Starting phenix.real_space_refine on Sat Jun 14 06:45:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzi_45068/06_2025/9bzi_45068_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzi_45068/06_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_45068/06_2025/9bzi_45068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzi_45068/06_2025/9bzi_45068.map" model { file = "/net/cci-nas-00/data/ceres_data/9bzi_45068/06_2025/9bzi_45068_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzi_45068/06_2025/9bzi_45068_neut.cif" } resolution = 3.99 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 9.05, per 1000 atoms: 0.56 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: 4.41 Conformation dependent library (CDL) restraints added in 1.9 seconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 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: 4.90 Time building geometry restraints manager: 4.59 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: 0.950 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 35.210 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.470 ------------------------------------------------------------------------------- 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 : 8.19 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (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 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE C 227 TYR 0.020 0.002 TYR D 179 ARG 0.003 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.15420 ( 871) hydrogen bonds : angle 6.51778 ( 2571) covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74022 (22134) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 1085 time to evaluate : 1.778 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: A 28 LYS cc_start: 0.8512 (mmtm) cc_final: 0.8197 (mtpp) REVERT: A 76 ASP cc_start: 0.8314 (m-30) cc_final: 0.7595 (m-30) REVERT: A 172 LEU cc_start: 0.8973 (mp) cc_final: 0.8533 (mp) REVERT: A 177 ASP cc_start: 0.8139 (t0) cc_final: 0.7844 (t0) REVERT: A 188 ILE cc_start: 0.8410 (mt) cc_final: 0.8038 (mt) REVERT: A 191 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7998 (mm-40) REVERT: A 192 LEU cc_start: 0.9026 (mt) cc_final: 0.8757 (mt) REVERT: A 202 ASN cc_start: 0.9096 (t0) cc_final: 0.8850 (t0) REVERT: A 258 ILE cc_start: 0.8947 (tp) cc_final: 0.8696 (tp) REVERT: A 349 LEU cc_start: 0.8369 (mt) cc_final: 0.8151 (mt) REVERT: A 385 VAL cc_start: 0.8659 (t) cc_final: 0.8384 (t) REVERT: A 391 VAL cc_start: 0.9431 (p) cc_final: 0.9206 (p) REVERT: A 407 ILE cc_start: 0.8631 (mt) cc_final: 0.8167 (mt) REVERT: A 420 MET cc_start: 0.7021 (mmm) cc_final: 0.6672 (mmm) REVERT: A 485 ARG cc_start: 0.7711 (mtm-85) cc_final: 0.7475 (mtm-85) REVERT: A 501 GLN cc_start: 0.8151 (tt0) cc_final: 0.7773 (tt0) REVERT: A 502 ARG cc_start: 0.7804 (tpt170) cc_final: 0.7592 (tpt170) REVERT: A 546 LEU cc_start: 0.8784 (mt) cc_final: 0.8545 (mt) REVERT: A 550 MET cc_start: 0.6690 (mtm) cc_final: 0.6097 (mtm) REVERT: A 590 SER cc_start: 0.8929 (p) cc_final: 0.8284 (p) REVERT: A 631 ASP cc_start: 0.7859 (m-30) cc_final: 0.7398 (m-30) REVERT: B 12 LEU cc_start: 0.8337 (mt) cc_final: 0.8041 (mt) REVERT: B 118 TYR cc_start: 0.7321 (t80) cc_final: 0.7033 (t80) REVERT: B 122 ILE cc_start: 0.8630 (mt) cc_final: 0.8426 (mt) REVERT: B 191 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8221 (mm-40) REVERT: B 192 LEU cc_start: 0.9085 (mt) cc_final: 0.8856 (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: 0.8585 (t) REVERT: B 265 LYS cc_start: 0.8645 (mmtt) cc_final: 0.8285 (mmmt) REVERT: B 286 ASP cc_start: 0.6672 (OUTLIER) cc_final: 0.6427 (m-30) REVERT: B 315 ASP cc_start: 0.7898 (p0) cc_final: 0.7672 (p0) REVERT: B 322 MET cc_start: 0.7167 (mmm) cc_final: 0.6747 (mmt) REVERT: B 358 ILE cc_start: 0.8977 (mm) cc_final: 0.8722 (mm) REVERT: B 366 LYS cc_start: 0.8571 (ptpp) cc_final: 0.8226 (ttpp) REVERT: B 378 PHE cc_start: 0.8476 (p90) cc_final: 0.8095 (p90) REVERT: B 384 GLU cc_start: 0.8921 (pm20) cc_final: 0.8628 (pm20) REVERT: B 458 MET cc_start: 0.8140 (mmm) cc_final: 0.7818 (tpp) REVERT: B 468 LEU cc_start: 0.8484 (tp) cc_final: 0.8144 (tp) REVERT: B 471 TYR cc_start: 0.8185 (t80) cc_final: 0.7848 (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: 0.6560 (t) REVERT: B 645 GLN cc_start: 0.8234 (tp-100) cc_final: 0.7972 (tp40) REVERT: B 670 ILE cc_start: 0.9064 (mt) cc_final: 0.8827 (mt) REVERT: B 687 THR cc_start: 0.7737 (m) cc_final: 0.7353 (p) REVERT: C 95 MET cc_start: 0.5372 (tmm) cc_final: 0.4520 (tmm) REVERT: C 131 LEU cc_start: 0.5653 (OUTLIER) cc_final: 0.5425 (tp) REVERT: C 153 LEU cc_start: 0.6621 (tp) cc_final: 0.6001 (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: 0.3608 (t80) REVERT: D 17 PHE cc_start: 0.6374 (p90) cc_final: 0.6066 (p90) REVERT: D 43 THR cc_start: 0.7141 (p) cc_final: 0.6896 (p) REVERT: D 89 VAL cc_start: 0.7381 (t) cc_final: 0.6655 (t) REVERT: D 178 PHE cc_start: 0.6753 (m-80) cc_final: 0.5556 (m-80) REVERT: D 265 ASN cc_start: 0.4532 (m-40) cc_final: 0.3777 (m110) outliers start: 23 outliers final: 7 residues processed: 1094 average time/residue: 0.3111 time to fit residues: 482.3625 Evaluate side-chains 721 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 711 time to evaluate : 1.970 ------------------------------------------------------------------------------- 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 162 optimal weight: 8.9990 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 150 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 112 optimal weight: 0.5980 chunk 174 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 370 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS ** 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 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 181 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: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.115506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.086872 restraints weight = 40947.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.090054 restraints weight = 21220.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.092090 restraints weight = 13303.215| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 16386 Z= 0.230 Angle : 0.757 14.832 22134 Z= 0.397 Chirality : 0.047 0.188 2360 Planarity : 0.004 0.046 2818 Dihedral : 11.751 169.953 2258 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.78 % Allowed : 21.27 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.19), residues: 1932 helix: 1.25 (0.15), residues: 1126 sheet: 0.31 (0.43), residues: 126 loop : 0.48 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 30 HIS 0.012 0.002 HIS C 201 PHE 0.034 0.003 PHE D 172 TYR 0.021 0.002 TYR B 527 ARG 0.007 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.05059 ( 871) hydrogen bonds : angle 5.35040 ( 2571) covalent geometry : bond 0.00504 (16386) covalent geometry : angle 0.75679 (22134) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 789 time to evaluate : 1.788 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 49 HIS cc_start: 0.8458 (t70) cc_final: 0.8251 (t70) REVERT: A 53 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8652 (mt-10) REVERT: A 76 ASP cc_start: 0.9055 (m-30) cc_final: 0.8601 (m-30) REVERT: A 107 LYS cc_start: 0.8570 (OUTLIER) cc_final: 0.8318 (mmmm) REVERT: A 166 GLU cc_start: 0.8230 (mm-30) cc_final: 0.8030 (mm-30) REVERT: A 174 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7634 (mt-10) REVERT: A 191 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8374 (mm-40) REVERT: A 232 ASN cc_start: 0.9336 (OUTLIER) cc_final: 0.9077 (m-40) REVERT: A 250 TYR cc_start: 0.8810 (m-80) cc_final: 0.8600 (m-80) REVERT: A 291 LEU cc_start: 0.9599 (mt) cc_final: 0.9226 (mt) REVERT: A 335 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7820 (mt-10) REVERT: A 378 PHE cc_start: 0.9011 (p90) cc_final: 0.8680 (p90) REVERT: A 436 LEU cc_start: 0.9452 (mt) cc_final: 0.9079 (mt) REVERT: A 444 ASP cc_start: 0.7678 (t0) cc_final: 0.6970 (t70) REVERT: A 447 ASN cc_start: 0.8428 (m-40) cc_final: 0.7894 (t0) REVERT: A 471 TYR cc_start: 0.9051 (t80) cc_final: 0.8556 (t80) REVERT: A 515 ASP cc_start: 0.9094 (m-30) cc_final: 0.8767 (m-30) REVERT: A 528 PHE cc_start: 0.8804 (m-80) cc_final: 0.8552 (m-80) REVERT: A 546 LEU cc_start: 0.9729 (mt) cc_final: 0.9369 (mt) REVERT: A 550 MET cc_start: 0.6676 (mtm) cc_final: 0.6011 (mtm) REVERT: A 595 MET cc_start: 0.9286 (mmp) cc_final: 0.9000 (mmp) REVERT: A 615 MET cc_start: 0.9171 (mmt) cc_final: 0.8864 (mmm) REVERT: A 640 MET cc_start: 0.9155 (tpp) cc_final: 0.8873 (tpp) REVERT: A 645 GLN cc_start: 0.8896 (tp40) cc_final: 0.8377 (tp-100) REVERT: A 647 HIS cc_start: 0.8925 (m-70) cc_final: 0.8525 (m-70) REVERT: A 648 ILE cc_start: 0.9587 (mm) cc_final: 0.9256 (mm) REVERT: A 650 GLN cc_start: 0.8696 (mt0) cc_final: 0.8420 (mt0) REVERT: A 686 ARG cc_start: 0.8128 (ttm-80) cc_final: 0.7909 (ttm-80) REVERT: B 18 ILE cc_start: 0.9610 (mp) cc_final: 0.9294 (pt) REVERT: B 82 LYS cc_start: 0.9571 (mtpp) cc_final: 0.9259 (ptpp) REVERT: B 95 MET cc_start: 0.9031 (tpt) cc_final: 0.8713 (tpp) REVERT: B 99 LYS cc_start: 0.9348 (OUTLIER) cc_final: 0.8678 (tptp) REVERT: B 102 ASN cc_start: 0.9419 (m110) cc_final: 0.9140 (m110) REVERT: B 150 GLN cc_start: 0.9574 (tp40) cc_final: 0.9336 (tp-100) REVERT: B 181 ASP cc_start: 0.8805 (m-30) cc_final: 0.8304 (m-30) REVERT: B 184 ARG cc_start: 0.9476 (tpp80) cc_final: 0.9221 (tpp80) REVERT: B 227 MET cc_start: 0.9226 (mtt) cc_final: 0.8990 (mtt) REVERT: B 257 ASP cc_start: 0.8663 (m-30) cc_final: 0.8405 (m-30) REVERT: B 322 MET cc_start: 0.9128 (mmm) cc_final: 0.8875 (mmt) REVERT: B 341 LYS cc_start: 0.9557 (mmtm) cc_final: 0.9348 (mmmt) REVERT: B 348 MET cc_start: 0.8544 (tmm) cc_final: 0.8169 (tpt) REVERT: B 352 GLU cc_start: 0.8269 (mm-30) cc_final: 0.5902 (mm-30) REVERT: B 387 GLN cc_start: 0.8865 (mt0) cc_final: 0.8632 (mp10) REVERT: B 393 SER cc_start: 0.9337 (m) cc_final: 0.8726 (p) REVERT: B 402 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7580 (tm-30) REVERT: B 471 TYR cc_start: 0.9338 (t80) cc_final: 0.8451 (t80) REVERT: B 475 ASN cc_start: 0.9114 (m-40) cc_final: 0.8547 (m-40) REVERT: B 515 ASP cc_start: 0.9205 (m-30) cc_final: 0.8821 (m-30) REVERT: B 570 MET cc_start: 0.8287 (OUTLIER) cc_final: 0.7638 (mtm) REVERT: B 583 SER cc_start: 0.8890 (m) cc_final: 0.8382 (p) REVERT: B 620 SER cc_start: 0.9364 (OUTLIER) cc_final: 0.9106 (p) REVERT: B 632 MET cc_start: 0.8665 (mtm) cc_final: 0.8411 (mtm) REVERT: B 645 GLN cc_start: 0.9333 (tp-100) cc_final: 0.8814 (tp-100) REVERT: C 21 PHE cc_start: 0.9369 (m-80) cc_final: 0.8949 (m-80) REVERT: C 30 TRP cc_start: 0.7648 (p-90) cc_final: 0.7016 (t60) REVERT: C 86 ARG cc_start: 0.4103 (mpt180) cc_final: 0.3688 (mpt180) REVERT: C 90 LEU cc_start: 0.9055 (mt) cc_final: 0.8784 (mt) REVERT: C 92 PHE cc_start: 0.9356 (t80) cc_final: 0.8362 (t80) REVERT: C 93 MET cc_start: 0.9466 (mtt) cc_final: 0.9168 (mtt) REVERT: C 95 MET cc_start: 0.9121 (tmm) cc_final: 0.8758 (tmm) REVERT: C 96 MET cc_start: 0.9102 (mmm) cc_final: 0.8092 (mmm) REVERT: C 101 HIS cc_start: 0.9065 (m170) cc_final: 0.8587 (m90) REVERT: C 109 PHE cc_start: 0.8423 (m-10) cc_final: 0.8184 (m-80) REVERT: C 130 TYR cc_start: 0.9593 (m-80) cc_final: 0.9293 (m-10) REVERT: C 145 ILE cc_start: 0.7748 (tp) cc_final: 0.7436 (tp) REVERT: C 155 LYS cc_start: 0.8818 (mttt) cc_final: 0.8393 (mmtt) REVERT: C 173 TYR cc_start: 0.8388 (t80) cc_final: 0.7790 (t80) REVERT: C 174 TYR cc_start: 0.8784 (OUTLIER) cc_final: 0.7903 (t80) REVERT: C 197 ASP cc_start: 0.9500 (m-30) cc_final: 0.9167 (m-30) REVERT: C 198 GLU cc_start: 0.9679 (mm-30) cc_final: 0.9269 (mm-30) REVERT: C 241 GLU cc_start: 0.9525 (mp0) cc_final: 0.9099 (mp0) REVERT: C 242 TYR cc_start: 0.9258 (t80) cc_final: 0.8694 (t80) REVERT: C 259 PHE cc_start: 0.8816 (t80) cc_final: 0.7943 (t80) REVERT: C 263 ASN cc_start: 0.9557 (m110) cc_final: 0.8657 (p0) REVERT: C 268 LEU cc_start: 0.9533 (mt) cc_final: 0.9181 (mt) REVERT: C 273 PHE cc_start: 0.7187 (m-10) cc_final: 0.6448 (m-10) REVERT: D 30 TRP cc_start: 0.8087 (p-90) cc_final: 0.7595 (p-90) REVERT: D 50 ASN cc_start: 0.8996 (m-40) cc_final: 0.8501 (p0) REVERT: D 96 MET cc_start: 0.8512 (mmm) cc_final: 0.8293 (mmt) REVERT: D 131 LEU cc_start: 0.8573 (tt) cc_final: 0.8276 (tp) REVERT: D 155 LYS cc_start: 0.8314 (mttt) cc_final: 0.7878 (mtmm) REVERT: D 167 LEU cc_start: 0.9728 (mt) cc_final: 0.9310 (mt) REVERT: D 168 PHE cc_start: 0.8539 (m-80) cc_final: 0.7810 (m-80) REVERT: D 174 TYR cc_start: 0.8773 (t80) cc_final: 0.7913 (t80) REVERT: D 186 GLN cc_start: 0.7939 (mm-40) cc_final: 0.7580 (mm-40) REVERT: D 198 GLU cc_start: 0.8603 (pp20) cc_final: 0.8325 (pp20) REVERT: D 254 HIS cc_start: 0.8926 (m90) cc_final: 0.8722 (m-70) outliers start: 82 outliers final: 46 residues processed: 822 average time/residue: 0.2855 time to fit residues: 344.3285 Evaluate side-chains 747 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 695 time to evaluate : 1.904 ------------------------------------------------------------------------------- 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 224 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 306 ILE 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 27 ASP 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 312 GLN Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN 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 495 VAL Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 105 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 246 LEU Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 241 GLU 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 8 optimal weight: 2.9990 chunk 168 optimal weight: 10.0000 chunk 175 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 191 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 52 optimal weight: 0.9990 chunk 171 optimal weight: 6.9990 chunk 189 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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** ** A 588 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 HIS ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** D 23 ASN ** 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.116990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.087918 restraints weight = 41168.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.091176 restraints weight = 21647.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.093332 restraints weight = 13639.457| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3127 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.5502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16386 Z= 0.171 Angle : 0.722 14.197 22134 Z= 0.371 Chirality : 0.046 0.279 2360 Planarity : 0.004 0.035 2818 Dihedral : 11.449 179.656 2252 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.08 % Allowed : 24.53 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.19), residues: 1932 helix: 1.30 (0.15), residues: 1104 sheet: 0.60 (0.46), residues: 118 loop : 0.25 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 44 HIS 0.009 0.001 HIS D 201 PHE 0.039 0.002 PHE C 168 TYR 0.037 0.002 TYR D 142 ARG 0.006 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.04535 ( 871) hydrogen bonds : angle 5.22994 ( 2571) covalent geometry : bond 0.00374 (16386) covalent geometry : angle 0.72246 (22134) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 775 time to evaluate : 1.980 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.8981 (pm20) cc_final: 0.8717 (pm20) REVERT: A 138 LYS cc_start: 0.9202 (mmtt) cc_final: 0.8957 (mmtp) REVERT: A 147 GLN cc_start: 0.9081 (mt0) cc_final: 0.8597 (mt0) REVERT: A 174 GLU cc_start: 0.7929 (mt-10) cc_final: 0.7696 (mt-10) REVERT: A 211 GLU cc_start: 0.8304 (mm-30) cc_final: 0.8037 (mm-30) REVERT: A 255 HIS cc_start: 0.8820 (t-90) cc_final: 0.8574 (t-90) REVERT: A 294 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8761 (tm-30) REVERT: A 325 LYS cc_start: 0.9574 (mmmt) cc_final: 0.9098 (mmtp) REVERT: A 447 ASN cc_start: 0.8288 (m-40) cc_final: 0.7353 (m-40) REVERT: A 459 LYS cc_start: 0.9425 (OUTLIER) cc_final: 0.9080 (mtmm) REVERT: A 471 TYR cc_start: 0.9040 (t80) cc_final: 0.8637 (t80) REVERT: A 515 ASP cc_start: 0.9128 (m-30) cc_final: 0.8816 (m-30) REVERT: A 516 GLN cc_start: 0.8755 (mm-40) cc_final: 0.8396 (tp40) REVERT: A 526 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8609 (mp0) REVERT: A 528 PHE cc_start: 0.8837 (m-80) cc_final: 0.8608 (m-80) REVERT: A 546 LEU cc_start: 0.9699 (mt) cc_final: 0.9422 (mt) REVERT: A 590 SER cc_start: 0.9634 (t) cc_final: 0.9088 (p) REVERT: A 595 MET cc_start: 0.9200 (mmp) cc_final: 0.8833 (mmp) REVERT: A 645 GLN cc_start: 0.9068 (tp40) cc_final: 0.8372 (tp-100) REVERT: A 647 HIS cc_start: 0.8804 (m-70) cc_final: 0.8148 (m90) REVERT: A 648 ILE cc_start: 0.9562 (mm) cc_final: 0.9251 (mm) REVERT: A 650 GLN cc_start: 0.8810 (mt0) cc_final: 0.8508 (mt0) REVERT: B 18 ILE cc_start: 0.9621 (mp) cc_final: 0.9339 (pt) REVERT: B 54 LYS cc_start: 0.9596 (tttt) cc_final: 0.9295 (tttt) REVERT: B 82 LYS cc_start: 0.9586 (mtpp) cc_final: 0.9232 (ptpp) REVERT: B 95 MET cc_start: 0.9014 (tpt) cc_final: 0.8491 (tpp) REVERT: B 99 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.8617 (tptp) REVERT: B 102 ASN cc_start: 0.9453 (m110) cc_final: 0.9217 (m110) REVERT: B 107 LYS cc_start: 0.9248 (mmmm) cc_final: 0.8888 (mmmm) REVERT: B 111 LYS cc_start: 0.9561 (mmtp) cc_final: 0.9353 (mmtm) REVERT: B 112 LYS cc_start: 0.9168 (pptt) cc_final: 0.8873 (pttm) REVERT: B 184 ARG cc_start: 0.9487 (tpp80) cc_final: 0.9242 (tpp80) REVERT: B 232 ASN cc_start: 0.9430 (m-40) cc_final: 0.9174 (m-40) REVERT: B 263 ASP cc_start: 0.9188 (m-30) cc_final: 0.8929 (m-30) REVERT: B 322 MET cc_start: 0.9160 (mmm) cc_final: 0.8925 (mmt) REVERT: B 333 LYS cc_start: 0.9030 (tttm) cc_final: 0.8666 (tttm) REVERT: B 341 LYS cc_start: 0.9550 (mmtm) cc_final: 0.8922 (mmmm) REVERT: B 348 MET cc_start: 0.8623 (tmm) cc_final: 0.8239 (tpt) REVERT: B 362 ASP cc_start: 0.8486 (m-30) cc_final: 0.8150 (m-30) REVERT: B 375 LYS cc_start: 0.9204 (mmmm) cc_final: 0.8659 (mmmm) REVERT: B 393 SER cc_start: 0.9379 (m) cc_final: 0.8938 (p) REVERT: B 402 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7523 (tm-30) REVERT: B 431 LEU cc_start: 0.9518 (mm) cc_final: 0.9309 (mm) REVERT: B 471 TYR cc_start: 0.9112 (t80) cc_final: 0.8836 (t80) REVERT: B 475 ASN cc_start: 0.9089 (m-40) cc_final: 0.8744 (m110) REVERT: B 515 ASP cc_start: 0.9203 (m-30) cc_final: 0.8735 (m-30) REVERT: B 522 TYR cc_start: 0.8897 (m-10) cc_final: 0.8646 (m-10) REVERT: B 548 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7648 (mm-30) REVERT: B 550 MET cc_start: 0.8052 (mtp) cc_final: 0.7794 (mtp) REVERT: B 583 SER cc_start: 0.8920 (m) cc_final: 0.8353 (p) REVERT: B 588 GLN cc_start: 0.9278 (mm110) cc_final: 0.8923 (mm-40) REVERT: B 595 MET cc_start: 0.9373 (mmp) cc_final: 0.9111 (mmm) REVERT: B 620 SER cc_start: 0.9272 (OUTLIER) cc_final: 0.9041 (p) REVERT: B 645 GLN cc_start: 0.9358 (tp-100) cc_final: 0.8900 (tp40) REVERT: B 650 GLN cc_start: 0.8624 (mt0) cc_final: 0.7852 (mt0) REVERT: B 668 ASN cc_start: 0.8984 (m110) cc_final: 0.8461 (m-40) REVERT: C 20 MET cc_start: 0.9451 (tmm) cc_final: 0.9234 (tmm) REVERT: C 21 PHE cc_start: 0.9370 (m-80) cc_final: 0.8728 (m-80) REVERT: C 55 TYR cc_start: 0.8919 (t80) cc_final: 0.8577 (m-80) REVERT: C 90 LEU cc_start: 0.9107 (mt) cc_final: 0.8783 (mt) REVERT: C 92 PHE cc_start: 0.9499 (t80) cc_final: 0.9188 (t80) REVERT: C 109 PHE cc_start: 0.8367 (m-10) cc_final: 0.8124 (m-10) REVERT: C 133 LYS cc_start: 0.9312 (tptt) cc_final: 0.9090 (tppt) REVERT: C 155 LYS cc_start: 0.8855 (mttt) cc_final: 0.8503 (mmtt) REVERT: C 174 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.7370 (t80) REVERT: C 178 PHE cc_start: 0.8962 (m-80) cc_final: 0.8649 (t80) REVERT: C 197 ASP cc_start: 0.9587 (m-30) cc_final: 0.8987 (m-30) REVERT: C 198 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8937 (mm-30) REVERT: C 236 TYR cc_start: 0.9347 (t80) cc_final: 0.9078 (t80) REVERT: C 237 GLU cc_start: 0.9213 (pp20) cc_final: 0.8984 (pp20) REVERT: C 242 TYR cc_start: 0.9425 (t80) cc_final: 0.8736 (t80) REVERT: C 259 PHE cc_start: 0.9000 (t80) cc_final: 0.8278 (t80) REVERT: C 263 ASN cc_start: 0.9577 (m-40) cc_final: 0.8555 (p0) REVERT: C 314 PRO cc_start: 0.9248 (Cg_exo) cc_final: 0.8831 (Cg_endo) REVERT: D 20 MET cc_start: 0.9183 (ppp) cc_final: 0.8891 (ppp) REVERT: D 30 TRP cc_start: 0.8380 (p-90) cc_final: 0.8050 (p-90) REVERT: D 46 TYR cc_start: 0.9204 (m-80) cc_final: 0.8729 (m-80) REVERT: D 96 MET cc_start: 0.8120 (mmm) cc_final: 0.7714 (mmm) REVERT: D 131 LEU cc_start: 0.8724 (tt) cc_final: 0.8439 (tp) REVERT: D 155 LYS cc_start: 0.8150 (mttt) cc_final: 0.7681 (mtmt) REVERT: D 168 PHE cc_start: 0.8365 (m-80) cc_final: 0.7941 (m-80) REVERT: D 172 PHE cc_start: 0.8864 (m-80) cc_final: 0.8254 (m-80) REVERT: D 174 TYR cc_start: 0.8335 (t80) cc_final: 0.8045 (t80) REVERT: D 185 MET cc_start: 0.6531 (mmm) cc_final: 0.6275 (mmm) REVERT: D 268 LEU cc_start: 0.8926 (mm) cc_final: 0.8698 (mt) outliers start: 70 outliers final: 38 residues processed: 802 average time/residue: 0.2750 time to fit residues: 323.5424 Evaluate side-chains 757 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 715 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU 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 259 ASN Chi-restraints excluded: chain A residue 306 ILE 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 413 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 632 MET 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 239 GLN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 495 VAL 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 168 PHE 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 207 LEU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 243 THR 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 180 optimal weight: 0.8980 chunk 99 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 69 optimal weight: 0.0870 chunk 71 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 0.0070 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 304 HIS ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN C 107 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.121223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.091797 restraints weight = 40776.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.095115 restraints weight = 21153.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.097383 restraints weight = 13234.605| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.6120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16386 Z= 0.143 Angle : 0.741 14.163 22134 Z= 0.374 Chirality : 0.047 0.215 2360 Planarity : 0.004 0.045 2818 Dihedral : 10.814 160.474 2246 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.96 % Allowed : 26.46 % Favored : 69.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.19), residues: 1932 helix: 1.15 (0.15), residues: 1104 sheet: 0.21 (0.43), residues: 128 loop : 0.23 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 558 HIS 0.010 0.001 HIS D 201 PHE 0.041 0.002 PHE C 168 TYR 0.041 0.002 TYR B 574 ARG 0.008 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.04377 ( 871) hydrogen bonds : angle 5.18562 ( 2571) covalent geometry : bond 0.00321 (16386) covalent geometry : angle 0.74061 (22134) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 808 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 740 time to evaluate : 1.908 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: A 31 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8789 (pm20) REVERT: A 65 GLU cc_start: 0.8690 (mm-30) cc_final: 0.7955 (mm-30) REVERT: A 117 ARG cc_start: 0.8718 (mmm-85) cc_final: 0.8202 (mmm-85) REVERT: A 138 LYS cc_start: 0.9257 (mmtt) cc_final: 0.9019 (mmtp) REVERT: A 147 GLN cc_start: 0.9103 (mt0) cc_final: 0.8483 (mt0) REVERT: A 161 ARG cc_start: 0.8462 (ttm110) cc_final: 0.7778 (ptp-170) REVERT: A 232 ASN cc_start: 0.9417 (OUTLIER) cc_final: 0.8994 (m110) REVERT: A 250 TYR cc_start: 0.8769 (m-80) cc_final: 0.8526 (m-10) REVERT: A 255 HIS cc_start: 0.8879 (t-90) cc_final: 0.8073 (t-90) REVERT: A 294 GLU cc_start: 0.9061 (mm-30) cc_final: 0.8719 (tm-30) REVERT: A 325 LYS cc_start: 0.9568 (mmmt) cc_final: 0.9341 (mmtp) REVERT: A 335 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8110 (mp0) REVERT: A 403 ILE cc_start: 0.9147 (mm) cc_final: 0.8894 (mm) REVERT: A 447 ASN cc_start: 0.7352 (m-40) cc_final: 0.6800 (t0) REVERT: A 456 LYS cc_start: 0.9308 (ptpp) cc_final: 0.9071 (ptpp) REVERT: A 471 TYR cc_start: 0.9044 (t80) cc_final: 0.8583 (t80) REVERT: A 515 ASP cc_start: 0.9134 (m-30) cc_final: 0.8821 (m-30) REVERT: A 526 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8592 (mp0) REVERT: A 546 LEU cc_start: 0.9697 (mt) cc_final: 0.9449 (mt) REVERT: A 590 SER cc_start: 0.9575 (t) cc_final: 0.9040 (p) REVERT: A 595 MET cc_start: 0.9212 (mmp) cc_final: 0.8838 (mmp) REVERT: A 600 ARG cc_start: 0.8521 (OUTLIER) cc_final: 0.8313 (mtt-85) REVERT: A 606 TYR cc_start: 0.8337 (m-80) cc_final: 0.7958 (m-80) REVERT: A 639 ASP cc_start: 0.8620 (m-30) cc_final: 0.8229 (m-30) REVERT: A 640 MET cc_start: 0.9280 (tpp) cc_final: 0.8963 (tpp) REVERT: A 645 GLN cc_start: 0.8872 (tp40) cc_final: 0.8495 (tp-100) REVERT: A 647 HIS cc_start: 0.8721 (m-70) cc_final: 0.7975 (m90) REVERT: A 650 GLN cc_start: 0.8835 (mt0) cc_final: 0.8446 (mt0) REVERT: A 665 ARG cc_start: 0.9247 (OUTLIER) cc_final: 0.8431 (ttt-90) REVERT: B 8 LYS cc_start: 0.9240 (tptm) cc_final: 0.8981 (tptm) REVERT: B 82 LYS cc_start: 0.9609 (mtpp) cc_final: 0.9158 (ptpp) REVERT: B 95 MET cc_start: 0.9084 (tpt) cc_final: 0.8525 (tpp) REVERT: B 99 LYS cc_start: 0.9338 (OUTLIER) cc_final: 0.8697 (tptp) REVERT: B 102 ASN cc_start: 0.9475 (m110) cc_final: 0.9194 (m110) REVERT: B 107 LYS cc_start: 0.9321 (mmmm) cc_final: 0.9056 (mmmm) REVERT: B 111 LYS cc_start: 0.9555 (mmtp) cc_final: 0.9340 (mmtm) REVERT: B 112 LYS cc_start: 0.9218 (pptt) cc_final: 0.8983 (pttm) REVERT: B 168 VAL cc_start: 0.9298 (t) cc_final: 0.9020 (m) REVERT: B 181 ASP cc_start: 0.8772 (m-30) cc_final: 0.8493 (m-30) REVERT: B 184 ARG cc_start: 0.9476 (tpp80) cc_final: 0.9263 (tpp80) REVERT: B 274 ARG cc_start: 0.8557 (ttm110) cc_final: 0.8195 (ttm170) REVERT: B 333 LYS cc_start: 0.9125 (tttm) cc_final: 0.8780 (tttm) REVERT: B 341 LYS cc_start: 0.9281 (mmtm) cc_final: 0.9048 (mmmt) REVERT: B 348 MET cc_start: 0.8892 (tmm) cc_final: 0.8361 (tpt) REVERT: B 362 ASP cc_start: 0.8645 (m-30) cc_final: 0.8220 (m-30) REVERT: B 375 LYS cc_start: 0.9151 (mmmm) cc_final: 0.8544 (mmmm) REVERT: B 393 SER cc_start: 0.9335 (m) cc_final: 0.8917 (p) REVERT: B 402 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7657 (tm-30) REVERT: B 475 ASN cc_start: 0.9161 (m-40) cc_final: 0.8760 (m110) REVERT: B 483 GLU cc_start: 0.9467 (mp0) cc_final: 0.9186 (mp0) REVERT: B 515 ASP cc_start: 0.9259 (m-30) cc_final: 0.8737 (m-30) REVERT: B 548 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7698 (mm-30) REVERT: B 558 TRP cc_start: 0.9503 (m100) cc_final: 0.8735 (m100) REVERT: B 570 MET cc_start: 0.7091 (mtm) cc_final: 0.6394 (mtm) REVERT: B 583 SER cc_start: 0.9037 (m) cc_final: 0.8384 (p) REVERT: B 602 GLU cc_start: 0.8250 (pt0) cc_final: 0.7620 (pt0) REVERT: B 632 MET cc_start: 0.8140 (mtt) cc_final: 0.7697 (mtt) REVERT: B 645 GLN cc_start: 0.9323 (tp-100) cc_final: 0.8905 (tp40) REVERT: B 668 ASN cc_start: 0.9108 (m110) cc_final: 0.8573 (m110) REVERT: C 20 MET cc_start: 0.9475 (tmm) cc_final: 0.9212 (tmm) REVERT: C 21 PHE cc_start: 0.9484 (m-80) cc_final: 0.8778 (m-80) REVERT: C 55 TYR cc_start: 0.8978 (t80) cc_final: 0.8589 (m-80) REVERT: C 74 MET cc_start: 0.8762 (mtt) cc_final: 0.8483 (mtt) REVERT: C 90 LEU cc_start: 0.9199 (mt) cc_final: 0.8577 (mt) REVERT: C 92 PHE cc_start: 0.9524 (t80) cc_final: 0.8752 (t80) REVERT: C 95 MET cc_start: 0.9026 (tmm) cc_final: 0.8160 (tmm) REVERT: C 96 MET cc_start: 0.9087 (mmm) cc_final: 0.8348 (mmm) REVERT: C 109 PHE cc_start: 0.8300 (m-10) cc_final: 0.8039 (m-10) REVERT: C 155 LYS cc_start: 0.8997 (mttt) cc_final: 0.8634 (mmtt) REVERT: C 174 TYR cc_start: 0.8298 (OUTLIER) cc_final: 0.7364 (t80) REVERT: C 178 PHE cc_start: 0.8929 (m-80) cc_final: 0.7570 (m-80) REVERT: C 197 ASP cc_start: 0.9447 (m-30) cc_final: 0.9203 (m-30) REVERT: C 198 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8685 (mm-30) REVERT: C 242 TYR cc_start: 0.9468 (t80) cc_final: 0.8686 (t80) REVERT: C 246 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8812 (mm) REVERT: C 259 PHE cc_start: 0.9050 (t80) cc_final: 0.8350 (t80) REVERT: C 260 ILE cc_start: 0.8945 (pt) cc_final: 0.8553 (pp) REVERT: C 263 ASN cc_start: 0.9563 (m-40) cc_final: 0.9209 (p0) REVERT: C 266 LYS cc_start: 0.9456 (mttt) cc_final: 0.9113 (mmmt) REVERT: C 274 ASP cc_start: 0.8179 (p0) cc_final: 0.7566 (p0) REVERT: C 314 PRO cc_start: 0.9262 (Cg_exo) cc_final: 0.8678 (Cg_endo) REVERT: D 46 TYR cc_start: 0.9250 (m-80) cc_final: 0.8822 (m-10) REVERT: D 96 MET cc_start: 0.8182 (mmm) cc_final: 0.7867 (mmm) REVERT: D 129 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.9067 (ptpp) REVERT: D 131 LEU cc_start: 0.8820 (tt) cc_final: 0.8606 (tp) REVERT: D 168 PHE cc_start: 0.8481 (m-80) cc_final: 0.7578 (m-80) REVERT: D 169 TYR cc_start: 0.7679 (m-80) cc_final: 0.6979 (m-80) REVERT: D 210 GLN cc_start: 0.9289 (pp30) cc_final: 0.8882 (tp-100) REVERT: D 268 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8462 (mp) outliers start: 68 outliers final: 39 residues processed: 766 average time/residue: 0.3032 time to fit residues: 347.6694 Evaluate side-chains 720 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 672 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU 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 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 232 ASN Chi-restraints excluded: chain A residue 259 ASN 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 451 VAL Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 665 ARG 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 190 MET Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 381 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 72 THR 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 200 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 207 LEU 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 268 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 67 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 73 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 182 optimal weight: 8.9990 chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.112622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.084138 restraints weight = 43390.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.087161 restraints weight = 22491.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.089182 restraints weight = 14114.071| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3028 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3028 r_free = 0.3028 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3028 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.6690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 16386 Z= 0.269 Angle : 0.781 15.249 22134 Z= 0.404 Chirality : 0.049 0.276 2360 Planarity : 0.004 0.051 2818 Dihedral : 10.716 156.074 2246 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 21.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 5.59 % Allowed : 26.75 % Favored : 67.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 1932 helix: 0.94 (0.15), residues: 1117 sheet: -0.19 (0.43), residues: 128 loop : 0.21 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 30 HIS 0.009 0.002 HIS D 201 PHE 0.038 0.002 PHE C 172 TYR 0.041 0.002 TYR D 142 ARG 0.007 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.04492 ( 871) hydrogen bonds : angle 5.41708 ( 2571) covalent geometry : bond 0.00588 (16386) covalent geometry : angle 0.78081 (22134) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 704 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8105 (mm-30) REVERT: A 82 LYS cc_start: 0.9506 (mttm) cc_final: 0.9208 (mmtt) REVERT: A 95 MET cc_start: 0.8916 (mmm) cc_final: 0.8641 (tpp) REVERT: A 147 GLN cc_start: 0.9174 (mt0) cc_final: 0.8763 (mt0) REVERT: A 150 GLN cc_start: 0.9403 (tp40) cc_final: 0.8612 (tm-30) REVERT: A 174 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7791 (mt-10) REVERT: A 243 ARG cc_start: 0.8349 (ttp80) cc_final: 0.8101 (ppt170) REVERT: A 255 HIS cc_start: 0.8812 (t-90) cc_final: 0.8593 (t-90) REVERT: A 266 LYS cc_start: 0.8926 (ptmm) cc_final: 0.8364 (ptmm) REVERT: A 325 LYS cc_start: 0.9673 (mmmt) cc_final: 0.9395 (mmtp) REVERT: A 375 LYS cc_start: 0.8849 (mmtp) cc_final: 0.8183 (mmtm) REVERT: A 384 GLU cc_start: 0.8785 (OUTLIER) cc_final: 0.8116 (pm20) REVERT: A 446 ARG cc_start: 0.7399 (mmm-85) cc_final: 0.7128 (mmm160) REVERT: A 447 ASN cc_start: 0.7622 (m-40) cc_final: 0.7126 (t0) REVERT: A 456 LYS cc_start: 0.9282 (ptpp) cc_final: 0.9067 (ptpp) REVERT: A 471 TYR cc_start: 0.9251 (t80) cc_final: 0.8888 (t80) REVERT: A 515 ASP cc_start: 0.9082 (m-30) cc_final: 0.8864 (m-30) REVERT: A 590 SER cc_start: 0.9520 (t) cc_final: 0.9205 (p) REVERT: A 600 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.8280 (mtt-85) REVERT: A 639 ASP cc_start: 0.8572 (m-30) cc_final: 0.8208 (m-30) REVERT: A 645 GLN cc_start: 0.9202 (tp40) cc_final: 0.8886 (tp40) REVERT: A 647 HIS cc_start: 0.8925 (m-70) cc_final: 0.8654 (m-70) REVERT: B 82 LYS cc_start: 0.9568 (mtpp) cc_final: 0.9163 (ptpp) REVERT: B 95 MET cc_start: 0.9031 (tpt) cc_final: 0.8481 (tpp) REVERT: B 99 LYS cc_start: 0.9394 (tptp) cc_final: 0.8838 (tptp) REVERT: B 102 ASN cc_start: 0.9459 (m110) cc_final: 0.9193 (m110) REVERT: B 128 PHE cc_start: 0.9651 (t80) cc_final: 0.9419 (t80) REVERT: B 181 ASP cc_start: 0.8907 (m-30) cc_final: 0.8612 (m-30) REVERT: B 235 ARG cc_start: 0.9029 (ptp-110) cc_final: 0.8729 (mtm-85) REVERT: B 256 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8598 (tpt90) REVERT: B 257 ASP cc_start: 0.8700 (m-30) cc_final: 0.8432 (m-30) REVERT: B 274 ARG cc_start: 0.8567 (ttm110) cc_final: 0.8231 (ttm170) REVERT: B 306 ILE cc_start: 0.9458 (mt) cc_final: 0.9217 (mm) REVERT: B 317 MET cc_start: 0.8895 (pmm) cc_final: 0.8678 (pmm) REVERT: B 322 MET cc_start: 0.9051 (mmt) cc_final: 0.8753 (mmm) REVERT: B 348 MET cc_start: 0.8795 (tmm) cc_final: 0.8301 (tpt) REVERT: B 362 ASP cc_start: 0.8499 (m-30) cc_final: 0.8143 (m-30) REVERT: B 387 GLN cc_start: 0.8674 (mp10) cc_final: 0.8416 (mp10) REVERT: B 393 SER cc_start: 0.9377 (m) cc_final: 0.8732 (p) REVERT: B 402 GLU cc_start: 0.8418 (tm-30) cc_final: 0.7732 (tm-30) REVERT: B 471 TYR cc_start: 0.9312 (t80) cc_final: 0.8824 (t80) REVERT: B 475 ASN cc_start: 0.9289 (m-40) cc_final: 0.8868 (m-40) REVERT: B 483 GLU cc_start: 0.9480 (mp0) cc_final: 0.9195 (mp0) REVERT: B 500 ILE cc_start: 0.9646 (OUTLIER) cc_final: 0.9403 (tp) REVERT: B 515 ASP cc_start: 0.9182 (m-30) cc_final: 0.8726 (m-30) REVERT: B 548 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7719 (mm-30) REVERT: B 550 MET cc_start: 0.8148 (mtp) cc_final: 0.7832 (mtp) REVERT: B 561 LEU cc_start: 0.9710 (tp) cc_final: 0.9507 (tt) REVERT: B 570 MET cc_start: 0.7646 (mtm) cc_final: 0.7032 (mtm) REVERT: B 573 SER cc_start: 0.9649 (OUTLIER) cc_final: 0.9367 (p) REVERT: B 583 SER cc_start: 0.9035 (m) cc_final: 0.8494 (p) REVERT: B 602 GLU cc_start: 0.8374 (pt0) cc_final: 0.7706 (pt0) REVERT: B 610 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8545 (ptmm) REVERT: B 645 GLN cc_start: 0.9404 (tp40) cc_final: 0.8791 (tp40) REVERT: B 650 GLN cc_start: 0.8682 (mt0) cc_final: 0.8323 (mt0) REVERT: B 668 ASN cc_start: 0.9031 (m110) cc_final: 0.8484 (m110) REVERT: B 686 ARG cc_start: 0.8176 (ttm110) cc_final: 0.7654 (mtm-85) REVERT: C 17 PHE cc_start: 0.8465 (p90) cc_final: 0.7722 (p90) REVERT: C 20 MET cc_start: 0.9504 (tmm) cc_final: 0.8939 (ppp) REVERT: C 21 PHE cc_start: 0.9509 (m-80) cc_final: 0.7830 (m-80) REVERT: C 74 MET cc_start: 0.8866 (mtt) cc_final: 0.8558 (mtt) REVERT: C 92 PHE cc_start: 0.9590 (t80) cc_final: 0.8887 (t80) REVERT: C 95 MET cc_start: 0.9104 (tmm) cc_final: 0.7627 (tmm) REVERT: C 96 MET cc_start: 0.9088 (mmm) cc_final: 0.8452 (mmm) REVERT: C 109 PHE cc_start: 0.8303 (m-10) cc_final: 0.8043 (m-10) REVERT: C 155 LYS cc_start: 0.9272 (mttt) cc_final: 0.9021 (mttm) REVERT: C 174 TYR cc_start: 0.8320 (OUTLIER) cc_final: 0.7835 (t80) REVERT: C 242 TYR cc_start: 0.9411 (t80) cc_final: 0.8917 (t80) REVERT: C 259 PHE cc_start: 0.9136 (t80) cc_final: 0.8383 (t80) REVERT: C 260 ILE cc_start: 0.8973 (pt) cc_final: 0.8513 (pp) REVERT: C 263 ASN cc_start: 0.9576 (m-40) cc_final: 0.9326 (p0) REVERT: C 266 LYS cc_start: 0.9393 (mttt) cc_final: 0.9172 (mmmm) REVERT: C 269 MET cc_start: 0.9607 (ptt) cc_final: 0.9155 (ptt) REVERT: C 274 ASP cc_start: 0.8366 (p0) cc_final: 0.7843 (p0) REVERT: C 314 PRO cc_start: 0.9345 (Cg_exo) cc_final: 0.8826 (Cg_endo) REVERT: D 25 ASN cc_start: 0.9525 (t0) cc_final: 0.9304 (t0) REVERT: D 46 TYR cc_start: 0.9198 (m-80) cc_final: 0.8753 (m-10) REVERT: D 55 TYR cc_start: 0.8895 (t80) cc_final: 0.8629 (t80) REVERT: D 96 MET cc_start: 0.8243 (mmm) cc_final: 0.7944 (mmt) REVERT: D 129 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8816 (ptpp) REVERT: D 137 MET cc_start: 0.8533 (mmt) cc_final: 0.8111 (mpp) REVERT: D 155 LYS cc_start: 0.8250 (mttt) cc_final: 0.7793 (mttt) REVERT: D 168 PHE cc_start: 0.8753 (m-80) cc_final: 0.7556 (m-80) REVERT: D 174 TYR cc_start: 0.8785 (t80) cc_final: 0.8261 (t80) REVERT: D 268 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8627 (mt) outliers start: 96 outliers final: 62 residues processed: 743 average time/residue: 0.2704 time to fit residues: 296.8900 Evaluate side-chains 720 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 649 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 134 THR 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 179 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 215 ASP 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 306 ILE Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 632 MET 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 155 THR 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 224 VAL 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 391 VAL 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 495 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 611 THR 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 168 PHE 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 312 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 254 HIS 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 31 optimal weight: 7.9990 chunk 126 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 69 optimal weight: 3.9990 chunk 156 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 169 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN A 232 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 232 ASN ** 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 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.107116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.080551 restraints weight = 42245.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.083541 restraints weight = 21941.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.085527 restraints weight = 13737.789| |-----------------------------------------------------------------------------| r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.7083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16386 Z= 0.205 Angle : 0.774 14.299 22134 Z= 0.393 Chirality : 0.048 0.283 2360 Planarity : 0.004 0.039 2818 Dihedral : 10.498 149.513 2246 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 21.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.66 % Allowed : 31.00 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.19), residues: 1932 helix: 0.84 (0.15), residues: 1133 sheet: -0.23 (0.43), residues: 128 loop : 0.22 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP D 30 HIS 0.009 0.001 HIS D 201 PHE 0.030 0.002 PHE C 168 TYR 0.035 0.002 TYR D 142 ARG 0.005 0.001 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.04382 ( 871) hydrogen bonds : angle 5.33067 ( 2571) covalent geometry : bond 0.00458 (16386) covalent geometry : angle 0.77389 (22134) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 696 time to evaluate : 1.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8318 (mm-30) REVERT: A 82 LYS cc_start: 0.9529 (mttm) cc_final: 0.9220 (mmtm) REVERT: A 95 MET cc_start: 0.8914 (mmm) cc_final: 0.8637 (tpp) REVERT: A 147 GLN cc_start: 0.9212 (mt0) cc_final: 0.8759 (mt0) REVERT: A 150 GLN cc_start: 0.9439 (tp40) cc_final: 0.8544 (tm-30) REVERT: A 161 ARG cc_start: 0.8615 (ttm110) cc_final: 0.7777 (ptp-170) REVERT: A 174 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7426 (mt-10) REVERT: A 213 ILE cc_start: 0.9176 (mm) cc_final: 0.8884 (tp) REVERT: A 232 ASN cc_start: 0.8723 (m-40) cc_final: 0.8463 (m-40) REVERT: A 243 ARG cc_start: 0.8444 (ttp80) cc_final: 0.8011 (tmm160) REVERT: A 255 HIS cc_start: 0.8871 (t-90) cc_final: 0.8485 (t-90) REVERT: A 290 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8698 (tm-30) REVERT: A 295 ASP cc_start: 0.9309 (t0) cc_final: 0.9102 (t70) REVERT: A 325 LYS cc_start: 0.9657 (mmmt) cc_final: 0.9412 (mmtp) REVERT: A 375 LYS cc_start: 0.8850 (mmtp) cc_final: 0.8448 (mmtm) REVERT: A 389 SER cc_start: 0.9159 (OUTLIER) cc_final: 0.8611 (p) REVERT: A 413 SER cc_start: 0.9479 (m) cc_final: 0.9096 (t) REVERT: A 446 ARG cc_start: 0.7545 (mmm-85) cc_final: 0.7220 (mmm-85) REVERT: A 456 LYS cc_start: 0.9266 (ptpp) cc_final: 0.9046 (ptpp) REVERT: A 471 TYR cc_start: 0.9215 (t80) cc_final: 0.8920 (t80) REVERT: A 515 ASP cc_start: 0.9159 (m-30) cc_final: 0.8919 (m-30) REVERT: A 546 LEU cc_start: 0.9719 (mp) cc_final: 0.9347 (mt) REVERT: A 590 SER cc_start: 0.9468 (t) cc_final: 0.9088 (p) REVERT: A 600 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.8283 (mtt-85) REVERT: A 639 ASP cc_start: 0.8625 (m-30) cc_final: 0.8231 (m-30) REVERT: A 640 MET cc_start: 0.9394 (tpp) cc_final: 0.9011 (tpp) REVERT: A 645 GLN cc_start: 0.9139 (tp40) cc_final: 0.8858 (tp40) REVERT: A 647 HIS cc_start: 0.8865 (m-70) cc_final: 0.8621 (m-70) REVERT: B 8 LYS cc_start: 0.9249 (tptm) cc_final: 0.9006 (tptm) REVERT: B 82 LYS cc_start: 0.9568 (mtpp) cc_final: 0.9294 (mmtt) REVERT: B 95 MET cc_start: 0.9099 (tpt) cc_final: 0.8541 (tpp) REVERT: B 99 LYS cc_start: 0.9377 (tptp) cc_final: 0.8785 (tptp) REVERT: B 102 ASN cc_start: 0.9498 (m110) cc_final: 0.9238 (m110) REVERT: B 107 LYS cc_start: 0.9171 (mmmm) cc_final: 0.8956 (mmmt) REVERT: B 128 PHE cc_start: 0.9719 (t80) cc_final: 0.9378 (t80) REVERT: B 181 ASP cc_start: 0.8891 (m-30) cc_final: 0.8592 (m-30) REVERT: B 256 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8538 (tpt90) REVERT: B 257 ASP cc_start: 0.8713 (m-30) cc_final: 0.8460 (m-30) REVERT: B 263 ASP cc_start: 0.9075 (m-30) cc_final: 0.8835 (p0) REVERT: B 274 ARG cc_start: 0.8608 (ttm110) cc_final: 0.8219 (ttm170) REVERT: B 306 ILE cc_start: 0.9489 (mt) cc_final: 0.9224 (mm) REVERT: B 317 MET cc_start: 0.8754 (pmm) cc_final: 0.8535 (pmm) REVERT: B 348 MET cc_start: 0.8901 (tmm) cc_final: 0.8457 (tpt) REVERT: B 350 ARG cc_start: 0.9012 (mtp85) cc_final: 0.8396 (mtp85) REVERT: B 362 ASP cc_start: 0.8686 (m-30) cc_final: 0.8260 (m-30) REVERT: B 387 GLN cc_start: 0.8860 (mp10) cc_final: 0.8436 (mp10) REVERT: B 393 SER cc_start: 0.9306 (m) cc_final: 0.8645 (p) REVERT: B 402 GLU cc_start: 0.8550 (tm-30) cc_final: 0.7859 (tm-30) REVERT: B 471 TYR cc_start: 0.9304 (t80) cc_final: 0.8882 (t80) REVERT: B 475 ASN cc_start: 0.9303 (m-40) cc_final: 0.8846 (m-40) REVERT: B 483 GLU cc_start: 0.9472 (mp0) cc_final: 0.9257 (mp0) REVERT: B 500 ILE cc_start: 0.9631 (OUTLIER) cc_final: 0.9396 (tp) REVERT: B 515 ASP cc_start: 0.9235 (m-30) cc_final: 0.8746 (m-30) REVERT: B 548 GLU cc_start: 0.8297 (mm-30) cc_final: 0.7765 (mm-30) REVERT: B 550 MET cc_start: 0.8133 (mtp) cc_final: 0.7886 (mtp) REVERT: B 561 LEU cc_start: 0.9681 (tp) cc_final: 0.9451 (tt) REVERT: B 570 MET cc_start: 0.7663 (mtm) cc_final: 0.7065 (ttm) REVERT: B 602 GLU cc_start: 0.8514 (pt0) cc_final: 0.8297 (pt0) REVERT: B 610 LYS cc_start: 0.8915 (OUTLIER) cc_final: 0.8622 (ptmm) REVERT: B 645 GLN cc_start: 0.9410 (tp40) cc_final: 0.8932 (tp40) REVERT: B 650 GLN cc_start: 0.8649 (mt0) cc_final: 0.8341 (mt0) REVERT: B 668 ASN cc_start: 0.9117 (m110) cc_final: 0.8540 (m110) REVERT: B 683 TYR cc_start: 0.8958 (t80) cc_final: 0.8561 (t80) REVERT: C 17 PHE cc_start: 0.8614 (p90) cc_final: 0.7834 (p90) REVERT: C 20 MET cc_start: 0.9573 (tmm) cc_final: 0.8999 (ppp) REVERT: C 21 PHE cc_start: 0.9576 (m-80) cc_final: 0.8022 (m-80) REVERT: C 74 MET cc_start: 0.8967 (mtt) cc_final: 0.8583 (mtt) REVERT: C 92 PHE cc_start: 0.9632 (t80) cc_final: 0.8924 (t80) REVERT: C 95 MET cc_start: 0.9173 (tmm) cc_final: 0.7856 (tmm) REVERT: C 96 MET cc_start: 0.9170 (mmm) cc_final: 0.8539 (mmm) REVERT: C 143 LYS cc_start: 0.8769 (tptt) cc_final: 0.8472 (tptp) REVERT: C 155 LYS cc_start: 0.9340 (mttt) cc_final: 0.9099 (mttm) REVERT: C 174 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7884 (t80) REVERT: C 207 LEU cc_start: 0.9278 (mt) cc_final: 0.8688 (mt) REVERT: C 218 GLU cc_start: 0.9107 (mm-30) cc_final: 0.8841 (pm20) REVERT: C 219 GLU cc_start: 0.9373 (tt0) cc_final: 0.9155 (pm20) REVERT: C 242 TYR cc_start: 0.9404 (t80) cc_final: 0.9160 (t80) REVERT: C 259 PHE cc_start: 0.9282 (t80) cc_final: 0.8575 (t80) REVERT: C 263 ASN cc_start: 0.9609 (m-40) cc_final: 0.9370 (p0) REVERT: C 269 MET cc_start: 0.9612 (ptt) cc_final: 0.9196 (mmt) REVERT: C 274 ASP cc_start: 0.8277 (p0) cc_final: 0.7787 (p0) REVERT: C 314 PRO cc_start: 0.9376 (Cg_exo) cc_final: 0.8752 (Cg_endo) REVERT: D 33 GLU cc_start: 0.9074 (mp0) cc_final: 0.8248 (pp20) REVERT: D 46 TYR cc_start: 0.9243 (m-80) cc_final: 0.8684 (m-10) REVERT: D 55 TYR cc_start: 0.8871 (t80) cc_final: 0.8636 (t80) REVERT: D 71 ASN cc_start: 0.9413 (m110) cc_final: 0.8755 (p0) REVERT: D 96 MET cc_start: 0.8218 (mmm) cc_final: 0.7923 (mmm) REVERT: D 168 PHE cc_start: 0.8850 (m-80) cc_final: 0.7758 (m-80) REVERT: D 174 TYR cc_start: 0.8864 (t80) cc_final: 0.8369 (t80) REVERT: D 268 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8404 (mt) outliers start: 80 outliers final: 60 residues processed: 729 average time/residue: 0.2781 time to fit residues: 297.8468 Evaluate side-chains 729 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 662 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 134 THR 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 179 LEU Chi-restraints excluded: chain A residue 181 ASP 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 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 405 LEU 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 441 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 143 LEU 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 256 ARG Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN 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 500 ILE Chi-restraints excluded: chain B residue 573 SER Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 610 LYS 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 168 PHE 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 43 THR Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 254 HIS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 39 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 161 optimal weight: 10.0000 chunk 23 optimal weight: 0.0370 chunk 40 optimal weight: 0.1980 chunk 146 optimal weight: 6.9990 chunk 184 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 175 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN ** B 158 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 107 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.111237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.084199 restraints weight = 42135.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.087315 restraints weight = 21601.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.089368 restraints weight = 13372.391| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.7351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16386 Z= 0.164 Angle : 0.781 16.000 22134 Z= 0.394 Chirality : 0.048 0.279 2360 Planarity : 0.004 0.042 2818 Dihedral : 10.289 141.536 2246 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.66 % Allowed : 31.70 % Favored : 63.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.19), residues: 1932 helix: 0.90 (0.15), residues: 1112 sheet: -0.26 (0.44), residues: 124 loop : 0.06 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP C 30 HIS 0.010 0.001 HIS D 201 PHE 0.035 0.002 PHE B 156 TYR 0.033 0.002 TYR A 498 ARG 0.008 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 871) hydrogen bonds : angle 5.29747 ( 2571) covalent geometry : bond 0.00375 (16386) covalent geometry : angle 0.78062 (22134) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 707 time to evaluate : 1.932 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 31 GLU cc_start: 0.9146 (OUTLIER) cc_final: 0.8819 (pm20) REVERT: A 56 ASP cc_start: 0.9112 (m-30) cc_final: 0.8641 (m-30) REVERT: A 95 MET cc_start: 0.8883 (mmm) cc_final: 0.8658 (tpp) REVERT: A 147 GLN cc_start: 0.9191 (mt0) cc_final: 0.8679 (mt0) REVERT: A 150 GLN cc_start: 0.9444 (tp40) cc_final: 0.9031 (tp40) REVERT: A 161 ARG cc_start: 0.8660 (ttm110) cc_final: 0.7931 (ptp-170) REVERT: A 191 GLN cc_start: 0.7946 (mt0) cc_final: 0.7669 (mt0) REVERT: A 218 ASN cc_start: 0.9255 (t0) cc_final: 0.8801 (p0) REVERT: A 255 HIS cc_start: 0.8756 (t-90) cc_final: 0.8500 (t-90) REVERT: A 290 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8708 (tm-30) REVERT: A 325 LYS cc_start: 0.9643 (mmmt) cc_final: 0.9404 (mmtp) REVERT: A 362 ASP cc_start: 0.8251 (m-30) cc_final: 0.8008 (m-30) REVERT: A 375 LYS cc_start: 0.8862 (mmtp) cc_final: 0.8410 (mmtm) REVERT: A 389 SER cc_start: 0.9170 (OUTLIER) cc_final: 0.8951 (p) REVERT: A 399 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8603 (tm-30) REVERT: A 413 SER cc_start: 0.9469 (OUTLIER) cc_final: 0.9082 (t) REVERT: A 471 TYR cc_start: 0.9142 (t80) cc_final: 0.8883 (t80) REVERT: A 546 LEU cc_start: 0.9668 (mp) cc_final: 0.9290 (mt) REVERT: A 590 SER cc_start: 0.9505 (t) cc_final: 0.9089 (p) REVERT: A 599 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8254 (mm-30) REVERT: A 600 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7817 (mtt-85) REVERT: A 615 MET cc_start: 0.9284 (mmm) cc_final: 0.8908 (mmm) REVERT: A 628 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8728 (mm-30) REVERT: A 639 ASP cc_start: 0.8560 (m-30) cc_final: 0.8152 (m-30) REVERT: A 640 MET cc_start: 0.9424 (tpp) cc_final: 0.8978 (tpp) REVERT: A 645 GLN cc_start: 0.9083 (tp40) cc_final: 0.8809 (tp40) REVERT: B 8 LYS cc_start: 0.9283 (tptm) cc_final: 0.8994 (tptm) REVERT: B 75 GLU cc_start: 0.9149 (mp0) cc_final: 0.8782 (pm20) REVERT: B 82 LYS cc_start: 0.9568 (mtpp) cc_final: 0.9245 (mmtt) REVERT: B 95 MET cc_start: 0.9042 (tpt) cc_final: 0.8480 (tpp) REVERT: B 99 LYS cc_start: 0.9309 (tptp) cc_final: 0.8764 (tptp) REVERT: B 102 ASN cc_start: 0.9485 (m110) cc_final: 0.9281 (m110) REVERT: B 117 ARG cc_start: 0.9082 (mtp85) cc_final: 0.8864 (mtp85) REVERT: B 119 GLU cc_start: 0.9087 (mp0) cc_final: 0.8576 (mp0) REVERT: B 181 ASP cc_start: 0.8813 (m-30) cc_final: 0.8382 (m-30) REVERT: B 235 ARG cc_start: 0.9196 (mtm110) cc_final: 0.8895 (ptp-110) REVERT: B 250 TYR cc_start: 0.8793 (m-10) cc_final: 0.8410 (m-10) REVERT: B 256 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8214 (tpt90) REVERT: B 257 ASP cc_start: 0.8594 (m-30) cc_final: 0.8098 (m-30) REVERT: B 274 ARG cc_start: 0.8661 (ttm110) cc_final: 0.8309 (ttm170) REVERT: B 306 ILE cc_start: 0.9488 (mt) cc_final: 0.9226 (mm) REVERT: B 317 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8481 (pmm) REVERT: B 348 MET cc_start: 0.8942 (tmm) cc_final: 0.8515 (tpt) REVERT: B 350 ARG cc_start: 0.9049 (mtp85) cc_final: 0.8378 (mtp85) REVERT: B 358 ILE cc_start: 0.9651 (mm) cc_final: 0.9149 (tp) REVERT: B 362 ASP cc_start: 0.8642 (m-30) cc_final: 0.8235 (m-30) REVERT: B 387 GLN cc_start: 0.8846 (mp10) cc_final: 0.8384 (mp10) REVERT: B 393 SER cc_start: 0.9335 (m) cc_final: 0.8725 (p) REVERT: B 402 GLU cc_start: 0.8622 (tm-30) cc_final: 0.7942 (tm-30) REVERT: B 467 ASN cc_start: 0.9253 (m-40) cc_final: 0.9019 (m-40) REVERT: B 471 TYR cc_start: 0.9198 (t80) cc_final: 0.8812 (t80) REVERT: B 475 ASN cc_start: 0.9310 (m-40) cc_final: 0.8873 (m-40) REVERT: B 483 GLU cc_start: 0.9456 (mp0) cc_final: 0.9234 (mp0) REVERT: B 500 ILE cc_start: 0.9630 (OUTLIER) cc_final: 0.9369 (tp) REVERT: B 515 ASP cc_start: 0.9230 (m-30) cc_final: 0.8760 (m-30) REVERT: B 548 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7770 (mm-30) REVERT: B 570 MET cc_start: 0.7677 (mtm) cc_final: 0.7271 (mtm) REVERT: B 602 GLU cc_start: 0.8529 (pt0) cc_final: 0.7948 (pt0) REVERT: B 610 LYS cc_start: 0.8858 (OUTLIER) cc_final: 0.8590 (ptmm) REVERT: B 645 GLN cc_start: 0.9416 (tp40) cc_final: 0.8994 (tp40) REVERT: B 657 PHE cc_start: 0.8903 (m-80) cc_final: 0.8663 (m-80) REVERT: B 668 ASN cc_start: 0.9133 (m110) cc_final: 0.8613 (m110) REVERT: B 686 ARG cc_start: 0.8156 (ttm-80) cc_final: 0.7877 (mmt180) REVERT: C 17 PHE cc_start: 0.8576 (p90) cc_final: 0.7797 (p90) REVERT: C 20 MET cc_start: 0.9569 (tmm) cc_final: 0.8976 (ppp) REVERT: C 21 PHE cc_start: 0.9564 (m-80) cc_final: 0.8080 (m-80) REVERT: C 55 TYR cc_start: 0.8891 (t80) cc_final: 0.8189 (m-80) REVERT: C 74 MET cc_start: 0.8935 (mtt) cc_final: 0.8527 (mtt) REVERT: C 85 GLN cc_start: 0.8425 (mt0) cc_final: 0.7840 (mm-40) REVERT: C 92 PHE cc_start: 0.9642 (t80) cc_final: 0.8928 (t80) REVERT: C 95 MET cc_start: 0.9059 (tmm) cc_final: 0.7831 (tmm) REVERT: C 96 MET cc_start: 0.9161 (mmm) cc_final: 0.8520 (mmm) REVERT: C 143 LYS cc_start: 0.8703 (tptt) cc_final: 0.8393 (tptp) REVERT: C 174 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.7727 (t80) REVERT: C 178 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8561 (t80) REVERT: C 207 LEU cc_start: 0.9309 (mt) cc_final: 0.8761 (mt) REVERT: C 218 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8823 (pm20) REVERT: C 242 TYR cc_start: 0.9445 (t80) cc_final: 0.9154 (t80) REVERT: C 259 PHE cc_start: 0.9246 (t80) cc_final: 0.8622 (t80) REVERT: C 269 MET cc_start: 0.9552 (OUTLIER) cc_final: 0.9200 (mmt) REVERT: C 274 ASP cc_start: 0.8214 (p0) cc_final: 0.7782 (p0) REVERT: C 314 PRO cc_start: 0.9351 (Cg_exo) cc_final: 0.8741 (Cg_endo) REVERT: D 33 GLU cc_start: 0.9091 (mp0) cc_final: 0.8424 (pp20) REVERT: D 46 TYR cc_start: 0.9219 (m-80) cc_final: 0.8655 (m-10) REVERT: D 55 TYR cc_start: 0.8923 (t80) cc_final: 0.8683 (t80) REVERT: D 96 MET cc_start: 0.8154 (mmm) cc_final: 0.7868 (mmm) REVERT: D 129 LYS cc_start: 0.9192 (OUTLIER) cc_final: 0.8724 (ptpp) REVERT: D 168 PHE cc_start: 0.8832 (m-80) cc_final: 0.7647 (m-80) REVERT: D 174 TYR cc_start: 0.8848 (t80) cc_final: 0.8256 (t80) REVERT: D 185 MET cc_start: 0.7463 (mmp) cc_final: 0.7146 (mmp) outliers start: 80 outliers final: 48 residues processed: 732 average time/residue: 0.2726 time to fit residues: 297.6763 Evaluate side-chains 697 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 637 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 58 LEU 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 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 312 GLN Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 600 ARG Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 410 ASN 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 500 ILE Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 611 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 168 PHE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 80 HIS Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 254 HIS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 chunk 72 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 183 optimal weight: 7.9990 chunk 52 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 108 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 158 ASN ** 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 201 HIS ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 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 = 0.3543 r_free = 0.3543 target = 0.113266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.086237 restraints weight = 41548.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.089384 restraints weight = 21360.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.091477 restraints weight = 13318.621| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.7636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16386 Z= 0.154 Angle : 0.820 18.897 22134 Z= 0.407 Chirality : 0.049 0.286 2360 Planarity : 0.004 0.039 2818 Dihedral : 10.121 137.339 2246 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 20.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.79 % Allowed : 33.45 % Favored : 62.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.19), residues: 1932 helix: 0.90 (0.15), residues: 1100 sheet: -0.72 (0.41), residues: 142 loop : 0.02 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP C 30 HIS 0.020 0.001 HIS C 201 PHE 0.038 0.002 PHE C 172 TYR 0.027 0.001 TYR D 142 ARG 0.008 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.04376 ( 871) hydrogen bonds : angle 5.29088 ( 2571) covalent geometry : bond 0.00353 (16386) covalent geometry : angle 0.81970 (22134) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 689 time to evaluate : 1.837 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 12 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9116 (mp) REVERT: A 56 ASP cc_start: 0.9043 (m-30) cc_final: 0.8566 (m-30) REVERT: A 147 GLN cc_start: 0.9184 (mt0) cc_final: 0.8654 (mt0) REVERT: A 150 GLN cc_start: 0.9441 (tp40) cc_final: 0.9048 (tp40) REVERT: A 161 ARG cc_start: 0.8631 (ttm110) cc_final: 0.8010 (ptp-170) REVERT: A 243 ARG cc_start: 0.8453 (ttp80) cc_final: 0.8191 (ppt170) REVERT: A 290 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8724 (tm-30) REVERT: A 301 PHE cc_start: 0.8994 (m-10) cc_final: 0.8686 (m-10) REVERT: A 325 LYS cc_start: 0.9623 (mmmt) cc_final: 0.9408 (mmtp) REVERT: A 375 LYS cc_start: 0.8872 (mmtp) cc_final: 0.8351 (mmtm) REVERT: A 399 GLU cc_start: 0.8840 (tm-30) cc_final: 0.8628 (tm-30) REVERT: A 413 SER cc_start: 0.9453 (m) cc_final: 0.9088 (t) REVERT: A 471 TYR cc_start: 0.9110 (t80) cc_final: 0.8874 (t80) REVERT: A 546 LEU cc_start: 0.9644 (mp) cc_final: 0.9289 (mt) REVERT: A 590 SER cc_start: 0.9499 (t) cc_final: 0.9025 (p) REVERT: A 595 MET cc_start: 0.8650 (mmm) cc_final: 0.8417 (mtp) REVERT: A 600 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8422 (mtt180) REVERT: A 639 ASP cc_start: 0.8497 (m-30) cc_final: 0.8090 (m-30) REVERT: A 645 GLN cc_start: 0.9006 (tp40) cc_final: 0.8481 (tp-100) REVERT: B 8 LYS cc_start: 0.9232 (tptm) cc_final: 0.8964 (tptm) REVERT: B 75 GLU cc_start: 0.9140 (mp0) cc_final: 0.8871 (pm20) REVERT: B 82 LYS cc_start: 0.9544 (mtpp) cc_final: 0.9189 (mmtt) REVERT: B 95 MET cc_start: 0.9003 (tpt) cc_final: 0.8413 (tpp) REVERT: B 99 LYS cc_start: 0.9314 (tptp) cc_final: 0.8818 (tptp) REVERT: B 117 ARG cc_start: 0.9096 (mtp85) cc_final: 0.8866 (mtp85) REVERT: B 119 GLU cc_start: 0.9056 (mp0) cc_final: 0.8561 (mp0) REVERT: B 128 PHE cc_start: 0.9666 (t80) cc_final: 0.9412 (t80) REVERT: B 168 VAL cc_start: 0.9376 (t) cc_final: 0.9160 (m) REVERT: B 235 ARG cc_start: 0.9175 (mtm110) cc_final: 0.8570 (mtm110) REVERT: B 250 TYR cc_start: 0.8797 (m-10) cc_final: 0.8533 (m-10) REVERT: B 256 ARG cc_start: 0.8922 (OUTLIER) cc_final: 0.8217 (tpt90) REVERT: B 257 ASP cc_start: 0.8377 (m-30) cc_final: 0.7915 (m-30) REVERT: B 317 MET cc_start: 0.8659 (OUTLIER) cc_final: 0.8369 (pmm) REVERT: B 348 MET cc_start: 0.8925 (tmm) cc_final: 0.8472 (tpt) REVERT: B 350 ARG cc_start: 0.9046 (mtp85) cc_final: 0.8420 (mtp85) REVERT: B 358 ILE cc_start: 0.9670 (mm) cc_final: 0.9210 (tp) REVERT: B 362 ASP cc_start: 0.8596 (m-30) cc_final: 0.8206 (m-30) REVERT: B 387 GLN cc_start: 0.8664 (mp10) cc_final: 0.8173 (mp10) REVERT: B 393 SER cc_start: 0.9284 (m) cc_final: 0.8755 (p) REVERT: B 402 GLU cc_start: 0.8638 (tm-30) cc_final: 0.7974 (tm-30) REVERT: B 471 TYR cc_start: 0.9134 (t80) cc_final: 0.8845 (t80) REVERT: B 475 ASN cc_start: 0.9317 (m-40) cc_final: 0.8895 (m-40) REVERT: B 483 GLU cc_start: 0.9439 (mp0) cc_final: 0.9221 (mp0) REVERT: B 500 ILE cc_start: 0.9655 (OUTLIER) cc_final: 0.9448 (tp) REVERT: B 515 ASP cc_start: 0.9189 (m-30) cc_final: 0.8688 (m-30) REVERT: B 548 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7791 (mm-30) REVERT: B 570 MET cc_start: 0.8011 (mtm) cc_final: 0.7557 (ttm) REVERT: B 602 GLU cc_start: 0.8448 (pt0) cc_final: 0.7892 (pt0) REVERT: B 610 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8577 (ptmm) REVERT: B 645 GLN cc_start: 0.9414 (tp40) cc_final: 0.9027 (tp40) REVERT: B 668 ASN cc_start: 0.9126 (m110) cc_final: 0.8573 (m110) REVERT: B 683 TYR cc_start: 0.8877 (t80) cc_final: 0.8394 (t80) REVERT: B 686 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7787 (mpt-90) REVERT: C 20 MET cc_start: 0.9553 (tmm) cc_final: 0.9001 (ppp) REVERT: C 21 PHE cc_start: 0.9559 (m-80) cc_final: 0.8378 (m-80) REVERT: C 74 MET cc_start: 0.8810 (mtt) cc_final: 0.8395 (mtt) REVERT: C 79 GLU cc_start: 0.8869 (pt0) cc_final: 0.8547 (pt0) REVERT: C 85 GLN cc_start: 0.8424 (mt0) cc_final: 0.7856 (mm-40) REVERT: C 92 PHE cc_start: 0.9636 (t80) cc_final: 0.8900 (t80) REVERT: C 95 MET cc_start: 0.9108 (tmm) cc_final: 0.7742 (tmm) REVERT: C 96 MET cc_start: 0.9120 (mmm) cc_final: 0.8479 (mmm) REVERT: C 143 LYS cc_start: 0.8653 (tptt) cc_final: 0.8321 (tptp) REVERT: C 174 TYR cc_start: 0.8253 (OUTLIER) cc_final: 0.8009 (t80) REVERT: C 185 MET cc_start: 0.8349 (mmm) cc_final: 0.8141 (mmm) REVERT: C 218 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8896 (pm20) REVERT: C 259 PHE cc_start: 0.9376 (t80) cc_final: 0.8646 (t80) REVERT: C 269 MET cc_start: 0.9493 (OUTLIER) cc_final: 0.9157 (mmt) REVERT: C 278 GLU cc_start: 0.8115 (tp30) cc_final: 0.7760 (pp20) REVERT: C 314 PRO cc_start: 0.9374 (Cg_exo) cc_final: 0.8819 (Cg_endo) REVERT: D 30 TRP cc_start: 0.8192 (p-90) cc_final: 0.7536 (p-90) REVERT: D 33 GLU cc_start: 0.9101 (mp0) cc_final: 0.8312 (pp20) REVERT: D 46 TYR cc_start: 0.9207 (m-80) cc_final: 0.8683 (m-10) REVERT: D 96 MET cc_start: 0.8149 (mmm) cc_final: 0.7800 (mmm) REVERT: D 129 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8664 (ptpp) REVERT: D 168 PHE cc_start: 0.8629 (m-80) cc_final: 0.7559 (m-80) REVERT: D 174 TYR cc_start: 0.8927 (OUTLIER) cc_final: 0.8294 (t80) outliers start: 65 outliers final: 43 residues processed: 716 average time/residue: 0.2633 time to fit residues: 283.1959 Evaluate side-chains 708 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 655 time to evaluate : 1.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 58 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 194 LYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 312 GLN 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 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 652 ILE Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 610 LYS 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 168 PHE 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 D residue 80 HIS Chi-restraints excluded: chain D residue 129 LYS 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 207 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 111 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 182 optimal weight: 8.9990 chunk 107 optimal weight: 3.9990 chunk 77 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 115 optimal weight: 0.5980 chunk 127 optimal weight: 0.0970 chunk 188 optimal weight: 9.9990 chunk 27 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 49 HIS A 361 GLN B 102 ASN ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.115292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.087747 restraints weight = 41705.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.090991 restraints weight = 21739.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.093175 restraints weight = 13580.348| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.7908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16386 Z= 0.157 Angle : 0.859 22.227 22134 Z= 0.423 Chirality : 0.050 0.261 2360 Planarity : 0.004 0.085 2818 Dihedral : 10.003 137.591 2246 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.38 % Allowed : 34.91 % Favored : 61.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.19), residues: 1932 helix: 0.76 (0.15), residues: 1125 sheet: -1.02 (0.40), residues: 148 loop : 0.00 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 30 HIS 0.011 0.001 HIS C 201 PHE 0.033 0.002 PHE C 29 TYR 0.027 0.001 TYR B 571 ARG 0.007 0.001 ARG A 446 Details of bonding type rmsd hydrogen bonds : bond 0.04263 ( 871) hydrogen bonds : angle 5.35344 ( 2571) covalent geometry : bond 0.00356 (16386) covalent geometry : angle 0.85919 (22134) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 690 time to evaluate : 1.905 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: 0.9162 (tppt) cc_final: 0.8828 (tppt) REVERT: A 12 LEU cc_start: 0.9459 (mp) cc_final: 0.9225 (mt) REVERT: A 56 ASP cc_start: 0.9007 (m-30) cc_final: 0.8518 (m-30) REVERT: A 147 GLN cc_start: 0.9046 (mt0) cc_final: 0.8483 (mm-40) REVERT: A 150 GLN cc_start: 0.9489 (tp40) cc_final: 0.9056 (tp40) REVERT: A 161 ARG cc_start: 0.8644 (ttm110) cc_final: 0.7959 (ptp-170) REVERT: A 243 ARG cc_start: 0.8449 (ttp80) cc_final: 0.8056 (tmm160) REVERT: A 290 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8751 (tm-30) REVERT: A 301 PHE cc_start: 0.9003 (m-10) cc_final: 0.8775 (m-10) REVERT: A 317 MET cc_start: 0.8499 (ptp) cc_final: 0.8279 (ptp) REVERT: A 325 LYS cc_start: 0.9621 (mmmt) cc_final: 0.9405 (mmtp) REVERT: A 375 LYS cc_start: 0.8831 (mmtp) cc_final: 0.8284 (mmtm) REVERT: A 413 SER cc_start: 0.9476 (m) cc_final: 0.8977 (t) REVERT: A 471 TYR cc_start: 0.9061 (t80) cc_final: 0.8861 (t80) REVERT: A 505 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8341 (mt-10) REVERT: A 546 LEU cc_start: 0.9617 (mp) cc_final: 0.9258 (mt) REVERT: A 600 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.8153 (mtt-85) REVERT: A 636 LYS cc_start: 0.9424 (mttm) cc_final: 0.8982 (mmmm) REVERT: A 639 ASP cc_start: 0.8464 (m-30) cc_final: 0.8017 (m-30) REVERT: A 645 GLN cc_start: 0.8990 (tp40) cc_final: 0.8501 (tp-100) REVERT: B 75 GLU cc_start: 0.9168 (mp0) cc_final: 0.8910 (pm20) REVERT: B 82 LYS cc_start: 0.9531 (mtpp) cc_final: 0.9099 (mmtp) REVERT: B 95 MET cc_start: 0.8990 (tpt) cc_final: 0.8406 (tpp) REVERT: B 99 LYS cc_start: 0.9324 (tptp) cc_final: 0.8880 (tptp) REVERT: B 119 GLU cc_start: 0.9044 (mp0) cc_final: 0.8506 (mp0) REVERT: B 128 PHE cc_start: 0.9664 (t80) cc_final: 0.9415 (t80) REVERT: B 235 ARG cc_start: 0.9170 (mtm110) cc_final: 0.8537 (mtm110) REVERT: B 250 TYR cc_start: 0.8745 (m-10) cc_final: 0.8352 (m-10) REVERT: B 256 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8552 (ttp80) REVERT: B 317 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.8334 (pmm) REVERT: B 348 MET cc_start: 0.8926 (tmm) cc_final: 0.8484 (tpt) REVERT: B 350 ARG cc_start: 0.9110 (mtp85) cc_final: 0.8480 (mtp85) REVERT: B 358 ILE cc_start: 0.9676 (mm) cc_final: 0.9251 (tp) REVERT: B 362 ASP cc_start: 0.8667 (m-30) cc_final: 0.8241 (m-30) REVERT: B 387 GLN cc_start: 0.8649 (mp10) cc_final: 0.8402 (mp10) REVERT: B 393 SER cc_start: 0.9344 (m) cc_final: 0.8755 (p) REVERT: B 402 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8063 (tm-30) REVERT: B 471 TYR cc_start: 0.9131 (t80) cc_final: 0.8906 (t80) REVERT: B 474 GLN cc_start: 0.9283 (OUTLIER) cc_final: 0.9055 (mp10) REVERT: B 475 ASN cc_start: 0.9288 (m-40) cc_final: 0.8859 (m-40) REVERT: B 483 GLU cc_start: 0.9419 (mp0) cc_final: 0.9195 (mp0) REVERT: B 500 ILE cc_start: 0.9660 (OUTLIER) cc_final: 0.9442 (tp) REVERT: B 515 ASP cc_start: 0.9157 (m-30) cc_final: 0.8696 (m-30) REVERT: B 548 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7724 (mm-30) REVERT: B 570 MET cc_start: 0.8035 (mtm) cc_final: 0.7595 (mtm) REVERT: B 602 GLU cc_start: 0.8492 (pt0) cc_final: 0.7891 (pt0) REVERT: B 610 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8565 (ptmm) REVERT: B 645 GLN cc_start: 0.9412 (tp40) cc_final: 0.9036 (tp40) REVERT: B 668 ASN cc_start: 0.9113 (m110) cc_final: 0.8612 (m-40) REVERT: B 686 ARG cc_start: 0.8249 (ttm-80) cc_final: 0.7922 (mpt-90) REVERT: C 20 MET cc_start: 0.9581 (tmm) cc_final: 0.9049 (ppp) REVERT: C 21 PHE cc_start: 0.9578 (m-80) cc_final: 0.8422 (m-80) REVERT: C 74 MET cc_start: 0.8834 (mtt) cc_final: 0.8493 (mtt) REVERT: C 79 GLU cc_start: 0.8935 (pt0) cc_final: 0.8617 (pt0) REVERT: C 85 GLN cc_start: 0.8500 (mt0) cc_final: 0.7921 (mm-40) REVERT: C 92 PHE cc_start: 0.9639 (t80) cc_final: 0.8894 (t80) REVERT: C 95 MET cc_start: 0.9107 (tmm) cc_final: 0.7618 (tmm) REVERT: C 96 MET cc_start: 0.9144 (mmm) cc_final: 0.8473 (mmm) REVERT: C 143 LYS cc_start: 0.8665 (tptt) cc_final: 0.8325 (tptp) REVERT: C 218 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8907 (pm20) REVERT: C 259 PHE cc_start: 0.9368 (t80) cc_final: 0.8731 (t80) REVERT: C 269 MET cc_start: 0.9417 (OUTLIER) cc_final: 0.9181 (mmt) REVERT: C 274 ASP cc_start: 0.8131 (p0) cc_final: 0.7714 (p0) REVERT: C 314 PRO cc_start: 0.9366 (Cg_exo) cc_final: 0.8793 (Cg_endo) REVERT: D 33 GLU cc_start: 0.9164 (mp0) cc_final: 0.8335 (pp20) REVERT: D 46 TYR cc_start: 0.9220 (m-80) cc_final: 0.8732 (m-10) REVERT: D 96 MET cc_start: 0.8190 (mmm) cc_final: 0.7979 (mmm) REVERT: D 129 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8601 (ptpp) REVERT: D 168 PHE cc_start: 0.8636 (m-80) cc_final: 0.7500 (m-80) REVERT: D 174 TYR cc_start: 0.9033 (t80) cc_final: 0.8534 (t80) outliers start: 58 outliers final: 36 residues processed: 714 average time/residue: 0.2696 time to fit residues: 286.2807 Evaluate side-chains 708 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 664 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 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 194 LYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 312 GLN 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 436 LEU 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 681 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 500 ILE Chi-restraints excluded: chain B residue 610 LYS 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 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 129 LYS Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 207 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 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 137 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 160 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 127 optimal weight: 0.5980 chunk 68 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN ** 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 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** D 186 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 = 0.3548 r_free = 0.3548 target = 0.113362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.085722 restraints weight = 42174.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.088889 restraints weight = 22109.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.091036 restraints weight = 13928.332| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3133 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3133 r_free = 0.3133 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3133 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.8103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16386 Z= 0.185 Angle : 0.894 22.633 22134 Z= 0.445 Chirality : 0.051 0.313 2360 Planarity : 0.004 0.065 2818 Dihedral : 10.105 148.063 2244 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 23.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.38 % Allowed : 35.20 % Favored : 61.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.19), residues: 1932 helix: 0.70 (0.15), residues: 1124 sheet: -1.14 (0.40), residues: 148 loop : -0.01 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 30 HIS 0.008 0.001 HIS B 255 PHE 0.042 0.002 PHE A 261 TYR 0.032 0.002 TYR B 571 ARG 0.007 0.001 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.04381 ( 871) hydrogen bonds : angle 5.48053 ( 2571) covalent geometry : bond 0.00424 (16386) covalent geometry : angle 0.89380 (22134) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 673 time to evaluate : 1.737 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: 0.9198 (tppt) cc_final: 0.8883 (tppt) REVERT: A 12 LEU cc_start: 0.9473 (mp) cc_final: 0.9233 (mt) REVERT: A 39 ASP cc_start: 0.8971 (m-30) cc_final: 0.8709 (m-30) REVERT: A 56 ASP cc_start: 0.9128 (m-30) cc_final: 0.8688 (m-30) REVERT: A 117 ARG cc_start: 0.8804 (mmm-85) cc_final: 0.8477 (mmt90) REVERT: A 144 MET cc_start: 0.8643 (mmm) cc_final: 0.8426 (mmm) REVERT: A 147 GLN cc_start: 0.9111 (mt0) cc_final: 0.8585 (mt0) REVERT: A 150 GLN cc_start: 0.9487 (tp40) cc_final: 0.9042 (tp40) REVERT: A 161 ARG cc_start: 0.8680 (ttm110) cc_final: 0.8185 (ptp-170) REVERT: A 266 LYS cc_start: 0.8782 (ptmm) cc_final: 0.8520 (ptmm) REVERT: A 290 GLU cc_start: 0.9106 (tm-30) cc_final: 0.8748 (tm-30) REVERT: A 301 PHE cc_start: 0.9060 (m-10) cc_final: 0.8807 (m-10) REVERT: A 325 LYS cc_start: 0.9617 (mmmt) cc_final: 0.9416 (mmtp) REVERT: A 366 LYS cc_start: 0.9403 (ptpp) cc_final: 0.9110 (ptpp) REVERT: A 375 LYS cc_start: 0.8973 (mmtp) cc_final: 0.8287 (mmtm) REVERT: A 384 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8188 (pm20) REVERT: A 413 SER cc_start: 0.9455 (m) cc_final: 0.8962 (t) REVERT: A 471 TYR cc_start: 0.9133 (t80) cc_final: 0.8727 (t80) REVERT: A 475 ASN cc_start: 0.9027 (m-40) cc_final: 0.8628 (m110) REVERT: A 590 SER cc_start: 0.9576 (t) cc_final: 0.9002 (p) REVERT: A 595 MET cc_start: 0.8412 (mtp) cc_final: 0.8172 (mtp) REVERT: A 636 LYS cc_start: 0.9420 (mttm) cc_final: 0.9007 (mmmm) REVERT: A 639 ASP cc_start: 0.8528 (m-30) cc_final: 0.8107 (m-30) REVERT: A 645 GLN cc_start: 0.9035 (tp40) cc_final: 0.8531 (tp-100) REVERT: A 647 HIS cc_start: 0.8371 (m-70) cc_final: 0.8104 (m170) REVERT: B 75 GLU cc_start: 0.9171 (mp0) cc_final: 0.8958 (pm20) REVERT: B 82 LYS cc_start: 0.9512 (mtpp) cc_final: 0.9095 (mmtp) REVERT: B 95 MET cc_start: 0.9000 (tpt) cc_final: 0.8476 (tpp) REVERT: B 99 LYS cc_start: 0.9299 (tptp) cc_final: 0.8830 (tptp) REVERT: B 107 LYS cc_start: 0.8810 (mmmt) cc_final: 0.8561 (mmmt) REVERT: B 119 GLU cc_start: 0.9128 (mp0) cc_final: 0.8573 (mp0) REVERT: B 125 VAL cc_start: 0.9807 (t) cc_final: 0.9516 (p) REVERT: B 235 ARG cc_start: 0.9173 (mtm110) cc_final: 0.8614 (mtm110) REVERT: B 250 TYR cc_start: 0.8903 (m-10) cc_final: 0.8440 (m-10) REVERT: B 256 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8512 (ttp80) REVERT: B 317 MET cc_start: 0.8621 (OUTLIER) cc_final: 0.8320 (pmm) REVERT: B 348 MET cc_start: 0.8932 (tmm) cc_final: 0.8499 (tpt) REVERT: B 350 ARG cc_start: 0.9169 (mtp85) cc_final: 0.8512 (mtp85) REVERT: B 358 ILE cc_start: 0.9671 (mm) cc_final: 0.9310 (tp) REVERT: B 362 ASP cc_start: 0.8541 (m-30) cc_final: 0.8311 (m-30) REVERT: B 387 GLN cc_start: 0.8687 (mp10) cc_final: 0.8380 (mp10) REVERT: B 393 SER cc_start: 0.9340 (m) cc_final: 0.8676 (p) REVERT: B 402 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8114 (tm-30) REVERT: B 471 TYR cc_start: 0.9252 (t80) cc_final: 0.8902 (t80) REVERT: B 475 ASN cc_start: 0.9295 (m-40) cc_final: 0.8841 (m-40) REVERT: B 500 ILE cc_start: 0.9723 (OUTLIER) cc_final: 0.9517 (tp) REVERT: B 515 ASP cc_start: 0.9195 (m-30) cc_final: 0.8725 (m-30) REVERT: B 548 GLU cc_start: 0.8341 (mm-30) cc_final: 0.7794 (mm-30) REVERT: B 570 MET cc_start: 0.8325 (mtm) cc_final: 0.7936 (mtm) REVERT: B 583 SER cc_start: 0.9212 (m) cc_final: 0.8360 (t) REVERT: B 602 GLU cc_start: 0.8539 (pt0) cc_final: 0.7984 (pt0) REVERT: B 610 LYS cc_start: 0.8886 (OUTLIER) cc_final: 0.8610 (ptmm) REVERT: B 645 GLN cc_start: 0.9411 (tp40) cc_final: 0.8905 (tp40) REVERT: B 668 ASN cc_start: 0.9149 (m110) cc_final: 0.8601 (m110) REVERT: B 683 TYR cc_start: 0.8863 (t80) cc_final: 0.8365 (t80) REVERT: B 686 ARG cc_start: 0.8352 (ttm-80) cc_final: 0.7793 (mpt-90) REVERT: C 17 PHE cc_start: 0.8682 (p90) cc_final: 0.7849 (p90) REVERT: C 20 MET cc_start: 0.9596 (tmm) cc_final: 0.9081 (ppp) REVERT: C 21 PHE cc_start: 0.9589 (m-80) cc_final: 0.8196 (m-80) REVERT: C 74 MET cc_start: 0.9010 (mtt) cc_final: 0.8573 (mtt) REVERT: C 79 GLU cc_start: 0.8891 (pt0) cc_final: 0.8569 (pt0) REVERT: C 85 GLN cc_start: 0.8484 (mt0) cc_final: 0.7994 (mm110) REVERT: C 92 PHE cc_start: 0.9672 (t80) cc_final: 0.8929 (t80) REVERT: C 95 MET cc_start: 0.9029 (tmm) cc_final: 0.7529 (tmm) REVERT: C 96 MET cc_start: 0.9101 (mmm) cc_final: 0.8434 (mmm) REVERT: C 101 HIS cc_start: 0.8466 (m170) cc_final: 0.8207 (m170) REVERT: C 143 LYS cc_start: 0.8715 (tptt) cc_final: 0.8331 (tptp) REVERT: C 185 MET cc_start: 0.8442 (mmm) cc_final: 0.7882 (mmm) REVERT: C 189 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8106 (mm-30) REVERT: C 194 ILE cc_start: 0.9658 (mt) cc_final: 0.9390 (tp) REVERT: C 218 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8921 (pm20) REVERT: C 259 PHE cc_start: 0.9415 (t80) cc_final: 0.8751 (t80) REVERT: C 269 MET cc_start: 0.9525 (OUTLIER) cc_final: 0.9182 (mmt) REVERT: C 274 ASP cc_start: 0.8218 (p0) cc_final: 0.7809 (p0) REVERT: C 278 GLU cc_start: 0.8242 (tp30) cc_final: 0.7885 (pp20) REVERT: D 33 GLU cc_start: 0.9175 (mp0) cc_final: 0.8363 (pp20) REVERT: D 168 PHE cc_start: 0.8676 (m-80) cc_final: 0.7551 (m-80) REVERT: D 174 TYR cc_start: 0.9044 (t80) cc_final: 0.8590 (t80) REVERT: D 227 PHE cc_start: 0.9300 (t80) cc_final: 0.9013 (t80) outliers start: 58 outliers final: 43 residues processed: 696 average time/residue: 0.2723 time to fit residues: 284.8580 Evaluate side-chains 685 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 636 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 LEU 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 182 ILE Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 348 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 499 SER Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 602 GLU 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 143 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 317 MET 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 500 ILE Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain C residue 42 LEU 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 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 129 LYS Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 207 LEU Chi-restraints excluded: chain D residue 254 HIS 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 81 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 179 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 180 optimal weight: 0.7980 chunk 108 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 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 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.110906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.083241 restraints weight = 42367.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.086261 restraints weight = 22412.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.088335 restraints weight = 14285.071| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.8228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 16386 Z= 0.235 Angle : 0.919 22.913 22134 Z= 0.459 Chirality : 0.052 0.260 2360 Planarity : 0.004 0.044 2818 Dihedral : 10.149 148.079 2244 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 25.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.15 % Allowed : 36.54 % Favored : 60.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.19), residues: 1932 helix: 0.56 (0.15), residues: 1147 sheet: -1.20 (0.40), residues: 148 loop : -0.11 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 30 HIS 0.007 0.001 HIS C 201 PHE 0.043 0.003 PHE A 657 TYR 0.033 0.002 TYR B 357 ARG 0.008 0.001 ARG B 117 Details of bonding type rmsd hydrogen bonds : bond 0.04449 ( 871) hydrogen bonds : angle 5.57268 ( 2571) covalent geometry : bond 0.00531 (16386) covalent geometry : angle 0.91854 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7096.03 seconds wall clock time: 123 minutes 25.32 seconds (7405.32 seconds total)