Starting phenix.real_space_refine on Thu Sep 18 09:58:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzi_45068/09_2025/9bzi_45068_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzi_45068/09_2025/9bzi_45068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bzi_45068/09_2025/9bzi_45068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzi_45068/09_2025/9bzi_45068.map" model { file = "/net/cci-nas-00/data/ceres_data/9bzi_45068/09_2025/9bzi_45068_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzi_45068/09_2025/9bzi_45068_neut.cif" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.44, per 1000 atoms: 0.21 Number of scatterers: 16038 At special positions: 0 Unit cell: (96.33, 140.946, 130.806, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 617.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.51 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.986A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.953A 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: 3.575A 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: 3.693A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.628A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.073A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.676A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.878A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.027A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.068A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A 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: 3.668A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.359A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.479A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.499A 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: 7.229A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.064A 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: 4.048A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.72 Time building geometry restraints manager: 1.58 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: 4853 1.34 - 1.46: 3064 1.46 - 1.58: 8288 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.25e-02 6.40e+03 2.37e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.039 1.20e-02 6.94e+03 1.04e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.033 1.08e-02 8.57e+03 9.08e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.569 -0.032 1.17e-02 7.31e+03 7.45e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.574 -0.034 1.25e-02 6.40e+03 7.31e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 21579 2.10 - 4.19: 513 4.19 - 6.29: 37 6.29 - 8.39: 1 8.39 - 10.48: 4 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.64 -6.10 1.36e+00 5.41e-01 2.01e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.15 -4.44 1.15e+00 7.56e-01 1.49e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.25 -3.97 1.09e+00 8.42e-01 1.33e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.84 -4.34 1.23e+00 6.61e-01 1.25e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.69 -3.98 1.15e+00 7.56e-01 1.20e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 9471 35.79 - 71.58: 336 71.58 - 107.38: 37 107.38 - 143.17: 3 143.17 - 178.96: 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 -58.32 120.64 -178.96 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 301.68 151.22 150.46 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 31.88 148.09 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 9847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2150 0.094 - 0.188: 177 0.188 - 0.282: 29 0.282 - 0.376: 2 0.376 - 0.470: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.53e+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 4.66e+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 2.96e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.70e+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 " 0.018 2.00e-02 2.50e+03 1.12e-02 2.20e+00 pdb=" CG PHE D 92 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 169 " 0.017 2.00e-02 2.50e+03 9.95e-03 1.98e+00 pdb=" CG TYR C 169 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 169 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 169 " 0.008 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 129 2.51 - 3.11: 11556 3.11 - 3.70: 27051 3.70 - 4.30: 41551 4.30 - 4.90: 65481 Nonbonded interactions: 145768 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.012 3.040 ... (remaining 145763 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 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: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.320 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6702 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16386 Z= 0.315 Angle : 0.740 10.483 22134 Z= 0.463 Chirality : 0.058 0.470 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.907 178.960 6154 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.34 % Allowed : 15.27 % Favored : 83.39 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.18), residues: 1932 helix: 0.59 (0.14), residues: 1149 sheet: 0.46 (0.42), residues: 124 loop : 0.24 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74022 (22134) hydrogen bonds : bond 0.15420 ( 871) hydrogen bonds : angle 6.51778 ( 2571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 1085 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 28 LYS cc_start: 0.8512 (mmtm) cc_final: 0.8195 (mtpp) REVERT: A 76 ASP cc_start: 0.8314 (m-30) cc_final: 0.7600 (m-30) REVERT: A 172 LEU cc_start: 0.8973 (mp) cc_final: 0.8508 (mp) REVERT: A 177 ASP cc_start: 0.8139 (t0) cc_final: 0.7845 (t0) REVERT: A 188 ILE cc_start: 0.8410 (mt) cc_final: 0.8066 (mt) REVERT: A 192 LEU cc_start: 0.9026 (mt) cc_final: 0.8774 (mt) REVERT: A 202 ASN cc_start: 0.9096 (t0) cc_final: 0.8841 (t0) REVERT: A 258 ILE cc_start: 0.8947 (tp) cc_final: 0.8697 (tp) REVERT: A 349 LEU cc_start: 0.8369 (mt) cc_final: 0.8146 (mt) REVERT: A 385 VAL cc_start: 0.8659 (t) cc_final: 0.8370 (t) REVERT: A 391 VAL cc_start: 0.9431 (p) cc_final: 0.9198 (p) REVERT: A 407 ILE cc_start: 0.8631 (mt) cc_final: 0.8201 (mt) REVERT: A 420 MET cc_start: 0.7021 (mmm) cc_final: 0.6674 (mmm) REVERT: A 485 ARG cc_start: 0.7711 (mtm-85) cc_final: 0.7485 (mtm-85) REVERT: A 501 GLN cc_start: 0.8151 (tt0) cc_final: 0.7764 (tt0) REVERT: A 546 LEU cc_start: 0.8784 (mt) cc_final: 0.8563 (mt) REVERT: A 550 MET cc_start: 0.6690 (mtm) cc_final: 0.6082 (mtm) REVERT: A 590 SER cc_start: 0.8929 (p) cc_final: 0.8281 (p) REVERT: A 631 ASP cc_start: 0.7859 (m-30) cc_final: 0.7412 (m-30) REVERT: B 118 TYR cc_start: 0.7321 (t80) cc_final: 0.7008 (t80) REVERT: B 122 ILE cc_start: 0.8630 (mt) cc_final: 0.8429 (mt) REVERT: B 191 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8224 (mm-40) REVERT: B 192 LEU cc_start: 0.9085 (mt) cc_final: 0.8857 (mt) REVERT: B 204 SER cc_start: 0.8867 (m) cc_final: 0.8149 (t) REVERT: B 226 VAL cc_start: 0.8791 (t) cc_final: 0.8583 (t) REVERT: B 265 LYS cc_start: 0.8645 (mmtt) cc_final: 0.8296 (mmmt) REVERT: B 286 ASP cc_start: 0.6672 (OUTLIER) cc_final: 0.6449 (m-30) REVERT: B 358 ILE cc_start: 0.8977 (mm) cc_final: 0.8719 (mm) REVERT: B 366 LYS cc_start: 0.8571 (ptpp) cc_final: 0.8221 (ttpp) REVERT: B 378 PHE cc_start: 0.8476 (p90) cc_final: 0.8116 (p90) REVERT: B 384 GLU cc_start: 0.8921 (pm20) cc_final: 0.8626 (pm20) REVERT: B 458 MET cc_start: 0.8140 (mmm) cc_final: 0.7834 (tpp) REVERT: B 468 LEU cc_start: 0.8484 (tp) cc_final: 0.8145 (tp) REVERT: B 471 TYR cc_start: 0.8185 (t80) cc_final: 0.7850 (t80) REVERT: B 546 LEU cc_start: 0.8826 (mt) cc_final: 0.8281 (mt) REVERT: B 583 SER cc_start: 0.6929 (m) cc_final: 0.6561 (t) REVERT: B 645 GLN cc_start: 0.8234 (tp-100) cc_final: 0.7984 (tp40) REVERT: B 650 GLN cc_start: 0.8332 (mt0) cc_final: 0.7616 (mt0) REVERT: B 670 ILE cc_start: 0.9064 (mt) cc_final: 0.8820 (mt) REVERT: B 687 THR cc_start: 0.7737 (m) cc_final: 0.7350 (p) REVERT: C 95 MET cc_start: 0.5372 (tmm) cc_final: 0.4514 (tmm) REVERT: C 131 LEU cc_start: 0.5653 (OUTLIER) cc_final: 0.5417 (tp) REVERT: C 153 LEU cc_start: 0.6621 (tp) cc_final: 0.6016 (tp) REVERT: C 155 LYS cc_start: 0.7675 (mttt) cc_final: 0.7442 (mmtt) REVERT: C 174 TYR cc_start: 0.4327 (OUTLIER) cc_final: 0.3652 (t80) REVERT: D 17 PHE cc_start: 0.6374 (p90) cc_final: 0.6077 (p90) REVERT: D 43 THR cc_start: 0.7141 (p) cc_final: 0.6894 (p) REVERT: D 89 VAL cc_start: 0.7381 (t) cc_final: 0.6656 (t) REVERT: D 178 PHE cc_start: 0.6753 (m-80) cc_final: 0.5555 (m-80) REVERT: D 265 ASN cc_start: 0.4532 (m-40) cc_final: 0.3794 (m110) outliers start: 23 outliers final: 7 residues processed: 1094 average time/residue: 0.1471 time to fit residues: 230.8607 Evaluate side-chains 716 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 706 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.0870 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 1.9990 overall best weight: 2.0164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 304 HIS A 370 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN B 61 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 304 HIS B 329 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN C 234 GLN C 263 ASN ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 181 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.116844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.087043 restraints weight = 41524.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.090530 restraints weight = 20850.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.092633 restraints weight = 12802.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.094395 restraints weight = 9064.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.095725 restraints weight = 6842.366| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 16386 Z= 0.216 Angle : 0.752 14.563 22134 Z= 0.395 Chirality : 0.047 0.186 2360 Planarity : 0.004 0.044 2818 Dihedral : 11.730 169.060 2258 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.55 % Allowed : 21.68 % Favored : 73.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.21 (0.19), residues: 1932 helix: 1.20 (0.15), residues: 1128 sheet: 0.28 (0.43), residues: 126 loop : 0.44 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 243 TYR 0.021 0.002 TYR B 527 PHE 0.034 0.003 PHE D 172 TRP 0.025 0.003 TRP C 30 HIS 0.011 0.002 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00473 (16386) covalent geometry : angle 0.75249 (22134) hydrogen bonds : bond 0.04989 ( 871) hydrogen bonds : angle 5.32410 ( 2571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 784 time to evaluate : 0.668 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: A 76 ASP cc_start: 0.9031 (m-30) cc_final: 0.8784 (m-30) REVERT: A 107 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8236 (mmmm) REVERT: A 166 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7997 (mm-30) REVERT: A 174 GLU cc_start: 0.7828 (mt-10) cc_final: 0.7507 (mt-10) REVERT: A 191 GLN cc_start: 0.8552 (mm-40) cc_final: 0.8313 (mm-40) REVERT: A 221 LYS cc_start: 0.8834 (mmtp) cc_final: 0.8623 (mttp) REVERT: A 232 ASN cc_start: 0.9371 (OUTLIER) cc_final: 0.9102 (m-40) REVERT: A 250 TYR cc_start: 0.8769 (m-80) cc_final: 0.8475 (m-80) REVERT: A 255 HIS cc_start: 0.8901 (t-90) cc_final: 0.8097 (t-90) REVERT: A 257 ASP cc_start: 0.9250 (m-30) cc_final: 0.8991 (m-30) REVERT: A 291 LEU cc_start: 0.9577 (mt) cc_final: 0.9277 (mt) REVERT: A 335 GLU cc_start: 0.8334 (mt-10) cc_final: 0.7958 (mt-10) REVERT: A 378 PHE cc_start: 0.8988 (p90) cc_final: 0.8638 (p90) REVERT: A 415 ASN cc_start: 0.9261 (t0) cc_final: 0.8979 (t0) REVERT: A 436 LEU cc_start: 0.9371 (mt) cc_final: 0.8987 (mt) REVERT: A 447 ASN cc_start: 0.8375 (m-40) cc_final: 0.7719 (t0) REVERT: A 456 LYS cc_start: 0.9237 (mtpt) cc_final: 0.8801 (ptpp) REVERT: A 471 TYR cc_start: 0.8985 (t80) cc_final: 0.8514 (t80) REVERT: A 528 PHE cc_start: 0.8888 (m-80) cc_final: 0.8677 (m-80) REVERT: A 546 LEU cc_start: 0.9753 (mt) cc_final: 0.9417 (mt) REVERT: A 550 MET cc_start: 0.6605 (mtm) cc_final: 0.5867 (mtm) REVERT: A 595 MET cc_start: 0.9304 (mmp) cc_final: 0.9014 (mmp) REVERT: A 615 MET cc_start: 0.9224 (mmt) cc_final: 0.8853 (mmm) REVERT: A 640 MET cc_start: 0.9171 (tpp) cc_final: 0.8895 (tpp) REVERT: A 645 GLN cc_start: 0.8808 (tp40) cc_final: 0.8495 (tp-100) REVERT: A 647 HIS cc_start: 0.8932 (m-70) cc_final: 0.8342 (m-70) REVERT: A 686 ARG cc_start: 0.8224 (ttm-80) cc_final: 0.8003 (ttm-80) REVERT: B 16 ILE cc_start: 0.9490 (pt) cc_final: 0.9273 (pt) REVERT: B 18 ILE cc_start: 0.9626 (mp) cc_final: 0.9322 (pt) REVERT: B 82 LYS cc_start: 0.9591 (mtpp) cc_final: 0.9264 (ptpp) REVERT: B 95 MET cc_start: 0.9090 (tpt) cc_final: 0.8768 (tpp) REVERT: B 99 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.8628 (tptp) REVERT: B 102 ASN cc_start: 0.9430 (m110) cc_final: 0.9130 (m110) REVERT: B 150 GLN cc_start: 0.9573 (tp40) cc_final: 0.9355 (tp-100) REVERT: B 181 ASP cc_start: 0.8801 (m-30) cc_final: 0.8335 (m-30) REVERT: B 184 ARG cc_start: 0.9446 (tpp80) cc_final: 0.9189 (tpp80) REVERT: B 227 MET cc_start: 0.9276 (mtt) cc_final: 0.9005 (mtt) REVERT: B 235 ARG cc_start: 0.8775 (mtm110) cc_final: 0.8509 (mtm110) REVERT: B 250 TYR cc_start: 0.8999 (m-80) cc_final: 0.8744 (m-80) REVERT: B 257 ASP cc_start: 0.8781 (m-30) cc_final: 0.8462 (m-30) REVERT: B 322 MET cc_start: 0.9224 (mmm) cc_final: 0.8879 (mmt) REVERT: B 341 LYS cc_start: 0.9601 (mmtm) cc_final: 0.9370 (mmmt) REVERT: B 348 MET cc_start: 0.8632 (tmm) cc_final: 0.8227 (tpt) REVERT: B 393 SER cc_start: 0.9310 (m) cc_final: 0.8707 (p) REVERT: B 399 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8683 (mm-30) REVERT: B 402 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7520 (tm-30) REVERT: B 471 TYR cc_start: 0.9347 (t80) cc_final: 0.8460 (t80) REVERT: B 475 ASN cc_start: 0.9121 (m-40) cc_final: 0.8562 (m-40) REVERT: B 515 ASP cc_start: 0.9212 (m-30) cc_final: 0.8739 (m-30) REVERT: B 570 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.7960 (mtm) REVERT: B 583 SER cc_start: 0.8951 (m) cc_final: 0.8402 (p) REVERT: B 620 SER cc_start: 0.9400 (OUTLIER) cc_final: 0.9139 (p) REVERT: B 632 MET cc_start: 0.8615 (mtm) cc_final: 0.8381 (mtm) REVERT: B 645 GLN cc_start: 0.9304 (tp-100) cc_final: 0.8842 (tp40) REVERT: C 21 PHE cc_start: 0.9396 (m-80) cc_final: 0.8748 (m-80) REVERT: C 30 TRP cc_start: 0.7642 (p-90) cc_final: 0.6951 (t60) REVERT: C 90 LEU cc_start: 0.9020 (mt) cc_final: 0.8721 (mt) REVERT: C 92 PHE cc_start: 0.9403 (t80) cc_final: 0.8417 (t80) REVERT: C 93 MET cc_start: 0.9419 (mtt) cc_final: 0.9083 (mtt) REVERT: C 95 MET cc_start: 0.9094 (tmm) cc_final: 0.8772 (tmm) REVERT: C 96 MET cc_start: 0.9142 (mmm) cc_final: 0.8189 (mmm) REVERT: C 101 HIS cc_start: 0.9118 (m170) cc_final: 0.8671 (m170) REVERT: C 109 PHE cc_start: 0.8406 (m-10) cc_final: 0.8161 (m-10) REVERT: C 130 TYR cc_start: 0.9652 (m-80) cc_final: 0.9354 (m-10) REVERT: C 145 ILE cc_start: 0.7623 (tp) cc_final: 0.7266 (tp) REVERT: C 155 LYS cc_start: 0.8730 (mttt) cc_final: 0.8326 (mmtt) REVERT: C 157 MET cc_start: 0.9322 (mtt) cc_final: 0.9071 (mtt) REVERT: C 173 TYR cc_start: 0.8437 (t80) cc_final: 0.7928 (t80) REVERT: C 174 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.7833 (t80) REVERT: C 197 ASP cc_start: 0.9495 (m-30) cc_final: 0.9111 (m-30) REVERT: C 198 GLU cc_start: 0.9683 (mm-30) cc_final: 0.9307 (mm-30) REVERT: C 201 HIS cc_start: 0.8980 (m-70) cc_final: 0.8618 (m90) REVERT: C 241 GLU cc_start: 0.9589 (mp0) cc_final: 0.9134 (mp0) REVERT: C 242 TYR cc_start: 0.9357 (t80) cc_final: 0.8772 (t80) REVERT: C 259 PHE cc_start: 0.8985 (t80) cc_final: 0.7899 (t80) REVERT: C 263 ASN cc_start: 0.9612 (OUTLIER) cc_final: 0.8476 (p0) REVERT: C 268 LEU cc_start: 0.9528 (mt) cc_final: 0.9242 (mt) REVERT: D 30 TRP cc_start: 0.8056 (p-90) cc_final: 0.7483 (p-90) REVERT: D 50 ASN cc_start: 0.8985 (m-40) cc_final: 0.8480 (p0) REVERT: D 63 THR cc_start: 0.9321 (m) cc_final: 0.9106 (p) REVERT: D 96 MET cc_start: 0.8465 (mmm) cc_final: 0.8237 (mmt) REVERT: D 131 LEU cc_start: 0.8563 (tt) cc_final: 0.8179 (tp) REVERT: D 167 LEU cc_start: 0.9733 (mt) cc_final: 0.9302 (mt) REVERT: D 168 PHE cc_start: 0.8596 (m-80) cc_final: 0.7862 (m-80) REVERT: D 174 TYR cc_start: 0.8805 (t80) cc_final: 0.8360 (t80) REVERT: D 186 GLN cc_start: 0.7867 (mm-40) cc_final: 0.7633 (mm-40) REVERT: D 198 GLU cc_start: 0.8625 (pp20) cc_final: 0.8317 (pp20) REVERT: D 242 TYR cc_start: 0.8730 (t80) cc_final: 0.8497 (t80) REVERT: D 254 HIS cc_start: 0.8953 (m90) cc_final: 0.8719 (m-70) outliers start: 78 outliers final: 36 residues processed: 813 average time/residue: 0.1394 time to fit residues: 168.9090 Evaluate side-chains 742 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 698 time to evaluate : 0.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 266 LYS Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 180 ASN 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 239 GLN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 427 LYS Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 263 ASN Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 91 optimal weight: 10.0000 chunk 150 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 40 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 239 GLN A 370 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 338 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN B 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 HIS ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN D 23 ASN D 71 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 210 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.115947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.086995 restraints weight = 41872.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.090187 restraints weight = 21737.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.092302 restraints weight = 13643.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.093873 restraints weight = 9666.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.095053 restraints weight = 7422.180| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3164 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3164 r_free = 0.3164 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3164 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.5662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16386 Z= 0.181 Angle : 0.720 14.574 22134 Z= 0.371 Chirality : 0.047 0.267 2360 Planarity : 0.004 0.037 2818 Dihedral : 11.404 178.940 2250 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.14 % Allowed : 24.65 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.19), residues: 1932 helix: 1.23 (0.15), residues: 1113 sheet: 0.71 (0.46), residues: 114 loop : 0.20 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 243 TYR 0.035 0.002 TYR D 142 PHE 0.037 0.002 PHE C 172 TRP 0.011 0.002 TRP C 44 HIS 0.013 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00400 (16386) covalent geometry : angle 0.71989 (22134) hydrogen bonds : bond 0.04534 ( 871) hydrogen bonds : angle 5.25189 ( 2571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 755 time to evaluate : 0.488 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: A 76 ASP cc_start: 0.8982 (m-30) cc_final: 0.8628 (m-30) REVERT: A 161 ARG cc_start: 0.8413 (ttm110) cc_final: 0.8027 (ptm160) REVERT: A 174 GLU cc_start: 0.7860 (mt-10) cc_final: 0.7641 (mt-10) REVERT: A 211 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8063 (mm-30) REVERT: A 221 LYS cc_start: 0.8795 (mmtp) cc_final: 0.8576 (mttp) REVERT: A 250 TYR cc_start: 0.8833 (m-80) cc_final: 0.8578 (m-80) REVERT: A 254 PHE cc_start: 0.9282 (m-80) cc_final: 0.9061 (m-80) REVERT: A 257 ASP cc_start: 0.9035 (m-30) cc_final: 0.8815 (m-30) REVERT: A 325 LYS cc_start: 0.9683 (mmmt) cc_final: 0.9411 (mmtp) REVERT: A 335 GLU cc_start: 0.8217 (mt-10) cc_final: 0.8001 (mt-10) REVERT: A 360 PHE cc_start: 0.9090 (m-80) cc_final: 0.8861 (m-80) REVERT: A 447 ASN cc_start: 0.8447 (m-40) cc_final: 0.7803 (t0) REVERT: A 456 LYS cc_start: 0.9365 (OUTLIER) cc_final: 0.8913 (mtmm) REVERT: A 471 TYR cc_start: 0.9060 (t80) cc_final: 0.8664 (t80) REVERT: A 516 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8421 (tp-100) REVERT: A 546 LEU cc_start: 0.9729 (mt) cc_final: 0.9476 (mt) REVERT: A 590 SER cc_start: 0.9642 (t) cc_final: 0.8984 (p) REVERT: A 595 MET cc_start: 0.9222 (mmp) cc_final: 0.8881 (mmp) REVERT: A 615 MET cc_start: 0.9217 (mmt) cc_final: 0.8917 (mmm) REVERT: A 645 GLN cc_start: 0.9062 (tp40) cc_final: 0.8568 (tp-100) REVERT: A 650 GLN cc_start: 0.8859 (mt0) cc_final: 0.8319 (mm-40) REVERT: A 669 ARG cc_start: 0.9257 (tpp-160) cc_final: 0.8861 (tpp80) REVERT: B 18 ILE cc_start: 0.9623 (mp) cc_final: 0.9350 (pt) REVERT: B 54 LYS cc_start: 0.9601 (tttt) cc_final: 0.9250 (tttt) REVERT: B 82 LYS cc_start: 0.9595 (mtpp) cc_final: 0.9226 (ptpp) REVERT: B 95 MET cc_start: 0.9084 (tpt) cc_final: 0.8547 (tpp) REVERT: B 99 LYS cc_start: 0.9373 (OUTLIER) cc_final: 0.8654 (tptp) REVERT: B 102 ASN cc_start: 0.9454 (m110) cc_final: 0.9201 (m110) REVERT: B 107 LYS cc_start: 0.9274 (mmmm) cc_final: 0.8919 (mmmm) REVERT: B 150 GLN cc_start: 0.9590 (tp40) cc_final: 0.9169 (tp-100) REVERT: B 184 ARG cc_start: 0.9480 (tpp80) cc_final: 0.9241 (tpp80) REVERT: B 227 MET cc_start: 0.9227 (mtp) cc_final: 0.9023 (mtt) REVERT: B 232 ASN cc_start: 0.9492 (OUTLIER) cc_final: 0.9059 (m110) REVERT: B 235 ARG cc_start: 0.9026 (mtm110) cc_final: 0.8796 (ptp-110) REVERT: B 266 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8453 (ptpp) REVERT: B 274 ARG cc_start: 0.8561 (ttm110) cc_final: 0.8256 (ttm170) REVERT: B 322 MET cc_start: 0.9225 (mmm) cc_final: 0.8876 (mmt) REVERT: B 341 LYS cc_start: 0.9592 (mmtm) cc_final: 0.9249 (mmmt) REVERT: B 344 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8763 (pt0) REVERT: B 348 MET cc_start: 0.8686 (tmm) cc_final: 0.8319 (tpt) REVERT: B 362 ASP cc_start: 0.8554 (m-30) cc_final: 0.8190 (m-30) REVERT: B 393 SER cc_start: 0.9353 (m) cc_final: 0.8922 (p) REVERT: B 396 ASP cc_start: 0.8892 (p0) cc_final: 0.8530 (p0) REVERT: B 399 GLU cc_start: 0.9022 (tp30) cc_final: 0.8615 (mm-30) REVERT: B 402 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7521 (tm-30) REVERT: B 431 LEU cc_start: 0.9512 (mm) cc_final: 0.9296 (mm) REVERT: B 471 TYR cc_start: 0.9154 (t80) cc_final: 0.8906 (t80) REVERT: B 474 GLN cc_start: 0.9114 (mm-40) cc_final: 0.8908 (mm-40) REVERT: B 475 ASN cc_start: 0.9088 (m-40) cc_final: 0.8612 (m110) REVERT: B 515 ASP cc_start: 0.9185 (m-30) cc_final: 0.8692 (m-30) REVERT: B 548 GLU cc_start: 0.8067 (mm-30) cc_final: 0.7683 (mm-30) REVERT: B 550 MET cc_start: 0.8040 (mtp) cc_final: 0.7753 (mtp) REVERT: B 583 SER cc_start: 0.9023 (m) cc_final: 0.8476 (p) REVERT: B 584 ILE cc_start: 0.9464 (tp) cc_final: 0.9234 (tp) REVERT: B 588 GLN cc_start: 0.9312 (mm-40) cc_final: 0.8981 (mm-40) REVERT: B 595 MET cc_start: 0.9353 (mmp) cc_final: 0.9120 (mmm) REVERT: B 602 GLU cc_start: 0.8306 (pt0) cc_final: 0.7990 (pt0) REVERT: B 604 ARG cc_start: 0.8845 (mmp80) cc_final: 0.8358 (mmt-90) REVERT: B 632 MET cc_start: 0.8503 (mtm) cc_final: 0.8239 (mtm) REVERT: B 645 GLN cc_start: 0.9372 (tp40) cc_final: 0.8854 (tp40) REVERT: B 668 ASN cc_start: 0.9016 (m110) cc_final: 0.8483 (m-40) REVERT: C 21 PHE cc_start: 0.9386 (m-80) cc_final: 0.9067 (m-80) REVERT: C 90 LEU cc_start: 0.9087 (mt) cc_final: 0.8783 (mt) REVERT: C 92 PHE cc_start: 0.9501 (t80) cc_final: 0.9194 (t80) REVERT: C 109 PHE cc_start: 0.8349 (m-10) cc_final: 0.8148 (m-10) REVERT: C 134 LYS cc_start: 0.9476 (pttm) cc_final: 0.9271 (pttm) REVERT: C 155 LYS cc_start: 0.8900 (mttt) cc_final: 0.8556 (mmtt) REVERT: C 174 TYR cc_start: 0.8700 (OUTLIER) cc_final: 0.7625 (t80) REVERT: C 194 ILE cc_start: 0.9656 (mt) cc_final: 0.9422 (mt) REVERT: C 198 GLU cc_start: 0.9346 (mm-30) cc_final: 0.9030 (mm-30) REVERT: C 242 TYR cc_start: 0.9440 (t80) cc_final: 0.8613 (t80) REVERT: C 259 PHE cc_start: 0.9076 (t80) cc_final: 0.8551 (t80) REVERT: C 266 LYS cc_start: 0.9427 (mttt) cc_final: 0.9076 (mmmt) REVERT: C 314 PRO cc_start: 0.9226 (Cg_exo) cc_final: 0.8671 (Cg_endo) REVERT: D 20 MET cc_start: 0.9213 (ppp) cc_final: 0.8944 (ppp) REVERT: D 30 TRP cc_start: 0.8370 (p-90) cc_final: 0.7948 (p-90) REVERT: D 46 TYR cc_start: 0.9271 (m-80) cc_final: 0.8795 (m-80) REVERT: D 96 MET cc_start: 0.8128 (mmm) cc_final: 0.7745 (mmm) REVERT: D 131 LEU cc_start: 0.8756 (tt) cc_final: 0.8428 (tp) REVERT: D 155 LYS cc_start: 0.8145 (mttt) cc_final: 0.7658 (mtmm) REVERT: D 168 PHE cc_start: 0.8474 (m-80) cc_final: 0.7951 (m-80) REVERT: D 172 PHE cc_start: 0.8859 (m-80) cc_final: 0.8188 (m-80) REVERT: D 185 MET cc_start: 0.6491 (mmm) cc_final: 0.6249 (mmm) REVERT: D 242 TYR cc_start: 0.8809 (t80) cc_final: 0.8562 (t80) REVERT: D 254 HIS cc_start: 0.8944 (m90) cc_final: 0.8709 (m-70) REVERT: D 268 LEU cc_start: 0.8905 (mm) cc_final: 0.8683 (mt) outliers start: 71 outliers final: 39 residues processed: 779 average time/residue: 0.1315 time to fit residues: 152.1916 Evaluate side-chains 735 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 692 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 282 ILE Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 185 optimal weight: 10.0000 chunk 191 optimal weight: 0.2980 chunk 159 optimal weight: 9.9990 chunk 182 optimal weight: 8.9990 chunk 93 optimal weight: 1.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN A 239 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN B 158 ASN B 232 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 ASN C 127 GLN C 132 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.113060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.084409 restraints weight = 42051.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.087450 restraints weight = 21701.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.089555 restraints weight = 13789.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.091108 restraints weight = 9726.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.092247 restraints weight = 7419.170| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.6403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16386 Z= 0.220 Angle : 0.746 12.152 22134 Z= 0.384 Chirality : 0.048 0.220 2360 Planarity : 0.004 0.061 2818 Dihedral : 11.004 163.631 2248 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 5.36 % Allowed : 25.23 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.01 (0.19), residues: 1932 helix: 1.13 (0.15), residues: 1104 sheet: 0.20 (0.44), residues: 118 loop : 0.20 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 243 TYR 0.026 0.002 TYR D 142 PHE 0.036 0.002 PHE C 172 TRP 0.010 0.002 TRP C 44 HIS 0.012 0.002 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00480 (16386) covalent geometry : angle 0.74624 (22134) hydrogen bonds : bond 0.04468 ( 871) hydrogen bonds : angle 5.32143 ( 2571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 719 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9168 (tp) cc_final: 0.8950 (mp) REVERT: A 82 LYS cc_start: 0.9517 (mttm) cc_final: 0.9233 (mmtt) REVERT: A 107 LYS cc_start: 0.8734 (OUTLIER) cc_final: 0.8534 (mmmm) REVERT: A 150 GLN cc_start: 0.9490 (tp40) cc_final: 0.8615 (tm-30) REVERT: A 161 ARG cc_start: 0.8508 (ttm110) cc_final: 0.7860 (ptp-170) REVERT: A 172 LEU cc_start: 0.9446 (mp) cc_final: 0.9236 (mp) REVERT: A 174 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7696 (mt-10) REVERT: A 191 GLN cc_start: 0.8336 (mm-40) cc_final: 0.8109 (mm-40) REVERT: A 250 TYR cc_start: 0.8856 (m-80) cc_final: 0.8637 (m-80) REVERT: A 255 HIS cc_start: 0.8751 (t-90) cc_final: 0.8315 (t-90) REVERT: A 266 LYS cc_start: 0.9083 (ptpp) cc_final: 0.8789 (ptmm) REVERT: A 325 LYS cc_start: 0.9661 (mmmt) cc_final: 0.9375 (mmtp) REVERT: A 375 LYS cc_start: 0.8701 (mmtp) cc_final: 0.8106 (mmtm) REVERT: A 447 ASN cc_start: 0.8087 (m-40) cc_final: 0.7334 (t0) REVERT: A 456 LYS cc_start: 0.9359 (OUTLIER) cc_final: 0.8983 (mtmm) REVERT: A 471 TYR cc_start: 0.9187 (t80) cc_final: 0.8743 (t80) REVERT: A 493 MET cc_start: 0.8995 (tmm) cc_final: 0.8641 (tmm) REVERT: A 546 LEU cc_start: 0.9711 (mt) cc_final: 0.9458 (mt) REVERT: A 590 SER cc_start: 0.9554 (t) cc_final: 0.9176 (p) REVERT: A 595 MET cc_start: 0.9223 (mmp) cc_final: 0.8879 (mmp) REVERT: A 600 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.8238 (mtt-85) REVERT: A 639 ASP cc_start: 0.8693 (m-30) cc_final: 0.8318 (m-30) REVERT: A 640 MET cc_start: 0.9331 (tpp) cc_final: 0.8947 (tpp) REVERT: A 645 GLN cc_start: 0.9070 (tp40) cc_final: 0.8784 (tp40) REVERT: A 650 GLN cc_start: 0.8947 (mt0) cc_final: 0.8501 (mt0) REVERT: A 669 ARG cc_start: 0.9267 (tpp-160) cc_final: 0.8920 (tpp80) REVERT: B 8 LYS cc_start: 0.9206 (tptm) cc_final: 0.8901 (tptm) REVERT: B 18 ILE cc_start: 0.9641 (mp) cc_final: 0.9293 (pt) REVERT: B 54 LYS cc_start: 0.9623 (tttt) cc_final: 0.9230 (tttp) REVERT: B 82 LYS cc_start: 0.9568 (mtpp) cc_final: 0.9202 (ptpp) REVERT: B 95 MET cc_start: 0.9072 (tpt) cc_final: 0.8548 (tpp) REVERT: B 99 LYS cc_start: 0.9407 (tptp) cc_final: 0.8841 (tptp) REVERT: B 102 ASN cc_start: 0.9460 (m110) cc_final: 0.9176 (m110) REVERT: B 184 ARG cc_start: 0.9509 (tpp80) cc_final: 0.9285 (tpp80) REVERT: B 232 ASN cc_start: 0.9341 (OUTLIER) cc_final: 0.8547 (m110) REVERT: B 235 ARG cc_start: 0.9008 (mtm180) cc_final: 0.8657 (mtm-85) REVERT: B 256 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8573 (tpt90) REVERT: B 257 ASP cc_start: 0.8809 (m-30) cc_final: 0.8487 (m-30) REVERT: B 266 LYS cc_start: 0.9135 (mtpp) cc_final: 0.8591 (ptpp) REVERT: B 274 ARG cc_start: 0.8606 (ttm110) cc_final: 0.8304 (ttm170) REVERT: B 322 MET cc_start: 0.9208 (mmm) cc_final: 0.8961 (mmt) REVERT: B 333 LYS cc_start: 0.9059 (tttm) cc_final: 0.8737 (tttm) REVERT: B 341 LYS cc_start: 0.9611 (mmtm) cc_final: 0.9294 (mmmt) REVERT: B 344 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8573 (pt0) REVERT: B 348 MET cc_start: 0.8711 (tmm) cc_final: 0.8275 (tpt) REVERT: B 362 ASP cc_start: 0.8590 (m-30) cc_final: 0.8206 (m-30) REVERT: B 393 SER cc_start: 0.9390 (m) cc_final: 0.8882 (p) REVERT: B 396 ASP cc_start: 0.8976 (p0) cc_final: 0.8575 (p0) REVERT: B 399 GLU cc_start: 0.8981 (tp30) cc_final: 0.8644 (mm-30) REVERT: B 402 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7724 (tm-30) REVERT: B 471 TYR cc_start: 0.9314 (t80) cc_final: 0.8563 (t80) REVERT: B 475 ASN cc_start: 0.9196 (m-40) cc_final: 0.8683 (m110) REVERT: B 483 GLU cc_start: 0.9440 (mp0) cc_final: 0.9144 (mp0) REVERT: B 515 ASP cc_start: 0.9158 (m-30) cc_final: 0.8693 (m-30) REVERT: B 546 LEU cc_start: 0.9570 (mt) cc_final: 0.9318 (mm) REVERT: B 548 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7662 (mm-30) REVERT: B 558 TRP cc_start: 0.9492 (m100) cc_final: 0.8710 (m100) REVERT: B 570 MET cc_start: 0.7000 (mtm) cc_final: 0.5556 (mtm) REVERT: B 583 SER cc_start: 0.9095 (m) cc_final: 0.8480 (p) REVERT: B 632 MET cc_start: 0.8331 (mtm) cc_final: 0.7672 (mtt) REVERT: B 645 GLN cc_start: 0.9389 (tp40) cc_final: 0.8892 (tp-100) REVERT: B 668 ASN cc_start: 0.9089 (m110) cc_final: 0.8687 (m-40) REVERT: B 686 ARG cc_start: 0.8366 (ttm170) cc_final: 0.8061 (mpt-90) REVERT: C 17 PHE cc_start: 0.8362 (p90) cc_final: 0.7533 (p90) REVERT: C 20 MET cc_start: 0.9467 (tmm) cc_final: 0.9196 (tmm) REVERT: C 21 PHE cc_start: 0.9433 (m-80) cc_final: 0.8276 (m-80) REVERT: C 55 TYR cc_start: 0.8616 (OUTLIER) cc_final: 0.7765 (m-10) REVERT: C 74 MET cc_start: 0.8792 (mtt) cc_final: 0.8511 (pmm) REVERT: C 92 PHE cc_start: 0.9559 (t80) cc_final: 0.8830 (t80) REVERT: C 96 MET cc_start: 0.9037 (mmm) cc_final: 0.8349 (mmm) REVERT: C 109 PHE cc_start: 0.8381 (m-10) cc_final: 0.8102 (m-10) REVERT: C 134 LYS cc_start: 0.9561 (pttm) cc_final: 0.9334 (pttm) REVERT: C 155 LYS cc_start: 0.9159 (mttt) cc_final: 0.8905 (mttm) REVERT: C 174 TYR cc_start: 0.8225 (OUTLIER) cc_final: 0.7322 (t80) REVERT: C 198 GLU cc_start: 0.9415 (mm-30) cc_final: 0.8828 (mm-30) REVERT: C 242 TYR cc_start: 0.9417 (t80) cc_final: 0.8730 (t80) REVERT: C 259 PHE cc_start: 0.9074 (t80) cc_final: 0.8794 (t80) REVERT: C 269 MET cc_start: 0.9646 (ptt) cc_final: 0.9263 (mmt) REVERT: C 274 ASP cc_start: 0.8479 (p0) cc_final: 0.7911 (p0) REVERT: C 314 PRO cc_start: 0.9251 (Cg_exo) cc_final: 0.8660 (Cg_endo) REVERT: D 30 TRP cc_start: 0.8389 (p-90) cc_final: 0.7558 (p-90) REVERT: D 46 TYR cc_start: 0.9241 (m-10) cc_final: 0.8768 (m-10) REVERT: D 96 MET cc_start: 0.8234 (mmm) cc_final: 0.7665 (mmm) REVERT: D 131 LEU cc_start: 0.8904 (tt) cc_final: 0.8596 (tp) REVERT: D 155 LYS cc_start: 0.8229 (mttt) cc_final: 0.7783 (mtmm) REVERT: D 168 PHE cc_start: 0.8611 (m-80) cc_final: 0.7595 (m-80) REVERT: D 169 TYR cc_start: 0.8416 (m-80) cc_final: 0.7335 (m-80) REVERT: D 174 TYR cc_start: 0.8917 (t80) cc_final: 0.8584 (t80) REVERT: D 242 TYR cc_start: 0.8853 (t80) cc_final: 0.8487 (t80) REVERT: D 268 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8605 (mp) outliers start: 92 outliers final: 56 residues processed: 755 average time/residue: 0.1296 time to fit residues: 145.4873 Evaluate side-chains 724 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 660 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 2.9990 chunk 46 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 126 optimal weight: 0.7980 chunk 129 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 122 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 168 optimal weight: 9.9990 chunk 157 optimal weight: 8.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 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 = 0.3507 r_free = 0.3507 target = 0.113801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.085634 restraints weight = 41400.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.088633 restraints weight = 21193.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.090800 restraints weight = 13502.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.092285 restraints weight = 9489.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.093384 restraints weight = 7227.343| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3124 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3124 r_free = 0.3124 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3124 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.6713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16386 Z= 0.173 Angle : 0.753 13.563 22134 Z= 0.381 Chirality : 0.047 0.259 2360 Planarity : 0.004 0.039 2818 Dihedral : 10.608 157.802 2246 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 19.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.55 % Allowed : 28.55 % Favored : 66.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.92 (0.19), residues: 1932 helix: 1.04 (0.15), residues: 1114 sheet: 0.08 (0.45), residues: 118 loop : 0.19 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 225 TYR 0.025 0.002 TYR B 522 PHE 0.039 0.002 PHE C 168 TRP 0.006 0.001 TRP D 124 HIS 0.013 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00391 (16386) covalent geometry : angle 0.75349 (22134) hydrogen bonds : bond 0.04344 ( 871) hydrogen bonds : angle 5.25695 ( 2571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 775 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 697 time to evaluate : 0.620 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: A 51 LEU cc_start: 0.9229 (tp) cc_final: 0.9017 (mp) REVERT: A 65 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8258 (mm-30) REVERT: A 82 LYS cc_start: 0.9529 (mttm) cc_final: 0.9220 (mmtt) REVERT: A 150 GLN cc_start: 0.9467 (tp40) cc_final: 0.8493 (tm-30) REVERT: A 161 ARG cc_start: 0.8640 (ttm110) cc_final: 0.7920 (ptp-170) REVERT: A 172 LEU cc_start: 0.9398 (mp) cc_final: 0.9174 (mp) REVERT: A 191 GLN cc_start: 0.8294 (mm-40) cc_final: 0.8071 (mm-40) REVERT: A 205 LYS cc_start: 0.8741 (mttp) cc_final: 0.8526 (mmtp) REVERT: A 221 LYS cc_start: 0.8763 (mttp) cc_final: 0.8467 (mttm) REVERT: A 250 TYR cc_start: 0.8785 (m-80) cc_final: 0.8573 (m-80) REVERT: A 255 HIS cc_start: 0.8896 (t-90) cc_final: 0.8379 (t-90) REVERT: A 325 LYS cc_start: 0.9647 (mmmt) cc_final: 0.9389 (mmtp) REVERT: A 375 LYS cc_start: 0.8710 (mmtp) cc_final: 0.8046 (mmtm) REVERT: A 389 SER cc_start: 0.9079 (OUTLIER) cc_final: 0.8865 (p) REVERT: A 413 SER cc_start: 0.9450 (m) cc_final: 0.9079 (t) REVERT: A 447 ASN cc_start: 0.8160 (m-40) cc_final: 0.7406 (t0) REVERT: A 456 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9013 (mtmm) REVERT: A 471 TYR cc_start: 0.9102 (t80) cc_final: 0.8684 (t80) REVERT: A 493 MET cc_start: 0.8903 (tmm) cc_final: 0.8554 (tmm) REVERT: A 546 LEU cc_start: 0.9726 (mt) cc_final: 0.9477 (mt) REVERT: A 590 SER cc_start: 0.9511 (t) cc_final: 0.9058 (p) REVERT: A 600 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8196 (mtt-85) REVERT: A 639 ASP cc_start: 0.8660 (m-30) cc_final: 0.8249 (m-30) REVERT: A 645 GLN cc_start: 0.9061 (tp40) cc_final: 0.8809 (tp40) REVERT: A 669 ARG cc_start: 0.9264 (tpp-160) cc_final: 0.8915 (tpp80) REVERT: B 82 LYS cc_start: 0.9572 (mtpp) cc_final: 0.9117 (ptpp) REVERT: B 95 MET cc_start: 0.9078 (tpt) cc_final: 0.8528 (tpp) REVERT: B 99 LYS cc_start: 0.9354 (tptp) cc_final: 0.8773 (tptp) REVERT: B 102 ASN cc_start: 0.9477 (m110) cc_final: 0.9188 (m110) REVERT: B 161 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8868 (mtt-85) REVERT: B 168 VAL cc_start: 0.9378 (t) cc_final: 0.9150 (m) REVERT: B 181 ASP cc_start: 0.8815 (m-30) cc_final: 0.8479 (m-30) REVERT: B 232 ASN cc_start: 0.9309 (OUTLIER) cc_final: 0.8778 (m110) REVERT: B 235 ARG cc_start: 0.9185 (mtm180) cc_final: 0.8804 (mtm-85) REVERT: B 256 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8632 (tpt90) REVERT: B 257 ASP cc_start: 0.8891 (m-30) cc_final: 0.8561 (m-30) REVERT: B 266 LYS cc_start: 0.9169 (mtpp) cc_final: 0.8507 (ptpp) REVERT: B 274 ARG cc_start: 0.8642 (ttm110) cc_final: 0.8317 (ttm170) REVERT: B 306 ILE cc_start: 0.9447 (mt) cc_final: 0.9205 (mm) REVERT: B 322 MET cc_start: 0.9296 (mmm) cc_final: 0.8988 (mmt) REVERT: B 333 LYS cc_start: 0.9064 (tttm) cc_final: 0.8775 (tttm) REVERT: B 341 LYS cc_start: 0.9613 (mmtm) cc_final: 0.9250 (mmmt) REVERT: B 344 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8608 (pt0) REVERT: B 348 MET cc_start: 0.8781 (tmm) cc_final: 0.8431 (tpt) REVERT: B 362 ASP cc_start: 0.8687 (m-30) cc_final: 0.8261 (m-30) REVERT: B 393 SER cc_start: 0.9346 (m) cc_final: 0.8819 (p) REVERT: B 399 GLU cc_start: 0.9062 (OUTLIER) cc_final: 0.8788 (mm-30) REVERT: B 402 GLU cc_start: 0.8424 (tm-30) cc_final: 0.7764 (tm-30) REVERT: B 471 TYR cc_start: 0.9289 (t80) cc_final: 0.8447 (t80) REVERT: B 475 ASN cc_start: 0.9228 (m-40) cc_final: 0.8673 (m-40) REVERT: B 483 GLU cc_start: 0.9451 (mp0) cc_final: 0.9160 (mp0) REVERT: B 515 ASP cc_start: 0.9193 (m-30) cc_final: 0.8685 (m-30) REVERT: B 548 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7695 (mm-30) REVERT: B 550 MET cc_start: 0.8125 (mtp) cc_final: 0.7793 (mtp) REVERT: B 558 TRP cc_start: 0.9515 (m100) cc_final: 0.8689 (m100) REVERT: B 561 LEU cc_start: 0.9733 (tp) cc_final: 0.9517 (tt) REVERT: B 602 GLU cc_start: 0.8697 (pt0) cc_final: 0.8112 (pt0) REVERT: B 604 ARG cc_start: 0.8558 (mmt-90) cc_final: 0.8160 (mmt-90) REVERT: B 645 GLN cc_start: 0.9408 (tp40) cc_final: 0.8947 (tp40) REVERT: B 650 GLN cc_start: 0.8323 (mt0) cc_final: 0.8056 (mt0) REVERT: B 668 ASN cc_start: 0.9087 (m110) cc_final: 0.8638 (m-40) REVERT: B 683 TYR cc_start: 0.8943 (t80) cc_final: 0.8487 (t80) REVERT: B 686 ARG cc_start: 0.8315 (ttm170) cc_final: 0.7924 (mtm-85) REVERT: C 20 MET cc_start: 0.9524 (tmm) cc_final: 0.9204 (tmm) REVERT: C 21 PHE cc_start: 0.9496 (m-80) cc_final: 0.8817 (m-80) REVERT: C 55 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.7885 (m-80) REVERT: C 74 MET cc_start: 0.8709 (mtt) cc_final: 0.8441 (mtt) REVERT: C 92 PHE cc_start: 0.9552 (t80) cc_final: 0.8918 (t80) REVERT: C 96 MET cc_start: 0.9085 (mmm) cc_final: 0.8508 (mmm) REVERT: C 109 PHE cc_start: 0.8296 (m-10) cc_final: 0.7854 (m-10) REVERT: C 143 LYS cc_start: 0.8828 (tptt) cc_final: 0.8598 (tppt) REVERT: C 155 LYS cc_start: 0.9209 (mttt) cc_final: 0.8991 (mttm) REVERT: C 174 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.7603 (t80) REVERT: C 178 PHE cc_start: 0.9092 (OUTLIER) cc_final: 0.8827 (t80) REVERT: C 218 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8767 (pm20) REVERT: C 242 TYR cc_start: 0.9440 (t80) cc_final: 0.9080 (t80) REVERT: C 259 PHE cc_start: 0.9142 (t80) cc_final: 0.8471 (t80) REVERT: C 260 ILE cc_start: 0.9011 (pt) cc_final: 0.8789 (pp) REVERT: C 269 MET cc_start: 0.9558 (OUTLIER) cc_final: 0.9223 (mmt) REVERT: C 274 ASP cc_start: 0.8543 (p0) cc_final: 0.8039 (p0) REVERT: C 314 PRO cc_start: 0.9211 (Cg_exo) cc_final: 0.8615 (Cg_endo) REVERT: D 30 TRP cc_start: 0.8285 (p-90) cc_final: 0.7452 (p-90) REVERT: D 46 TYR cc_start: 0.9269 (m-10) cc_final: 0.8786 (m-10) REVERT: D 71 ASN cc_start: 0.9417 (m110) cc_final: 0.9199 (m110) REVERT: D 96 MET cc_start: 0.8215 (mmm) cc_final: 0.7759 (mmm) REVERT: D 131 LEU cc_start: 0.8964 (tt) cc_final: 0.8681 (tp) REVERT: D 168 PHE cc_start: 0.8664 (m-80) cc_final: 0.7598 (m-80) REVERT: D 169 TYR cc_start: 0.8307 (m-80) cc_final: 0.7643 (m-80) REVERT: D 174 TYR cc_start: 0.8939 (t80) cc_final: 0.8560 (t80) REVERT: D 242 TYR cc_start: 0.8986 (t80) cc_final: 0.8602 (t80) REVERT: D 268 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8538 (mt) outliers start: 78 outliers final: 48 residues processed: 730 average time/residue: 0.1328 time to fit residues: 143.8274 Evaluate side-chains 709 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 649 time to evaluate : 0.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 182 ILE Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 494 MET Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 0.0980 chunk 183 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 27 optimal weight: 0.0170 chunk 136 optimal weight: 2.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 107 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.117669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.088526 restraints weight = 40982.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.091776 restraints weight = 21358.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.093860 restraints weight = 13492.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.095475 restraints weight = 9776.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.096617 restraints weight = 7495.249| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.7057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16386 Z= 0.142 Angle : 0.767 15.550 22134 Z= 0.382 Chirality : 0.047 0.271 2360 Planarity : 0.004 0.041 2818 Dihedral : 10.132 144.499 2246 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.31 % Allowed : 29.95 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.84 (0.19), residues: 1932 helix: 1.08 (0.15), residues: 1104 sheet: -0.68 (0.40), residues: 152 loop : 0.19 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 243 TYR 0.020 0.001 TYR D 55 PHE 0.040 0.002 PHE C 168 TRP 0.008 0.001 TRP D 124 HIS 0.011 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00320 (16386) covalent geometry : angle 0.76671 (22134) hydrogen bonds : bond 0.04242 ( 871) hydrogen bonds : angle 5.19700 ( 2571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 726 time to evaluate : 0.671 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: A 65 GLU cc_start: 0.8514 (mm-30) cc_final: 0.8173 (mm-30) REVERT: A 82 LYS cc_start: 0.9502 (mttm) cc_final: 0.9211 (mmtt) REVERT: A 161 ARG cc_start: 0.8536 (ttm110) cc_final: 0.7784 (ptp-170) REVERT: A 221 LYS cc_start: 0.8893 (mttp) cc_final: 0.8604 (mttm) REVERT: A 266 LYS cc_start: 0.8875 (ptmm) cc_final: 0.8398 (ptmm) REVERT: A 290 GLU cc_start: 0.9089 (tm-30) cc_final: 0.8681 (tm-30) REVERT: A 325 LYS cc_start: 0.9629 (mmmt) cc_final: 0.9410 (mmtp) REVERT: A 389 SER cc_start: 0.9061 (OUTLIER) cc_final: 0.8851 (p) REVERT: A 413 SER cc_start: 0.9449 (m) cc_final: 0.8993 (t) REVERT: A 443 THR cc_start: 0.8753 (t) cc_final: 0.8470 (t) REVERT: A 447 ASN cc_start: 0.8194 (m-40) cc_final: 0.7461 (t0) REVERT: A 456 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.8982 (mtmm) REVERT: A 471 TYR cc_start: 0.9021 (t80) cc_final: 0.8657 (t80) REVERT: A 493 MET cc_start: 0.8865 (tmm) cc_final: 0.8518 (tmm) REVERT: A 494 MET cc_start: 0.9177 (mtp) cc_final: 0.8604 (mtp) REVERT: A 546 LEU cc_start: 0.9674 (mt) cc_final: 0.9460 (mt) REVERT: A 590 SER cc_start: 0.9477 (t) cc_final: 0.8937 (p) REVERT: A 595 MET cc_start: 0.9141 (mmm) cc_final: 0.8495 (mmm) REVERT: A 600 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7790 (mtt-85) REVERT: A 606 TYR cc_start: 0.8122 (m-80) cc_final: 0.7908 (m-80) REVERT: A 639 ASP cc_start: 0.8574 (m-30) cc_final: 0.8109 (m-30) REVERT: A 640 MET cc_start: 0.9464 (tpp) cc_final: 0.9139 (tpp) REVERT: A 645 GLN cc_start: 0.8992 (tp40) cc_final: 0.8508 (tp-100) REVERT: A 669 ARG cc_start: 0.9246 (tpp-160) cc_final: 0.8887 (tpp80) REVERT: B 82 LYS cc_start: 0.9562 (mtpp) cc_final: 0.9149 (ptpp) REVERT: B 95 MET cc_start: 0.9020 (tpt) cc_final: 0.8453 (tpp) REVERT: B 99 LYS cc_start: 0.9334 (tptp) cc_final: 0.8810 (tptp) REVERT: B 102 ASN cc_start: 0.9496 (m110) cc_final: 0.9278 (m110) REVERT: B 181 ASP cc_start: 0.8745 (m-30) cc_final: 0.8433 (m-30) REVERT: B 232 ASN cc_start: 0.9249 (OUTLIER) cc_final: 0.8640 (m110) REVERT: B 235 ARG cc_start: 0.9175 (mtm180) cc_final: 0.8687 (mtm-85) REVERT: B 263 ASP cc_start: 0.9082 (m-30) cc_final: 0.8650 (p0) REVERT: B 266 LYS cc_start: 0.9117 (mtpp) cc_final: 0.8609 (ptpp) REVERT: B 274 ARG cc_start: 0.8667 (ttm110) cc_final: 0.8377 (ttm170) REVERT: B 306 ILE cc_start: 0.9460 (mt) cc_final: 0.9227 (mm) REVERT: B 322 MET cc_start: 0.9302 (mmm) cc_final: 0.8980 (mmt) REVERT: B 333 LYS cc_start: 0.9093 (tttm) cc_final: 0.8791 (tttm) REVERT: B 341 LYS cc_start: 0.9622 (mmtm) cc_final: 0.9250 (mmmt) REVERT: B 344 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8557 (pt0) REVERT: B 348 MET cc_start: 0.8744 (tmm) cc_final: 0.8419 (tpt) REVERT: B 362 ASP cc_start: 0.8705 (m-30) cc_final: 0.8295 (m-30) REVERT: B 375 LYS cc_start: 0.9189 (mmmm) cc_final: 0.8628 (mmmm) REVERT: B 393 SER cc_start: 0.9379 (m) cc_final: 0.8865 (p) REVERT: B 399 GLU cc_start: 0.9065 (OUTLIER) cc_final: 0.8703 (mp0) REVERT: B 402 GLU cc_start: 0.8446 (tm-30) cc_final: 0.7689 (tm-30) REVERT: B 447 ASN cc_start: 0.8705 (m-40) cc_final: 0.8033 (m-40) REVERT: B 471 TYR cc_start: 0.9174 (t80) cc_final: 0.8629 (t80) REVERT: B 475 ASN cc_start: 0.9197 (m-40) cc_final: 0.8691 (m110) REVERT: B 483 GLU cc_start: 0.9441 (mp0) cc_final: 0.9180 (mp0) REVERT: B 500 ILE cc_start: 0.9803 (tp) cc_final: 0.9535 (tp) REVERT: B 515 ASP cc_start: 0.9103 (m-30) cc_final: 0.8638 (m-30) REVERT: B 546 LEU cc_start: 0.9578 (mt) cc_final: 0.9346 (mm) REVERT: B 548 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7653 (mm-30) REVERT: B 558 TRP cc_start: 0.9474 (m100) cc_final: 0.8728 (m100) REVERT: B 602 GLU cc_start: 0.8606 (pt0) cc_final: 0.8232 (pt0) REVERT: B 645 GLN cc_start: 0.9395 (tp40) cc_final: 0.8989 (tp-100) REVERT: B 650 GLN cc_start: 0.8549 (mt0) cc_final: 0.8319 (mt0) REVERT: B 668 ASN cc_start: 0.9045 (m110) cc_final: 0.8495 (m110) REVERT: B 683 TYR cc_start: 0.8824 (t80) cc_final: 0.8265 (t80) REVERT: B 686 ARG cc_start: 0.8310 (ttm170) cc_final: 0.7872 (mtm-85) REVERT: C 20 MET cc_start: 0.9508 (tmm) cc_final: 0.9212 (ppp) REVERT: C 21 PHE cc_start: 0.9471 (m-80) cc_final: 0.8652 (m-80) REVERT: C 55 TYR cc_start: 0.8746 (t80) cc_final: 0.8002 (m-80) REVERT: C 74 MET cc_start: 0.8771 (mtt) cc_final: 0.8556 (mtt) REVERT: C 85 GLN cc_start: 0.8164 (mt0) cc_final: 0.7604 (mm-40) REVERT: C 92 PHE cc_start: 0.9598 (t80) cc_final: 0.9056 (t80) REVERT: C 96 MET cc_start: 0.9073 (mmm) cc_final: 0.8491 (mmm) REVERT: C 143 LYS cc_start: 0.8740 (tptt) cc_final: 0.8515 (tppt) REVERT: C 174 TYR cc_start: 0.8029 (OUTLIER) cc_final: 0.7671 (t80) REVERT: C 178 PHE cc_start: 0.9091 (OUTLIER) cc_final: 0.8860 (t80) REVERT: C 194 ILE cc_start: 0.9633 (mt) cc_final: 0.9310 (tp) REVERT: C 218 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8793 (pm20) REVERT: C 242 TYR cc_start: 0.9444 (t80) cc_final: 0.9053 (t80) REVERT: C 246 LEU cc_start: 0.9137 (tp) cc_final: 0.8913 (mm) REVERT: C 259 PHE cc_start: 0.9247 (t80) cc_final: 0.8585 (t80) REVERT: C 260 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8635 (pp) REVERT: C 269 MET cc_start: 0.9480 (ptt) cc_final: 0.9192 (mmt) REVERT: C 274 ASP cc_start: 0.8418 (p0) cc_final: 0.7942 (p0) REVERT: C 314 PRO cc_start: 0.9257 (Cg_exo) cc_final: 0.8669 (Cg_endo) REVERT: D 25 ASN cc_start: 0.9441 (t0) cc_final: 0.9043 (t0) REVERT: D 30 TRP cc_start: 0.8024 (p-90) cc_final: 0.7241 (p-90) REVERT: D 46 TYR cc_start: 0.9269 (m-80) cc_final: 0.8799 (m-10) REVERT: D 51 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7671 (mm-30) REVERT: D 71 ASN cc_start: 0.9437 (m110) cc_final: 0.9223 (m110) REVERT: D 96 MET cc_start: 0.8161 (mmm) cc_final: 0.7713 (mmm) REVERT: D 131 LEU cc_start: 0.8951 (tt) cc_final: 0.8676 (tp) REVERT: D 168 PHE cc_start: 0.8640 (m-80) cc_final: 0.7674 (m-80) REVERT: D 169 TYR cc_start: 0.8110 (m-80) cc_final: 0.7638 (m-80) REVERT: D 174 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.8399 (t80) REVERT: D 242 TYR cc_start: 0.8984 (t80) cc_final: 0.8647 (t80) outliers start: 74 outliers final: 44 residues processed: 752 average time/residue: 0.1335 time to fit residues: 149.4678 Evaluate side-chains 711 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 658 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 441 GLU Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 21 PHE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 186 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN C 201 HIS ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 210 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.117547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.088732 restraints weight = 40745.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.091985 restraints weight = 21412.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.093912 restraints weight = 13618.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.095517 restraints weight = 9997.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.096701 restraints weight = 7691.667| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.7345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16386 Z= 0.151 Angle : 0.793 16.365 22134 Z= 0.393 Chirality : 0.048 0.265 2360 Planarity : 0.004 0.050 2818 Dihedral : 10.006 135.878 2246 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.31 % Allowed : 31.59 % Favored : 64.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.19), residues: 1932 helix: 1.05 (0.15), residues: 1103 sheet: -0.92 (0.38), residues: 162 loop : 0.19 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 235 TYR 0.027 0.001 TYR D 55 PHE 0.043 0.002 PHE C 172 TRP 0.008 0.001 TRP D 124 HIS 0.019 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00348 (16386) covalent geometry : angle 0.79349 (22134) hydrogen bonds : bond 0.04236 ( 871) hydrogen bonds : angle 5.21137 ( 2571) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 707 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.8980 (m-30) cc_final: 0.8717 (m-30) REVERT: A 82 LYS cc_start: 0.9512 (mttm) cc_final: 0.9304 (mmtt) REVERT: A 95 MET cc_start: 0.9042 (mmm) cc_final: 0.8596 (tpp) REVERT: A 150 GLN cc_start: 0.9432 (tp40) cc_final: 0.8991 (tp40) REVERT: A 161 ARG cc_start: 0.8521 (ttm110) cc_final: 0.7866 (ptp-170) REVERT: A 171 PHE cc_start: 0.9524 (m-80) cc_final: 0.9263 (m-10) REVERT: A 221 LYS cc_start: 0.8864 (mttp) cc_final: 0.8601 (mttm) REVERT: A 255 HIS cc_start: 0.8800 (t-90) cc_final: 0.8435 (t-90) REVERT: A 266 LYS cc_start: 0.8777 (ptmm) cc_final: 0.8258 (ptmm) REVERT: A 290 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8708 (tm-30) REVERT: A 295 ASP cc_start: 0.9274 (t0) cc_final: 0.8909 (t0) REVERT: A 325 LYS cc_start: 0.9622 (mmmt) cc_final: 0.9412 (mmtp) REVERT: A 390 GLN cc_start: 0.8912 (mt0) cc_final: 0.8667 (mt0) REVERT: A 396 ASP cc_start: 0.8627 (p0) cc_final: 0.8388 (p0) REVERT: A 413 SER cc_start: 0.9482 (m) cc_final: 0.9017 (t) REVERT: A 456 LYS cc_start: 0.9346 (OUTLIER) cc_final: 0.8873 (mtmm) REVERT: A 471 TYR cc_start: 0.9089 (t80) cc_final: 0.8749 (t80) REVERT: A 493 MET cc_start: 0.8829 (tmm) cc_final: 0.8484 (tmm) REVERT: A 516 GLN cc_start: 0.9294 (mt0) cc_final: 0.8880 (mp10) REVERT: A 546 LEU cc_start: 0.9637 (mt) cc_final: 0.9412 (mt) REVERT: A 595 MET cc_start: 0.9116 (mmm) cc_final: 0.8579 (mmm) REVERT: A 599 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8141 (mm-30) REVERT: A 600 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7989 (mtt-85) REVERT: A 606 TYR cc_start: 0.8241 (m-80) cc_final: 0.7988 (m-80) REVERT: A 639 ASP cc_start: 0.8569 (m-30) cc_final: 0.8103 (m-30) REVERT: A 640 MET cc_start: 0.9492 (tpp) cc_final: 0.8998 (tpp) REVERT: A 645 GLN cc_start: 0.8999 (tp40) cc_final: 0.8507 (tp-100) REVERT: B 8 LYS cc_start: 0.9250 (tptm) cc_final: 0.9038 (tptm) REVERT: B 79 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8748 (mm-30) REVERT: B 82 LYS cc_start: 0.9551 (mtpp) cc_final: 0.9187 (ptpp) REVERT: B 95 MET cc_start: 0.9025 (tpt) cc_final: 0.8519 (tpp) REVERT: B 99 LYS cc_start: 0.9329 (tptp) cc_final: 0.8874 (tptp) REVERT: B 102 ASN cc_start: 0.9507 (m110) cc_final: 0.9281 (m110) REVERT: B 112 LYS cc_start: 0.9221 (pptt) cc_final: 0.9011 (pttm) REVERT: B 119 GLU cc_start: 0.9039 (mp0) cc_final: 0.8478 (mp0) REVERT: B 181 ASP cc_start: 0.8707 (m-30) cc_final: 0.8338 (m-30) REVERT: B 232 ASN cc_start: 0.9264 (m110) cc_final: 0.8607 (m110) REVERT: B 235 ARG cc_start: 0.9180 (mtm180) cc_final: 0.8659 (mtm-85) REVERT: B 236 TYR cc_start: 0.9278 (t80) cc_final: 0.8381 (t80) REVERT: B 250 TYR cc_start: 0.8805 (m-10) cc_final: 0.8398 (m-10) REVERT: B 256 ARG cc_start: 0.8967 (OUTLIER) cc_final: 0.8502 (ttp80) REVERT: B 266 LYS cc_start: 0.9157 (mtpp) cc_final: 0.8614 (ptpp) REVERT: B 274 ARG cc_start: 0.8669 (ttm110) cc_final: 0.8335 (ttm170) REVERT: B 322 MET cc_start: 0.9312 (mmm) cc_final: 0.8977 (mmt) REVERT: B 333 LYS cc_start: 0.9089 (tttm) cc_final: 0.8864 (ttmm) REVERT: B 341 LYS cc_start: 0.9632 (mmtm) cc_final: 0.9254 (mmmt) REVERT: B 344 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8583 (pt0) REVERT: B 348 MET cc_start: 0.8799 (tmm) cc_final: 0.8399 (tpt) REVERT: B 350 ARG cc_start: 0.8992 (mtp85) cc_final: 0.8423 (mtp85) REVERT: B 362 ASP cc_start: 0.8723 (m-30) cc_final: 0.8134 (m-30) REVERT: B 393 SER cc_start: 0.9326 (m) cc_final: 0.8974 (p) REVERT: B 399 GLU cc_start: 0.9110 (OUTLIER) cc_final: 0.8718 (mp0) REVERT: B 402 GLU cc_start: 0.8548 (tm-30) cc_final: 0.7777 (tm-30) REVERT: B 471 TYR cc_start: 0.9135 (t80) cc_final: 0.8605 (t80) REVERT: B 475 ASN cc_start: 0.9198 (m-40) cc_final: 0.8718 (m110) REVERT: B 483 GLU cc_start: 0.9439 (mp0) cc_final: 0.9205 (mp0) REVERT: B 515 ASP cc_start: 0.9113 (m-30) cc_final: 0.8641 (m-30) REVERT: B 548 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7712 (mm-30) REVERT: B 558 TRP cc_start: 0.9424 (m100) cc_final: 0.8801 (m100) REVERT: B 570 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7772 (mtp) REVERT: B 571 TYR cc_start: 0.8273 (t80) cc_final: 0.8012 (t80) REVERT: B 602 GLU cc_start: 0.8667 (pt0) cc_final: 0.8417 (pt0) REVERT: B 645 GLN cc_start: 0.9401 (tp40) cc_final: 0.8989 (tp-100) REVERT: B 650 GLN cc_start: 0.8497 (mt0) cc_final: 0.8236 (mt0) REVERT: B 668 ASN cc_start: 0.9095 (m110) cc_final: 0.8541 (m110) REVERT: B 686 ARG cc_start: 0.8348 (ttm170) cc_final: 0.8072 (mtt90) REVERT: C 20 MET cc_start: 0.9445 (tmm) cc_final: 0.9107 (ppp) REVERT: C 21 PHE cc_start: 0.9448 (m-80) cc_final: 0.8414 (m-80) REVERT: C 74 MET cc_start: 0.8705 (mtt) cc_final: 0.8472 (mtt) REVERT: C 85 GLN cc_start: 0.8324 (mt0) cc_final: 0.7726 (mm-40) REVERT: C 92 PHE cc_start: 0.9597 (t80) cc_final: 0.9057 (t80) REVERT: C 96 MET cc_start: 0.9026 (mmm) cc_final: 0.8488 (mmm) REVERT: C 110 MET cc_start: 0.7466 (mpp) cc_final: 0.7114 (mtt) REVERT: C 146 GLN cc_start: 0.8396 (tp40) cc_final: 0.8066 (tp40) REVERT: C 174 TYR cc_start: 0.7984 (OUTLIER) cc_final: 0.7680 (t80) REVERT: C 184 LEU cc_start: 0.7073 (mm) cc_final: 0.6373 (tt) REVERT: C 218 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8760 (pm20) REVERT: C 223 GLU cc_start: 0.9299 (tm-30) cc_final: 0.8753 (pt0) REVERT: C 242 TYR cc_start: 0.9494 (t80) cc_final: 0.9249 (t80) REVERT: C 259 PHE cc_start: 0.9349 (t80) cc_final: 0.8740 (t80) REVERT: C 269 MET cc_start: 0.9456 (OUTLIER) cc_final: 0.9215 (mmt) REVERT: C 274 ASP cc_start: 0.8375 (p0) cc_final: 0.7916 (p0) REVERT: C 314 PRO cc_start: 0.9287 (Cg_exo) cc_final: 0.8720 (Cg_endo) REVERT: D 30 TRP cc_start: 0.8139 (p-90) cc_final: 0.7535 (p-90) REVERT: D 46 TYR cc_start: 0.9265 (m-80) cc_final: 0.8780 (m-10) REVERT: D 51 GLU cc_start: 0.7813 (mm-30) cc_final: 0.7534 (mm-30) REVERT: D 96 MET cc_start: 0.8032 (mmm) cc_final: 0.7712 (mmm) REVERT: D 131 LEU cc_start: 0.9000 (tt) cc_final: 0.8774 (tp) REVERT: D 149 ASP cc_start: 0.9231 (m-30) cc_final: 0.8955 (m-30) REVERT: D 168 PHE cc_start: 0.8644 (m-80) cc_final: 0.7647 (m-80) REVERT: D 169 TYR cc_start: 0.8155 (m-80) cc_final: 0.7512 (m-80) REVERT: D 174 TYR cc_start: 0.9003 (OUTLIER) cc_final: 0.8360 (t80) REVERT: D 198 GLU cc_start: 0.8726 (pp20) cc_final: 0.8519 (pp20) REVERT: D 242 TYR cc_start: 0.9022 (t80) cc_final: 0.8677 (t80) outliers start: 74 outliers final: 49 residues processed: 737 average time/residue: 0.1277 time to fit residues: 140.0748 Evaluate side-chains 719 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 662 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 456 LYS Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 21 PHE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 61 optimal weight: 0.0970 chunk 19 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 chunk 153 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 214 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 = 0.3464 r_free = 0.3464 target = 0.107971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.080244 restraints weight = 42391.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.083314 restraints weight = 22117.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.085383 restraints weight = 13944.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.086788 restraints weight = 9803.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.087839 restraints weight = 7518.035| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3078 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.7612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 16386 Z= 0.251 Angle : 0.848 18.436 22134 Z= 0.429 Chirality : 0.050 0.296 2360 Planarity : 0.004 0.047 2818 Dihedral : 10.195 140.907 2246 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 24.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.55 % Allowed : 32.40 % Favored : 63.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.19), residues: 1932 helix: 0.96 (0.15), residues: 1119 sheet: -0.93 (0.39), residues: 152 loop : 0.14 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 164 TYR 0.032 0.002 TYR D 142 PHE 0.030 0.002 PHE B 156 TRP 0.010 0.002 TRP B 623 HIS 0.013 0.002 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00558 (16386) covalent geometry : angle 0.84792 (22134) hydrogen bonds : bond 0.04397 ( 871) hydrogen bonds : angle 5.46222 ( 2571) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 669 time to evaluate : 0.438 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 39 ASP cc_start: 0.9026 (m-30) cc_final: 0.8734 (m-30) REVERT: A 82 LYS cc_start: 0.9533 (mttm) cc_final: 0.9207 (mmmt) REVERT: A 95 MET cc_start: 0.9051 (mmm) cc_final: 0.8765 (tpp) REVERT: A 117 ARG cc_start: 0.8883 (mmm-85) cc_final: 0.8511 (mmt90) REVERT: A 150 GLN cc_start: 0.9516 (tp40) cc_final: 0.8476 (tm-30) REVERT: A 161 ARG cc_start: 0.8681 (ttm110) cc_final: 0.7883 (ptp-170) REVERT: A 174 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7898 (mt-10) REVERT: A 188 ILE cc_start: 0.9533 (mt) cc_final: 0.9297 (mm) REVERT: A 191 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7467 (mt0) REVERT: A 255 HIS cc_start: 0.8726 (t-90) cc_final: 0.8427 (t-90) REVERT: A 266 LYS cc_start: 0.8824 (ptmm) cc_final: 0.8273 (ptmm) REVERT: A 290 GLU cc_start: 0.9210 (tm-30) cc_final: 0.8857 (tm-30) REVERT: A 325 LYS cc_start: 0.9633 (mmmt) cc_final: 0.9431 (mmtp) REVERT: A 366 LYS cc_start: 0.9397 (ptpp) cc_final: 0.9171 (ptpp) REVERT: A 390 GLN cc_start: 0.8935 (mt0) cc_final: 0.8645 (mt0) REVERT: A 396 ASP cc_start: 0.8713 (p0) cc_final: 0.8412 (p0) REVERT: A 413 SER cc_start: 0.9445 (m) cc_final: 0.8983 (t) REVERT: A 447 ASN cc_start: 0.8067 (m-40) cc_final: 0.7414 (t0) REVERT: A 471 TYR cc_start: 0.9219 (t80) cc_final: 0.9001 (t80) REVERT: A 493 MET cc_start: 0.8852 (tmm) cc_final: 0.8372 (tmm) REVERT: A 516 GLN cc_start: 0.9357 (mt0) cc_final: 0.9017 (mp10) REVERT: A 590 SER cc_start: 0.9546 (t) cc_final: 0.8999 (p) REVERT: A 595 MET cc_start: 0.9309 (mmm) cc_final: 0.8956 (mmm) REVERT: A 639 ASP cc_start: 0.8659 (m-30) cc_final: 0.8251 (m-30) REVERT: A 645 GLN cc_start: 0.9119 (tp40) cc_final: 0.8843 (tp40) REVERT: A 659 LYS cc_start: 0.9029 (mmtm) cc_final: 0.8785 (mmtt) REVERT: B 8 LYS cc_start: 0.9302 (tptm) cc_final: 0.9012 (tptm) REVERT: B 75 GLU cc_start: 0.9170 (mp0) cc_final: 0.8898 (pm20) REVERT: B 82 LYS cc_start: 0.9561 (mtpp) cc_final: 0.9234 (mmtt) REVERT: B 95 MET cc_start: 0.9116 (tpt) cc_final: 0.8570 (tpp) REVERT: B 99 LYS cc_start: 0.9326 (tptp) cc_final: 0.8811 (tptp) REVERT: B 102 ASN cc_start: 0.9493 (m110) cc_final: 0.9228 (m110) REVERT: B 107 LYS cc_start: 0.8967 (mmmt) cc_final: 0.8737 (mmmt) REVERT: B 119 GLU cc_start: 0.9149 (mp0) cc_final: 0.8568 (mp0) REVERT: B 181 ASP cc_start: 0.8777 (m-30) cc_final: 0.8445 (m-30) REVERT: B 232 ASN cc_start: 0.9266 (m110) cc_final: 0.8987 (m-40) REVERT: B 235 ARG cc_start: 0.9226 (mtm180) cc_final: 0.8776 (ptp-110) REVERT: B 250 TYR cc_start: 0.8988 (m-10) cc_final: 0.8432 (m-10) REVERT: B 256 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8538 (ttp80) REVERT: B 266 LYS cc_start: 0.9259 (mtpp) cc_final: 0.8697 (ptpp) REVERT: B 274 ARG cc_start: 0.8690 (ttm110) cc_final: 0.8340 (ttm170) REVERT: B 322 MET cc_start: 0.9292 (mmm) cc_final: 0.9083 (mmt) REVERT: B 341 LYS cc_start: 0.9650 (mmtm) cc_final: 0.9265 (mmmt) REVERT: B 344 GLU cc_start: 0.9178 (mt-10) cc_final: 0.8426 (pt0) REVERT: B 348 MET cc_start: 0.8853 (tmm) cc_final: 0.8467 (tpt) REVERT: B 350 ARG cc_start: 0.9101 (mtp85) cc_final: 0.8436 (mtp85) REVERT: B 362 ASP cc_start: 0.8754 (m-30) cc_final: 0.8163 (m-30) REVERT: B 375 LYS cc_start: 0.9235 (mmmm) cc_final: 0.8655 (mmmm) REVERT: B 393 SER cc_start: 0.9292 (m) cc_final: 0.8867 (p) REVERT: B 399 GLU cc_start: 0.9170 (OUTLIER) cc_final: 0.8773 (mm-30) REVERT: B 402 GLU cc_start: 0.8631 (tm-30) cc_final: 0.7866 (tm-30) REVERT: B 475 ASN cc_start: 0.9375 (m-40) cc_final: 0.9110 (m110) REVERT: B 515 ASP cc_start: 0.9177 (m-30) cc_final: 0.8673 (m-30) REVERT: B 539 LYS cc_start: 0.9214 (mmmt) cc_final: 0.8974 (mptt) REVERT: B 548 GLU cc_start: 0.8319 (mm-30) cc_final: 0.7777 (mm-30) REVERT: B 570 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.8070 (tpp) REVERT: B 645 GLN cc_start: 0.9431 (tp40) cc_final: 0.8893 (tp-100) REVERT: B 668 ASN cc_start: 0.9151 (m110) cc_final: 0.8816 (m-40) REVERT: C 17 PHE cc_start: 0.8702 (p90) cc_final: 0.7813 (p90) REVERT: C 20 MET cc_start: 0.9486 (tmm) cc_final: 0.9152 (ppp) REVERT: C 21 PHE cc_start: 0.9493 (m-80) cc_final: 0.8169 (m-80) REVERT: C 85 GLN cc_start: 0.8467 (mt0) cc_final: 0.7891 (mm-40) REVERT: C 92 PHE cc_start: 0.9618 (t80) cc_final: 0.9138 (t80) REVERT: C 96 MET cc_start: 0.9074 (mmm) cc_final: 0.8584 (mmm) REVERT: C 110 MET cc_start: 0.7552 (mpp) cc_final: 0.7324 (mtt) REVERT: C 146 GLN cc_start: 0.8465 (tp40) cc_final: 0.8265 (tp40) REVERT: C 189 GLU cc_start: 0.8842 (mm-30) cc_final: 0.8284 (mm-30) REVERT: C 194 ILE cc_start: 0.9678 (mt) cc_final: 0.9452 (tp) REVERT: C 207 LEU cc_start: 0.9285 (mt) cc_final: 0.8741 (mt) REVERT: C 218 GLU cc_start: 0.9150 (mm-30) cc_final: 0.8819 (pm20) REVERT: C 242 TYR cc_start: 0.9521 (t80) cc_final: 0.9165 (t80) REVERT: C 259 PHE cc_start: 0.9350 (t80) cc_final: 0.8749 (t80) REVERT: C 269 MET cc_start: 0.9587 (ptt) cc_final: 0.9186 (mmp) REVERT: C 274 ASP cc_start: 0.8416 (p0) cc_final: 0.7996 (p0) REVERT: D 30 TRP cc_start: 0.8389 (p-90) cc_final: 0.7214 (p-90) REVERT: D 33 GLU cc_start: 0.9217 (mp0) cc_final: 0.8412 (pp20) REVERT: D 79 GLU cc_start: 0.8802 (pt0) cc_final: 0.8506 (tm-30) REVERT: D 80 HIS cc_start: 0.9017 (m170) cc_final: 0.7869 (m170) REVERT: D 168 PHE cc_start: 0.8792 (m-80) cc_final: 0.7752 (m-80) REVERT: D 169 TYR cc_start: 0.8519 (m-80) cc_final: 0.7818 (m-80) REVERT: D 174 TYR cc_start: 0.9085 (OUTLIER) cc_final: 0.8545 (t80) REVERT: D 242 TYR cc_start: 0.9050 (t80) cc_final: 0.8541 (t80) outliers start: 78 outliers final: 62 residues processed: 700 average time/residue: 0.1205 time to fit residues: 126.3770 Evaluate side-chains 707 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 640 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 191 GLN Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 21 PHE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 149 optimal weight: 8.9990 chunk 16 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 0.0030 chunk 88 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 387 GLN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 181 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.113719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.085717 restraints weight = 41345.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.088873 restraints weight = 21460.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.091034 restraints weight = 13540.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.092494 restraints weight = 9516.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.093606 restraints weight = 7268.168| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.7859 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= 0.163 Angle : 0.876 18.096 22134 Z= 0.434 Chirality : 0.050 0.292 2360 Planarity : 0.004 0.049 2818 Dihedral : 10.007 136.115 2244 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 21.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.38 % Allowed : 34.85 % Favored : 61.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.19), residues: 1932 helix: 0.87 (0.15), residues: 1113 sheet: -0.96 (0.40), residues: 148 loop : 0.07 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 164 TYR 0.044 0.002 TYR C 262 PHE 0.043 0.002 PHE A 261 TRP 0.012 0.001 TRP D 124 HIS 0.014 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00374 (16386) covalent geometry : angle 0.87643 (22134) hydrogen bonds : bond 0.04423 ( 871) hydrogen bonds : angle 5.42335 ( 2571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 676 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9092 (tppt) cc_final: 0.8625 (tppt) REVERT: A 56 ASP cc_start: 0.8899 (m-30) cc_final: 0.8487 (m-30) REVERT: A 95 MET cc_start: 0.8982 (mmm) cc_final: 0.8684 (tpp) REVERT: A 150 GLN cc_start: 0.9538 (tp40) cc_final: 0.9114 (tp40) REVERT: A 161 ARG cc_start: 0.8713 (ttm110) cc_final: 0.8054 (ptp-170) REVERT: A 191 GLN cc_start: 0.8156 (mm-40) cc_final: 0.7785 (mt0) REVERT: A 221 LYS cc_start: 0.8793 (mmtp) cc_final: 0.8553 (mttm) REVERT: A 255 HIS cc_start: 0.8599 (t-90) cc_final: 0.8369 (t-90) REVERT: A 266 LYS cc_start: 0.8744 (ptmm) cc_final: 0.8197 (ptmm) REVERT: A 290 GLU cc_start: 0.9214 (tm-30) cc_final: 0.8831 (tm-30) REVERT: A 301 PHE cc_start: 0.9059 (m-10) cc_final: 0.8722 (m-10) REVERT: A 375 LYS cc_start: 0.8832 (mmtp) cc_final: 0.7973 (mmtm) REVERT: A 390 GLN cc_start: 0.8992 (mt0) cc_final: 0.8774 (mt0) REVERT: A 413 SER cc_start: 0.9438 (m) cc_final: 0.8931 (t) REVERT: A 447 ASN cc_start: 0.8164 (m-40) cc_final: 0.7908 (t0) REVERT: A 493 MET cc_start: 0.8819 (tmm) cc_final: 0.8490 (tmm) REVERT: A 590 SER cc_start: 0.9542 (t) cc_final: 0.8829 (p) REVERT: A 595 MET cc_start: 0.9206 (mmm) cc_final: 0.8906 (mmm) REVERT: A 639 ASP cc_start: 0.8586 (m-30) cc_final: 0.8141 (m-30) REVERT: A 640 MET cc_start: 0.9492 (tpp) cc_final: 0.9126 (tpp) REVERT: A 645 GLN cc_start: 0.8997 (tp40) cc_final: 0.8521 (tp-100) REVERT: B 8 LYS cc_start: 0.9259 (tptm) cc_final: 0.8980 (tptm) REVERT: B 82 LYS cc_start: 0.9530 (mtpp) cc_final: 0.9158 (mmtt) REVERT: B 95 MET cc_start: 0.9031 (tpt) cc_final: 0.8079 (tpp) REVERT: B 99 LYS cc_start: 0.9310 (tptp) cc_final: 0.8815 (tptp) REVERT: B 102 ASN cc_start: 0.9527 (m110) cc_final: 0.9280 (m110) REVERT: B 119 GLU cc_start: 0.9047 (mp0) cc_final: 0.8490 (mp0) REVERT: B 125 VAL cc_start: 0.9797 (t) cc_final: 0.9503 (p) REVERT: B 181 ASP cc_start: 0.8711 (m-30) cc_final: 0.8364 (m-30) REVERT: B 235 ARG cc_start: 0.9186 (mtm180) cc_final: 0.8892 (ttm-80) REVERT: B 250 TYR cc_start: 0.8793 (m-10) cc_final: 0.8209 (m-10) REVERT: B 256 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8468 (ttp80) REVERT: B 266 LYS cc_start: 0.9250 (mtpp) cc_final: 0.8629 (ptpp) REVERT: B 274 ARG cc_start: 0.8704 (ttm110) cc_final: 0.8323 (ttm170) REVERT: B 322 MET cc_start: 0.9328 (mmm) cc_final: 0.9000 (mmt) REVERT: B 341 LYS cc_start: 0.9646 (mmtm) cc_final: 0.9247 (mmmt) REVERT: B 344 GLU cc_start: 0.9185 (mt-10) cc_final: 0.8581 (pt0) REVERT: B 348 MET cc_start: 0.8859 (tmm) cc_final: 0.8522 (tpt) REVERT: B 350 ARG cc_start: 0.9103 (mtp85) cc_final: 0.8474 (mtp85) REVERT: B 358 ILE cc_start: 0.9686 (mm) cc_final: 0.9313 (tp) REVERT: B 362 ASP cc_start: 0.8850 (m-30) cc_final: 0.8161 (m-30) REVERT: B 375 LYS cc_start: 0.9221 (mmmm) cc_final: 0.8638 (mmmm) REVERT: B 393 SER cc_start: 0.9237 (m) cc_final: 0.8957 (p) REVERT: B 396 ASP cc_start: 0.8883 (p0) cc_final: 0.8497 (p0) REVERT: B 399 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8728 (mm-30) REVERT: B 402 GLU cc_start: 0.8666 (tm-30) cc_final: 0.7947 (tm-30) REVERT: B 475 ASN cc_start: 0.9368 (m-40) cc_final: 0.9115 (m110) REVERT: B 483 GLU cc_start: 0.9369 (mp0) cc_final: 0.9123 (mp0) REVERT: B 515 ASP cc_start: 0.9111 (m-30) cc_final: 0.8632 (m-30) REVERT: B 539 LYS cc_start: 0.9271 (mmmt) cc_final: 0.9042 (mptt) REVERT: B 548 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7680 (mm-30) REVERT: B 571 TYR cc_start: 0.8597 (t80) cc_final: 0.8369 (t80) REVERT: B 586 TYR cc_start: 0.9272 (m-80) cc_final: 0.8987 (m-80) REVERT: B 602 GLU cc_start: 0.8662 (pt0) cc_final: 0.8391 (pm20) REVERT: B 645 GLN cc_start: 0.9381 (tp40) cc_final: 0.8978 (tp-100) REVERT: B 668 ASN cc_start: 0.9197 (m110) cc_final: 0.8742 (m-40) REVERT: B 683 TYR cc_start: 0.8881 (t80) cc_final: 0.8402 (t80) REVERT: B 686 ARG cc_start: 0.8241 (ttm-80) cc_final: 0.7848 (mmt180) REVERT: C 17 PHE cc_start: 0.8699 (p90) cc_final: 0.7844 (p90) REVERT: C 20 MET cc_start: 0.9443 (tmm) cc_final: 0.9115 (ppp) REVERT: C 21 PHE cc_start: 0.9480 (m-80) cc_final: 0.8247 (m-80) REVERT: C 30 TRP cc_start: 0.7214 (t60) cc_final: 0.6959 (t60) REVERT: C 74 MET cc_start: 0.8672 (mtt) cc_final: 0.8449 (pmm) REVERT: C 85 GLN cc_start: 0.8476 (mt0) cc_final: 0.7880 (mm-40) REVERT: C 92 PHE cc_start: 0.9623 (t80) cc_final: 0.9140 (t80) REVERT: C 96 MET cc_start: 0.9047 (mmm) cc_final: 0.8519 (mmm) REVERT: C 110 MET cc_start: 0.7364 (mpp) cc_final: 0.7159 (mtt) REVERT: C 207 LEU cc_start: 0.9288 (mt) cc_final: 0.8717 (mt) REVERT: C 218 GLU cc_start: 0.9128 (mm-30) cc_final: 0.8733 (pm20) REVERT: C 223 GLU cc_start: 0.9322 (tm-30) cc_final: 0.8806 (pt0) REVERT: C 242 TYR cc_start: 0.9506 (t80) cc_final: 0.9184 (t80) REVERT: C 259 PHE cc_start: 0.9355 (t80) cc_final: 0.8724 (t80) REVERT: C 269 MET cc_start: 0.9555 (OUTLIER) cc_final: 0.9220 (mmp) REVERT: C 274 ASP cc_start: 0.8440 (p0) cc_final: 0.8034 (p0) REVERT: D 30 TRP cc_start: 0.8024 (p-90) cc_final: 0.7224 (p-90) REVERT: D 33 GLU cc_start: 0.9171 (mp0) cc_final: 0.8490 (pp20) REVERT: D 51 GLU cc_start: 0.8057 (mm-30) cc_final: 0.7773 (mm-30) REVERT: D 96 MET cc_start: 0.7971 (mmm) cc_final: 0.7748 (mmm) REVERT: D 168 PHE cc_start: 0.8752 (m-80) cc_final: 0.7719 (m-80) REVERT: D 169 TYR cc_start: 0.8196 (m-80) cc_final: 0.7612 (m-80) REVERT: D 174 TYR cc_start: 0.9126 (OUTLIER) cc_final: 0.8487 (t80) REVERT: D 225 ARG cc_start: 0.8919 (mtt180) cc_final: 0.8441 (mtt180) REVERT: D 242 TYR cc_start: 0.9043 (t80) cc_final: 0.8646 (t80) outliers start: 58 outliers final: 47 residues processed: 694 average time/residue: 0.1154 time to fit residues: 120.0310 Evaluate side-chains 698 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 647 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 296 LYS Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 21 PHE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 189 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 132 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 127 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.113447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.086006 restraints weight = 41639.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.089108 restraints weight = 21562.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.091134 restraints weight = 13526.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.092647 restraints weight = 9525.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.093678 restraints weight = 7285.891| |-----------------------------------------------------------------------------| r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.8041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16386 Z= 0.179 Angle : 0.892 18.552 22134 Z= 0.443 Chirality : 0.051 0.262 2360 Planarity : 0.004 0.048 2818 Dihedral : 9.955 137.052 2244 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 22.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.44 % Allowed : 35.49 % Favored : 61.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.49 (0.19), residues: 1932 helix: 0.78 (0.15), residues: 1119 sheet: -1.05 (0.41), residues: 148 loop : 0.12 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 164 TYR 0.040 0.002 TYR C 262 PHE 0.036 0.002 PHE A 261 TRP 0.015 0.001 TRP D 124 HIS 0.014 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00419 (16386) covalent geometry : angle 0.89172 (22134) hydrogen bonds : bond 0.04392 ( 871) hydrogen bonds : angle 5.49652 ( 2571) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 644 time to evaluate : 0.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8980 (tppt) cc_final: 0.8661 (tppt) REVERT: A 12 LEU cc_start: 0.9668 (mt) cc_final: 0.9449 (mp) REVERT: A 39 ASP cc_start: 0.8944 (m-30) cc_final: 0.8648 (m-30) REVERT: A 95 MET cc_start: 0.8970 (mmm) cc_final: 0.8706 (tpp) REVERT: A 144 MET cc_start: 0.8377 (mmm) cc_final: 0.8012 (mmm) REVERT: A 150 GLN cc_start: 0.9500 (tp40) cc_final: 0.9107 (tp40) REVERT: A 161 ARG cc_start: 0.8737 (ttm110) cc_final: 0.8033 (ptp-170) REVERT: A 221 LYS cc_start: 0.8781 (mmtp) cc_final: 0.8523 (mttm) REVERT: A 255 HIS cc_start: 0.8551 (t-90) cc_final: 0.8343 (t-90) REVERT: A 266 LYS cc_start: 0.8724 (ptmm) cc_final: 0.8203 (ptmm) REVERT: A 290 GLU cc_start: 0.9198 (tm-30) cc_final: 0.8827 (tm-30) REVERT: A 301 PHE cc_start: 0.9087 (m-10) cc_final: 0.8713 (m-10) REVERT: A 375 LYS cc_start: 0.8724 (mmtp) cc_final: 0.8492 (mmtm) REVERT: A 413 SER cc_start: 0.9433 (m) cc_final: 0.8944 (t) REVERT: A 415 ASN cc_start: 0.8975 (t0) cc_final: 0.7958 (t0) REVERT: A 418 ASN cc_start: 0.9413 (m-40) cc_final: 0.8896 (m110) REVERT: A 493 MET cc_start: 0.8906 (tmm) cc_final: 0.8581 (tmm) REVERT: A 570 MET cc_start: 0.8805 (mtp) cc_final: 0.8403 (ptp) REVERT: A 590 SER cc_start: 0.9527 (t) cc_final: 0.8863 (p) REVERT: A 595 MET cc_start: 0.9217 (mmm) cc_final: 0.8897 (mmm) REVERT: A 639 ASP cc_start: 0.8585 (m-30) cc_final: 0.8161 (m-30) REVERT: A 645 GLN cc_start: 0.9019 (tp40) cc_final: 0.8546 (tp-100) REVERT: A 686 ARG cc_start: 0.8225 (ttm-80) cc_final: 0.7945 (mtp85) REVERT: B 8 LYS cc_start: 0.9252 (tptm) cc_final: 0.8968 (tptm) REVERT: B 82 LYS cc_start: 0.9508 (mtpp) cc_final: 0.9103 (mmtp) REVERT: B 95 MET cc_start: 0.9008 (tpt) cc_final: 0.8081 (tpp) REVERT: B 99 LYS cc_start: 0.9319 (tptp) cc_final: 0.8843 (tptp) REVERT: B 102 ASN cc_start: 0.9510 (m110) cc_final: 0.9272 (m110) REVERT: B 109 ASN cc_start: 0.9520 (m-40) cc_final: 0.9290 (m-40) REVERT: B 119 GLU cc_start: 0.9044 (mp0) cc_final: 0.8472 (mp0) REVERT: B 168 VAL cc_start: 0.9412 (t) cc_final: 0.9159 (m) REVERT: B 181 ASP cc_start: 0.8644 (m-30) cc_final: 0.8014 (m-30) REVERT: B 235 ARG cc_start: 0.9144 (mtm180) cc_final: 0.8941 (mtm-85) REVERT: B 250 TYR cc_start: 0.8899 (m-10) cc_final: 0.8441 (m-10) REVERT: B 256 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8522 (ttp80) REVERT: B 266 LYS cc_start: 0.9243 (mtpp) cc_final: 0.8622 (ptpp) REVERT: B 274 ARG cc_start: 0.8711 (ttm110) cc_final: 0.8353 (ttm110) REVERT: B 322 MET cc_start: 0.9289 (mmm) cc_final: 0.8949 (mmt) REVERT: B 341 LYS cc_start: 0.9636 (mmtm) cc_final: 0.9258 (mmmt) REVERT: B 344 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8354 (pt0) REVERT: B 348 MET cc_start: 0.8823 (tmm) cc_final: 0.8513 (tpt) REVERT: B 350 ARG cc_start: 0.9104 (mtp85) cc_final: 0.8510 (mtp85) REVERT: B 358 ILE cc_start: 0.9714 (mm) cc_final: 0.9406 (tp) REVERT: B 362 ASP cc_start: 0.8781 (m-30) cc_final: 0.8339 (m-30) REVERT: B 375 LYS cc_start: 0.9237 (mmmm) cc_final: 0.8648 (mmmm) REVERT: B 387 GLN cc_start: 0.8659 (mp10) cc_final: 0.8195 (mp10) REVERT: B 393 SER cc_start: 0.9297 (m) cc_final: 0.9076 (p) REVERT: B 396 ASP cc_start: 0.8918 (p0) cc_final: 0.8448 (p0) REVERT: B 399 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8528 (mp0) REVERT: B 402 GLU cc_start: 0.8767 (tm-30) cc_final: 0.8084 (tm-30) REVERT: B 475 ASN cc_start: 0.9370 (m-40) cc_final: 0.9135 (m110) REVERT: B 483 GLU cc_start: 0.9349 (mp0) cc_final: 0.9128 (mp0) REVERT: B 515 ASP cc_start: 0.9090 (m-30) cc_final: 0.8607 (m-30) REVERT: B 539 LYS cc_start: 0.9288 (mmmt) cc_final: 0.9064 (mptt) REVERT: B 548 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7659 (mm-30) REVERT: B 586 TYR cc_start: 0.9201 (m-80) cc_final: 0.8963 (m-80) REVERT: B 599 GLU cc_start: 0.8806 (pm20) cc_final: 0.8513 (pm20) REVERT: B 602 GLU cc_start: 0.8619 (pt0) cc_final: 0.8410 (pm20) REVERT: B 645 GLN cc_start: 0.9404 (tp40) cc_final: 0.9004 (tp40) REVERT: B 668 ASN cc_start: 0.9208 (m110) cc_final: 0.8815 (m-40) REVERT: B 683 TYR cc_start: 0.8918 (t80) cc_final: 0.8378 (t80) REVERT: B 686 ARG cc_start: 0.8192 (ttm-80) cc_final: 0.7954 (mmt180) REVERT: C 17 PHE cc_start: 0.8740 (p90) cc_final: 0.7890 (p90) REVERT: C 20 MET cc_start: 0.9416 (tmm) cc_final: 0.9126 (ppp) REVERT: C 21 PHE cc_start: 0.9467 (m-80) cc_final: 0.8308 (m-80) REVERT: C 55 TYR cc_start: 0.8145 (t80) cc_final: 0.7501 (m-80) REVERT: C 74 MET cc_start: 0.8666 (mtt) cc_final: 0.8443 (pmm) REVERT: C 85 GLN cc_start: 0.8501 (mt0) cc_final: 0.7991 (mm-40) REVERT: C 92 PHE cc_start: 0.9612 (t80) cc_final: 0.9151 (t80) REVERT: C 96 MET cc_start: 0.9030 (mmm) cc_final: 0.8507 (mmm) REVERT: C 207 LEU cc_start: 0.9308 (mt) cc_final: 0.8758 (mt) REVERT: C 218 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8742 (pm20) REVERT: C 223 GLU cc_start: 0.9313 (tm-30) cc_final: 0.8827 (pt0) REVERT: C 237 GLU cc_start: 0.9533 (mp0) cc_final: 0.9074 (pm20) REVERT: C 242 TYR cc_start: 0.9468 (t80) cc_final: 0.9139 (t80) REVERT: C 259 PHE cc_start: 0.9331 (t80) cc_final: 0.9073 (t80) REVERT: C 269 MET cc_start: 0.9510 (OUTLIER) cc_final: 0.9250 (mmp) REVERT: C 274 ASP cc_start: 0.8427 (p0) cc_final: 0.8005 (p0) REVERT: D 30 TRP cc_start: 0.8153 (p-90) cc_final: 0.7322 (p-90) REVERT: D 33 GLU cc_start: 0.9177 (mp0) cc_final: 0.8477 (pp20) REVERT: D 51 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7592 (mm-30) REVERT: D 96 MET cc_start: 0.8023 (mmm) cc_final: 0.7795 (mmm) REVERT: D 168 PHE cc_start: 0.8724 (m-80) cc_final: 0.7662 (m-80) REVERT: D 169 TYR cc_start: 0.8228 (m-80) cc_final: 0.7549 (m-80) REVERT: D 172 PHE cc_start: 0.8914 (m-80) cc_final: 0.8668 (t80) REVERT: D 174 TYR cc_start: 0.9203 (OUTLIER) cc_final: 0.8584 (t80) REVERT: D 183 LYS cc_start: 0.7905 (ptpt) cc_final: 0.7614 (ptpp) outliers start: 59 outliers final: 48 residues processed: 665 average time/residue: 0.1080 time to fit residues: 107.9616 Evaluate side-chains 687 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 635 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 112 LYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 399 GLU Chi-restraints excluded: chain B residue 405 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 679 ILE Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 21 PHE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 2.9990 chunk 1 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 148 optimal weight: 0.7980 chunk 125 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 GLN A 646 GLN B 150 GLN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 418 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 186 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.116159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.088703 restraints weight = 41382.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.091739 restraints weight = 21401.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.093794 restraints weight = 13577.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.095303 restraints weight = 9519.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.096403 restraints weight = 7255.503| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.8209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16386 Z= 0.164 Angle : 0.896 17.821 22134 Z= 0.444 Chirality : 0.051 0.268 2360 Planarity : 0.004 0.049 2818 Dihedral : 9.852 137.239 2244 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 22.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.03 % Allowed : 35.90 % Favored : 61.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.19), residues: 1932 helix: 0.72 (0.15), residues: 1115 sheet: -1.07 (0.41), residues: 148 loop : 0.05 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 164 TYR 0.038 0.002 TYR C 262 PHE 0.054 0.002 PHE B 129 TRP 0.025 0.002 TRP D 124 HIS 0.015 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00378 (16386) covalent geometry : angle 0.89600 (22134) hydrogen bonds : bond 0.04383 ( 871) hydrogen bonds : angle 5.46008 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3481.24 seconds wall clock time: 61 minutes 1.34 seconds (3661.34 seconds total)