVERT: A 628 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8437 (mm-30) REVERT: B 79 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8421 (mm-30) REVERT: B 103 ASP cc_start: 0.9044 (m-30) cc_final: 0.8843 (m-30) REVERT: B 108 THR cc_start: 0.8742 (OUTLIER) cc_final: 0.7311 (p) REVERT: B 111 LYS cc_start: 0.9425 (mmtp) cc_final: 0.8914 (mmtm) REVERT: B 253 ILE cc_start: 0.9545 (tt) cc_final: 0.9223 (tt) REVERT: B 263 ASP cc_start: 0.8863 (m-30) cc_final: 0.8449 (m-30) REVERT: B 272 ASP cc_start: 0.8776 (p0) cc_final: 0.8487 (p0) REVERT: B 288 PHE cc_start: 0.9345 (t80) cc_final: 0.9082 (t80) REVERT: B 336 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.8989 (ttmm) REVERT: B 355 TYR cc_start: 0.8496 (m-80) cc_final: 0.7955 (m-80) REVERT: B 362 ASP cc_start: 0.8376 (m-30) cc_final: 0.8077 (m-30) REVERT: B 384 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.7318 (pm20) REVERT: B 515 ASP cc_start: 0.8873 (m-30) cc_final: 0.8293 (m-30) REVERT: B 599 GLU cc_start: 0.8336 (pt0) cc_final: 0.8065 (pt0) REVERT: B 615 MET cc_start: 0.9542 (mmp) cc_final: 0.9312 (mmp) REVERT: C 21 PHE cc_start: 0.9234 (m-80) cc_final: 0.8893 (m-80) REVERT: C 56 MET cc_start: 0.6954 (ptm) cc_final: 0.5941 (ttm) REVERT: C 122 PHE cc_start: 0.8810 (m-80) cc_final: 0.8568 (m-80) REVERT: C 162 TYR cc_start: 0.8952 (m-80) cc_final: 0.7833 (m-80) REVERT: C 163 LEU cc_start: 0.9686 (mt) cc_final: 0.9445 (pp) REVERT: C 189 GLU cc_start: 0.8952 (tp30) cc_final: 0.8594 (tp30) REVERT: C 193 LEU cc_start: 0.9430 (mt) cc_final: 0.9136 (mt) REVERT: C 196 ARG cc_start: 0.9096 (ptm160) cc_final: 0.8828 (ptt90) REVERT: C 244 GLU cc_start: 0.9485 (pt0) cc_final: 0.9139 (pp20) REVERT: C 259 PHE cc_start: 0.8391 (t80) cc_final: 0.8174 (t80) REVERT: D 24 GLN cc_start: 0.8885 (tp40) cc_final: 0.8645 (tp40) REVERT: D 28 GLN cc_start: 0.8096 (mt0) cc_final: 0.7520 (mt0) REVERT: D 30 TRP cc_start: 0.6973 (p-90) cc_final: 0.6069 (p-90) REVERT: D 74 MET cc_start: 0.6593 (OUTLIER) cc_final: 0.6333 (tpt) REVERT: D 132 GLN cc_start: 0.8380 (OUTLIER) cc_final: 0.8020 (mm110) REVERT: D 133 LYS cc_start: 0.9423 (tppt) cc_final: 0.8883 (mtmt) REVERT: D 154 PHE cc_start: 0.7868 (t80) cc_final: 0.7420 (t80) REVERT: D 196 ARG cc_start: 0.8901 (ttt180) cc_final: 0.8481 (ptm160) REVERT: D 197 ASP cc_start: 0.8830 (m-30) cc_final: 0.8408 (m-30) outliers start: 79 outliers final: 53 residues processed: 542 average time/residue: 0.2665 time to fit residues: 215.5499 Evaluate side-chains 537 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 475 time to evaluate : 1.861 ------------------------------------------------------------------------------- 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 179 LEU 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 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 431 LEU 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 599 GLU 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 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 157 MET Chi-restraints excluded: chain C residue 211 GLU 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 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 166 PHE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 39 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 161 optimal weight: 10.0000 chunk 23 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 184 optimal weight: 20.0000 chunk 119 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN 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 = 0.3820 r_free = 0.3820 target = 0.150251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.099998 restraints weight = 27507.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.103587 restraints weight = 11351.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.105784 restraints weight = 6518.539| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 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 = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16386 Z= 0.161 Angle : 0.663 12.698 22134 Z= 0.341 Chirality : 0.044 0.373 2360 Planarity : 0.003 0.051 2818 Dihedral : 10.179 154.195 2246 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.96 % Allowed : 24.36 % 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: 1.11 (0.19), residues: 1932 helix: 1.25 (0.15), residues: 1134 sheet: -0.57 (0.41), residues: 148 loop : 0.37 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 44 HIS 0.004 0.001 HIS B 438 PHE 0.031 0.002 PHE C 172 TYR 0.030 0.001 TYR C 169 ARG 0.008 0.001 ARG B 686 Details of bonding type rmsd hydrogen bonds : bond 0.04056 ( 871) hydrogen bonds : angle 4.86213 ( 2571) covalent geometry : bond 0.00363 (16386) covalent geometry : angle 0.66291 (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 578 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 510 time to evaluate : 1.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ASP cc_start: 0.8690 (m-30) cc_final: 0.8427 (m-30) REVERT: A 106 LEU cc_start: 0.9085 (tp) cc_final: 0.8854 (tp) REVERT: A 144 MET cc_start: 0.8913 (mtm) cc_final: 0.8305 (mtm) REVERT: A 147 GLN cc_start: 0.9055 (mt0) cc_final: 0.8643 (mt0) REVERT: A 148 GLU cc_start: 0.8484 (mt-10) cc_final: 0.8163 (mt-10) REVERT: A 209 LYS cc_start: 0.9040 (tttm) cc_final: 0.8528 (ttmm) REVERT: A 250 TYR cc_start: 0.9083 (m-80) cc_final: 0.8736 (m-80) REVERT: A 251 LEU cc_start: 0.9353 (tp) cc_final: 0.9041 (tp) REVERT: A 259 ASN cc_start: 0.9074 (m-40) cc_final: 0.8493 (m-40) REVERT: A 263 ASP cc_start: 0.8751 (m-30) cc_final: 0.8388 (m-30) REVERT: A 276 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8552 (ptpp) REVERT: A 277 THR cc_start: 0.8350 (p) cc_final: 0.8087 (t) REVERT: A 286 ASP cc_start: 0.8746 (t0) cc_final: 0.8454 (t0) REVERT: A 350 ARG cc_start: 0.9185 (mtp85) cc_final: 0.8145 (mtp85) REVERT: A 357 TYR cc_start: 0.9067 (m-10) cc_final: 0.8737 (m-10) REVERT: A 379 SER cc_start: 0.9257 (t) cc_final: 0.8835 (t) REVERT: A 384 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.6722 (pm20) REVERT: A 486 ASP cc_start: 0.8528 (t0) cc_final: 0.8246 (t0) REVERT: A 493 MET cc_start: 0.9130 (tmm) cc_final: 0.8874 (tmm) REVERT: A 583 SER cc_start: 0.9278 (OUTLIER) cc_final: 0.8949 (t) REVERT: A 589 SER cc_start: 0.9323 (m) cc_final: 0.9038 (p) REVERT: A 628 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8438 (mm-30) REVERT: A 645 GLN cc_start: 0.9220 (tp40) cc_final: 0.8986 (tp-100) REVERT: B 47 PHE cc_start: 0.8529 (t80) cc_final: 0.8294 (t80) REVERT: B 111 LYS cc_start: 0.9394 (mmtp) cc_final: 0.8908 (mmtm) REVERT: B 149 TYR cc_start: 0.9264 (t80) cc_final: 0.9038 (t80) REVERT: B 263 ASP cc_start: 0.8830 (m-30) cc_final: 0.8411 (m-30) REVERT: B 320 ASN cc_start: 0.8848 (m-40) cc_final: 0.8640 (m110) REVERT: B 355 TYR cc_start: 0.8384 (m-80) cc_final: 0.7891 (m-80) REVERT: B 362 ASP cc_start: 0.8322 (m-30) cc_final: 0.7748 (m-30) REVERT: B 384 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.7342 (pm20) REVERT: B 394 TYR cc_start: 0.9223 (m-80) cc_final: 0.8452 (m-80) REVERT: B 515 ASP cc_start: 0.8823 (m-30) cc_final: 0.8269 (m-30) REVERT: B 571 TYR cc_start: 0.8792 (t80) cc_final: 0.7735 (t80) REVERT: B 586 TYR cc_start: 0.8820 (m-80) cc_final: 0.8613 (m-80) REVERT: B 599 GLU cc_start: 0.8314 (pt0) cc_final: 0.8062 (pt0) REVERT: B 610 LYS cc_start: 0.8979 (ptpt) cc_final: 0.8729 (ptmm) REVERT: C 21 PHE cc_start: 0.9266 (m-80) cc_final: 0.8897 (m-80) REVERT: C 110 MET cc_start: 0.8299 (mpp) cc_final: 0.8083 (mpp) REVERT: C 122 PHE cc_start: 0.8805 (m-80) cc_final: 0.8574 (m-80) REVERT: C 154 PHE cc_start: 0.9102 (t80) cc_final: 0.8826 (t80) REVERT: C 162 TYR cc_start: 0.8931 (m-80) cc_final: 0.7783 (m-80) REVERT: C 189 GLU cc_start: 0.8966 (tp30) cc_final: 0.8610 (tp30) REVERT: C 193 LEU cc_start: 0.9451 (mt) cc_final: 0.9132 (mt) REVERT: C 196 ARG cc_start: 0.9156 (ptm160) cc_final: 0.8836 (ptt90) REVERT: C 244 GLU cc_start: 0.9467 (pt0) cc_final: 0.9109 (pp20) REVERT: C 259 PHE cc_start: 0.8490 (t80) cc_final: 0.8196 (t80) REVERT: D 24 GLN cc_start: 0.8962 (tp40) cc_final: 0.8171 (tp40) REVERT: D 25 ASN cc_start: 0.8681 (t0) cc_final: 0.8171 (t0) REVERT: D 28 GLN cc_start: 0.8237 (mt0) cc_final: 0.7547 (mt0) REVERT: D 31 LEU cc_start: 0.8490 (mt) cc_final: 0.8180 (mt) REVERT: D 44 TRP cc_start: 0.8332 (t-100) cc_final: 0.7984 (t-100) REVERT: D 56 MET cc_start: 0.8065 (ptp) cc_final: 0.7807 (mmp) REVERT: D 69 GLN cc_start: 0.8128 (tp40) cc_final: 0.7638 (pt0) REVERT: D 132 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7994 (mm110) REVERT: D 133 LYS cc_start: 0.9580 (tppt) cc_final: 0.9096 (mtpt) REVERT: D 154 PHE cc_start: 0.7939 (t80) cc_final: 0.7481 (t80) REVERT: D 184 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7483 (mt) REVERT: D 197 ASP cc_start: 0.8806 (m-30) cc_final: 0.8509 (m-30) REVERT: D 233 ASN cc_start: 0.9200 (m-40) cc_final: 0.8890 (m110) REVERT: D 245 ASP cc_start: 0.7838 (t0) cc_final: 0.7452 (m-30) outliers start: 68 outliers final: 43 residues processed: 545 average time/residue: 0.2633 time to fit residues: 214.7149 Evaluate side-chains 528 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 479 time to evaluate : 1.912 ------------------------------------------------------------------------------- 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 226 VAL Chi-restraints excluded: chain A residue 256 ARG Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 306 ILE 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 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 232 ASN 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 147 LYS Chi-restraints excluded: chain C residue 157 MET Chi-restraints excluded: chain C residue 211 GLU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 132 GLN Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 176 LEU Chi-restraints excluded: chain D residue 184 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 159 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 chunk 180 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 650 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 80 HIS 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 = 0.3844 r_free = 0.3844 target = 0.151529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.101560 restraints weight = 27214.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.105182 restraints weight = 11431.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107359 restraints weight = 6524.238| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16386 Z= 0.147 Angle : 0.683 14.149 22134 Z= 0.353 Chirality : 0.044 0.380 2360 Planarity : 0.004 0.055 2818 Dihedral : 9.693 150.199 2246 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.61 % Allowed : 25.87 % 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: 1.11 (0.19), residues: 1932 helix: 1.27 (0.15), residues: 1120 sheet: -0.27 (0.43), residues: 140 loop : 0.23 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 44 HIS 0.003 0.001 HIS A 438 PHE 0.035 0.002 PHE C 168 TYR 0.032 0.002 TYR D 142 ARG 0.008 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04005 ( 871) hydrogen bonds : angle 4.86667 ( 2571) covalent geometry : bond 0.00333 (16386) covalent geometry : angle 0.68322 (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 578 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 516 time to evaluate : 1.695 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: 0.8691 (m-30) cc_final: 0.8480 (m-30) REVERT: A 106 LEU cc_start: 0.9050 (tp) cc_final: 0.8737 (tp) REVERT: A 144 MET cc_start: 0.8816 (mtm) cc_final: 0.8204 (mtm) REVERT: A 148 GLU cc_start: 0.8475 (mt-10) cc_final: 0.8176 (mt-10) REVERT: A 209 LYS cc_start: 0.9026 (tttm) cc_final: 0.8621 (ttmm) REVERT: A 250 TYR cc_start: 0.9082 (m-80) cc_final: 0.8727 (m-80) REVERT: A 251 LEU cc_start: 0.9316 (tp) cc_final: 0.9002 (tp) REVERT: A 259 ASN cc_start: 0.9039 (m-40) cc_final: 0.8451 (m-40) REVERT: A 263 ASP cc_start: 0.8711 (m-30) cc_final: 0.8399 (m-30) REVERT: A 277 THR cc_start: 0.8289 (p) cc_final: 0.8034 (t) REVERT: A 286 ASP cc_start: 0.8677 (t0) cc_final: 0.8416 (t0) REVERT: A 350 ARG cc_start: 0.9220 (mtp85) cc_final: 0.8174 (mtp85) REVERT: A 357 TYR cc_start: 0.9033 (m-10) cc_final: 0.8684 (m-10) REVERT: A 379 SER cc_start: 0.9275 (t) cc_final: 0.8844 (t) REVERT: A 384 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.6771 (pm20) REVERT: A 486 ASP cc_start: 0.8487 (t0) cc_final: 0.8274 (t0) REVERT: A 493 MET cc_start: 0.9100 (tmm) cc_final: 0.8833 (tmm) REVERT: A 583 SER cc_start: 0.9233 (OUTLIER) cc_final: 0.8928 (t) REVERT: A 589 SER cc_start: 0.9307 (m) cc_final: 0.9020 (p) REVERT: A 628 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8447 (mm-30) REVERT: A 645 GLN cc_start: 0.9103 (tp40) cc_final: 0.8891 (tp-100) REVERT: B 47 PHE cc_start: 0.8505 (t80) cc_final: 0.8247 (t80) REVERT: B 108 THR cc_start: 0.8738 (OUTLIER) cc_final: 0.8238 (p) REVERT: B 111 LYS cc_start: 0.9369 (mmtp) cc_final: 0.9138 (mptt) REVERT: B 263 ASP cc_start: 0.8792 (m-30) cc_final: 0.8357 (m-30) REVERT: B 274 ARG cc_start: 0.8244 (ttm110) cc_final: 0.7316 (ptp-110) REVERT: B 362 ASP cc_start: 0.8254 (m-30) cc_final: 0.7769 (m-30) REVERT: B 394 TYR cc_start: 0.9235 (m-80) cc_final: 0.8362 (m-80) REVERT: B 515 ASP cc_start: 0.8810 (m-30) cc_final: 0.8240 (m-30) REVERT: B 599 GLU cc_start: 0.8298 (pt0) cc_final: 0.8015 (pt0) REVERT: C 21 PHE cc_start: 0.9292 (m-80) cc_final: 0.8923 (m-80) REVERT: C 122 PHE cc_start: 0.8809 (m-80) cc_final: 0.8562 (m-80) REVERT: C 154 PHE cc_start: 0.9098 (t80) cc_final: 0.8835 (t80) REVERT: C 162 TYR cc_start: 0.8929 (m-80) cc_final: 0.7794 (m-80) REVERT: C 189 GLU cc_start: 0.8928 (tp30) cc_final: 0.8595 (tp30) REVERT: C 193 LEU cc_start: 0.9461 (mt) cc_final: 0.9151 (mt) REVERT: C 196 ARG cc_start: 0.9156 (ptm160) cc_final: 0.8855 (ptt90) REVERT: C 244 GLU cc_start: 0.9465 (pt0) cc_final: 0.9126 (pp20) REVERT: C 259 PHE cc_start: 0.8467 (t80) cc_final: 0.8175 (t80) REVERT: D 24 GLN cc_start: 0.8943 (tp40) cc_final: 0.8441 (tp40) REVERT: D 34 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.6733 (mp0) REVERT: D 44 TRP cc_start: 0.8393 (t-100) cc_final: 0.8010 (t-100) REVERT: D 69 GLN cc_start: 0.8064 (tp40) cc_final: 0.7661 (pt0) REVERT: D 119 ASN cc_start: 0.8958 (m110) cc_final: 0.8011 (p0) REVERT: D 123 GLU cc_start: 0.9118 (mm-30) cc_final: 0.8781 (mp0) REVERT: D 133 LYS cc_start: 0.9588 (tppt) cc_final: 0.9265 (pttt) REVERT: D 184 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7739 (mp) REVERT: D 197 ASP cc_start: 0.8829 (m-30) cc_final: 0.8484 (m-30) REVERT: D 245 ASP cc_start: 0.7841 (t0) cc_final: 0.7488 (m-30) outliers start: 62 outliers final: 44 residues processed: 550 average time/residue: 0.2638 time to fit residues: 217.3651 Evaluate side-chains 528 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 479 time to evaluate : 1.700 ------------------------------------------------------------------------------- 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 267 ILE Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 306 ILE 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 663 THR Chi-restraints excluded: chain A residue 667 LEU 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 349 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 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 B residue 667 LEU 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 211 GLU 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 132 GLN Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 227 PHE 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: 0.8980 chunk 182 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 115 optimal weight: 3.9990 chunk 127 optimal weight: 0.0270 chunk 188 optimal weight: 20.0000 chunk 27 optimal weight: 0.8980 chunk 50 optimal weight: 0.0770 overall best weight: 0.5196 ------------------------------------------------------------------------------- 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 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 132 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.153260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.103299 restraints weight = 27330.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.106925 restraints weight = 11272.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.109045 restraints weight = 6440.774| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16386 Z= 0.142 Angle : 0.705 15.781 22134 Z= 0.358 Chirality : 0.045 0.387 2360 Planarity : 0.004 0.048 2818 Dihedral : 9.248 140.068 2244 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.97 % Allowed : 26.75 % Favored : 70.28 % 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: 1.07 (0.19), residues: 1932 helix: 1.24 (0.15), residues: 1115 sheet: -0.32 (0.43), residues: 140 loop : 0.23 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 44 HIS 0.003 0.001 HIS B 438 PHE 0.035 0.001 PHE C 172 TYR 0.025 0.001 TYR D 142 ARG 0.008 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03998 ( 871) hydrogen bonds : angle 4.86612 ( 2571) covalent geometry : bond 0.00317 (16386) covalent geometry : angle 0.70483 (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 557 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 506 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.8801 (mp0) cc_final: 0.8346 (mp0) REVERT: A 103 ASP cc_start: 0.8718 (m-30) cc_final: 0.8516 (m-30) REVERT: A 106 LEU cc_start: 0.9038 (tp) cc_final: 0.8719 (tp) REVERT: A 144 MET cc_start: 0.8766 (mtm) cc_final: 0.8166 (mtm) REVERT: A 148 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8273 (mt-10) REVERT: A 209 LYS cc_start: 0.9026 (tttm) cc_final: 0.8659 (ttmm) REVERT: A 228 LYS cc_start: 0.8914 (ttmm) cc_final: 0.8417 (mttp) REVERT: A 250 TYR cc_start: 0.9074 (m-80) cc_final: 0.8756 (m-80) REVERT: A 259 ASN cc_start: 0.9028 (m-40) cc_final: 0.8463 (m-40) REVERT: A 263 ASP cc_start: 0.8650 (m-30) cc_final: 0.8306 (m-30) REVERT: A 277 THR cc_start: 0.8242 (p) cc_final: 0.8010 (t) REVERT: A 286 ASP cc_start: 0.8624 (t0) cc_final: 0.8348 (t0) REVERT: A 350 ARG cc_start: 0.9167 (mtp85) cc_final: 0.8073 (mtp85) REVERT: A 357 TYR cc_start: 0.9034 (m-10) cc_final: 0.8705 (m-10) REVERT: A 379 SER cc_start: 0.9261 (t) cc_final: 0.8806 (t) REVERT: A 384 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.6656 (pm20) REVERT: A 486 ASP cc_start: 0.8449 (t0) cc_final: 0.8234 (t0) REVERT: A 583 SER cc_start: 0.9225 (OUTLIER) cc_final: 0.8904 (t) REVERT: A 628 GLU cc_start: 0.8703 (mt-10) cc_final: 0.8418 (mm-30) REVERT: A 645 GLN cc_start: 0.9063 (tp40) cc_final: 0.8862 (tp-100) REVERT: B 47 PHE cc_start: 0.8514 (t80) cc_final: 0.8230 (t80) REVERT: B 108 THR cc_start: 0.8749 (OUTLIER) cc_final: 0.8240 (p) REVERT: B 111 LYS cc_start: 0.9352 (mmtp) cc_final: 0.9133 (mptt) REVERT: B 263 ASP cc_start: 0.8796 (m-30) cc_final: 0.8351 (m-30) REVERT: B 274 ARG cc_start: 0.8246 (ttm110) cc_final: 0.7398 (ptp-110) REVERT: B 362 ASP cc_start: 0.8064 (m-30) cc_final: 0.7839 (m-30) REVERT: B 394 TYR cc_start: 0.9238 (m-80) cc_final: 0.8330 (m-80) REVERT: B 515 ASP cc_start: 0.8797 (m-30) cc_final: 0.8233 (m-30) REVERT: B 571 TYR cc_start: 0.8696 (t80) cc_final: 0.7651 (t80) REVERT: B 599 GLU cc_start: 0.8299 (pt0) cc_final: 0.8020 (pt0) REVERT: C 21 PHE cc_start: 0.9266 (m-80) cc_final: 0.8851 (m-80) REVERT: C 74 MET cc_start: 0.7353 (mtm) cc_final: 0.7062 (pmm) REVERT: C 95 MET cc_start: 0.8940 (tmm) cc_final: 0.8680 (tmm) REVERT: C 122 PHE cc_start: 0.8719 (m-80) cc_final: 0.8505 (m-80) REVERT: C 154 PHE cc_start: 0.9122 (t80) cc_final: 0.8877 (t80) REVERT: C 162 TYR cc_start: 0.8897 (m-80) cc_final: 0.8492 (m-80) REVERT: C 189 GLU cc_start: 0.8907 (tp30) cc_final: 0.8579 (tp30) REVERT: C 193 LEU cc_start: 0.9403 (mt) cc_final: 0.9079 (mt) REVERT: C 196 ARG cc_start: 0.9121 (ptm160) cc_final: 0.8831 (ptt90) REVERT: C 259 PHE cc_start: 0.8521 (t80) cc_final: 0.8200 (t80) REVERT: C 281 ASP cc_start: 0.8050 (p0) cc_final: 0.7682 (t0) REVERT: D 24 GLN cc_start: 0.9065 (tp40) cc_final: 0.8788 (tp40) REVERT: D 56 MET cc_start: 0.8929 (mmp) cc_final: 0.7957 (ptp) REVERT: D 69 GLN cc_start: 0.8162 (tp40) cc_final: 0.7653 (pt0) REVERT: D 133 LYS cc_start: 0.9592 (tppt) cc_final: 0.9292 (pttt) REVERT: D 197 ASP cc_start: 0.8793 (m-30) cc_final: 0.8540 (m-30) REVERT: D 233 ASN cc_start: 0.9171 (m-40) cc_final: 0.8838 (m110) REVERT: D 245 ASP cc_start: 0.7843 (t0) cc_final: 0.7559 (m-30) outliers start: 51 outliers final: 38 residues processed: 535 average time/residue: 0.2660 time to fit residues: 213.9351 Evaluate side-chains 524 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 483 time to evaluate : 1.693 ------------------------------------------------------------------------------- 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 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 349 LEU Chi-restraints excluded: chain A residue 359 MET 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 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 410 ASN Chi-restraints excluded: chain B residue 411 LEU 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 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 211 GLU 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 161 VAL 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: 2.9990 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 160 optimal weight: 20.0000 chunk 106 optimal weight: 0.5980 chunk 120 optimal weight: 0.7980 chunk 135 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 127 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 70 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 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 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 132 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.151567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.101421 restraints weight = 27486.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.105062 restraints weight = 11410.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.107178 restraints weight = 6519.535| |-----------------------------------------------------------------------------| r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.6040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16386 Z= 0.179 Angle : 0.739 15.265 22134 Z= 0.375 Chirality : 0.046 0.383 2360 Planarity : 0.004 0.051 2818 Dihedral : 9.188 138.750 2244 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.91 % Allowed : 27.33 % Favored : 69.76 % 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: 1.15 (0.15), residues: 1118 sheet: -0.68 (0.41), residues: 152 loop : 0.25 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 44 HIS 0.004 0.001 HIS A 438 PHE 0.036 0.002 PHE C 172 TYR 0.027 0.002 TYR D 204 ARG 0.009 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 871) hydrogen bonds : angle 4.94507 ( 2571) covalent geometry : bond 0.00409 (16386) covalent geometry : angle 0.73923 (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 546 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 496 time to evaluate : 1.817 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: 0.8807 (mp0) cc_final: 0.8356 (mp0) REVERT: A 76 ASP cc_start: 0.8753 (m-30) cc_final: 0.8378 (m-30) REVERT: A 103 ASP cc_start: 0.8717 (m-30) cc_final: 0.8506 (m-30) REVERT: A 106 LEU cc_start: 0.9060 (tp) cc_final: 0.8730 (tp) REVERT: A 144 MET cc_start: 0.8807 (mtm) cc_final: 0.8233 (mtm) REVERT: A 148 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8226 (mt-10) REVERT: A 209 LYS cc_start: 0.9051 (tttm) cc_final: 0.8715 (ttmm) REVERT: A 250 TYR cc_start: 0.9096 (m-80) cc_final: 0.8760 (m-80) REVERT: A 259 ASN cc_start: 0.9033 (m-40) cc_final: 0.8469 (m-40) REVERT: A 263 ASP cc_start: 0.8661 (m-30) cc_final: 0.8339 (m-30) REVERT: A 277 THR cc_start: 0.8299 (p) cc_final: 0.8030 (t) REVERT: A 286 ASP cc_start: 0.8608 (t0) cc_final: 0.8379 (t0) REVERT: A 350 ARG cc_start: 0.9237 (mtp85) cc_final: 0.8180 (mtp85) REVERT: A 379 SER cc_start: 0.9246 (t) cc_final: 0.8787 (t) REVERT: A 384 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.6809 (pm20) REVERT: A 486 ASP cc_start: 0.8469 (t0) cc_final: 0.8256 (t0) REVERT: A 583 SER cc_start: 0.9269 (OUTLIER) cc_final: 0.8951 (t) REVERT: A 586 TYR cc_start: 0.8778 (m-10) cc_final: 0.8240 (m-80) REVERT: A 628 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8466 (mm-30) REVERT: B 108 THR cc_start: 0.8754 (OUTLIER) cc_final: 0.8220 (p) REVERT: B 111 LYS cc_start: 0.9382 (mmtp) cc_final: 0.9154 (mptt) REVERT: B 184 ARG cc_start: 0.9146 (tpp-160) cc_final: 0.8854 (tpp-160) REVERT: B 263 ASP cc_start: 0.8809 (m-30) cc_final: 0.8353 (m-30) REVERT: B 274 ARG cc_start: 0.8286 (ttm110) cc_final: 0.7434 (ptp-110) REVERT: B 362 ASP cc_start: 0.8130 (m-30) cc_final: 0.7910 (m-30) REVERT: B 515 ASP cc_start: 0.8790 (m-30) cc_final: 0.8226 (m-30) REVERT: B 571 TYR cc_start: 0.8749 (t80) cc_final: 0.7679 (t80) REVERT: B 595 MET cc_start: 0.8984 (mmm) cc_final: 0.8278 (mmm) REVERT: B 599 GLU cc_start: 0.8324 (pt0) cc_final: 0.8024 (pt0) REVERT: B 602 GLU cc_start: 0.8123 (pt0) cc_final: 0.7820 (pt0) REVERT: C 17 PHE cc_start: 0.8446 (p90) cc_final: 0.7914 (p90) REVERT: C 21 PHE cc_start: 0.9248 (m-80) cc_final: 0.8399 (m-80) REVERT: C 74 MET cc_start: 0.7374 (mtm) cc_final: 0.7106 (pmm) REVERT: C 95 MET cc_start: 0.8951 (tmm) cc_final: 0.8729 (tmm) REVERT: C 154 PHE cc_start: 0.9065 (t80) cc_final: 0.8825 (t80) REVERT: C 162 TYR cc_start: 0.8906 (m-80) cc_final: 0.8490 (m-80) REVERT: C 189 GLU cc_start: 0.8944 (tp30) cc_final: 0.8617 (tp30) REVERT: C 193 LEU cc_start: 0.9402 (mt) cc_final: 0.9078 (mt) REVERT: C 196 ARG cc_start: 0.9105 (ptm160) cc_final: 0.8895 (ptt90) REVERT: C 259 PHE cc_start: 0.8540 (t80) cc_final: 0.8223 (t80) REVERT: D 24 GLN cc_start: 0.9180 (tp40) cc_final: 0.8879 (tp40) REVERT: D 30 TRP cc_start: 0.7059 (p-90) cc_final: 0.6443 (p-90) REVERT: D 56 MET cc_start: 0.8908 (mmp) cc_final: 0.8031 (mtt) REVERT: D 69 GLN cc_start: 0.8216 (tp40) cc_final: 0.7743 (pt0) REVERT: D 74 MET cc_start: 0.5617 (tpt) cc_final: 0.4558 (ttp) REVERT: D 133 LYS cc_start: 0.9581 (tppt) cc_final: 0.9306 (pttm) REVERT: D 154 PHE cc_start: 0.7589 (t80) cc_final: 0.7331 (t80) REVERT: D 232 LEU cc_start: 0.8608 (mt) cc_final: 0.7922 (tt) REVERT: D 233 ASN cc_start: 0.9170 (m-40) cc_final: 0.8805 (m110) REVERT: D 245 ASP cc_start: 0.7843 (t0) cc_final: 0.7483 (m-30) REVERT: D 287 LEU cc_start: 0.7475 (mt) cc_final: 0.7004 (pp) outliers start: 50 outliers final: 41 residues processed: 521 average time/residue: 0.2662 time to fit residues: 207.6323 Evaluate side-chains 528 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 484 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 49 HIS Chi-restraints excluded: chain A residue 134 THR 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 279 SER Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 MET 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 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 410 ASN Chi-restraints excluded: chain B residue 411 LEU 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 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 211 GLU Chi-restraints excluded: chain C residue 280 GLU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 161 VAL 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: 3.9990 chunk 2 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 105 optimal weight: 0.7980 chunk 179 optimal weight: 9.9990 chunk 190 optimal weight: 0.9980 chunk 58 optimal weight: 3.9990 chunk 180 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 418 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 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 650 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN D 132 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.151835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.102684 restraints weight = 27462.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.106189 restraints weight = 11723.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.108417 restraints weight = 6837.559| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.6204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 16386 Z= 0.163 Angle : 0.759 14.725 22134 Z= 0.386 Chirality : 0.047 0.408 2360 Planarity : 0.004 0.049 2818 Dihedral : 9.128 137.248 2244 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.56 % Allowed : 27.86 % Favored : 69.58 % 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: 0.85 (0.19), residues: 1932 helix: 1.10 (0.15), residues: 1116 sheet: -0.73 (0.41), residues: 152 loop : 0.17 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 44 HIS 0.011 0.001 HIS D 201 PHE 0.037 0.002 PHE C 172 TYR 0.038 0.001 TYR D 142 ARG 0.008 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04108 ( 871) hydrogen bonds : angle 5.03206 ( 2571) covalent geometry : bond 0.00373 (16386) covalent geometry : angle 0.75927 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6336.92 seconds wall clock time: 111 minutes 29.47 seconds (6689.47 seconds total)