Starting phenix.real_space_refine on Sat May 17 16:22:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzi_45068/05_2025/9bzi_45068_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzi_45068/05_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_45068/05_2025/9bzi_45068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzi_45068/05_2025/9bzi_45068.map" model { file = "/net/cci-nas-00/data/ceres_data/9bzi_45068/05_2025/9bzi_45068_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzi_45068/05_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 8.84, per 1000 atoms: 0.55 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: 3.84 Conformation dependent library (CDL) restraints added in 1.8 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: 1.60 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: 4.98 Time building geometry restraints manager: 4.32 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: 0.960 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: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 33.930 Find NCS groups from input model: 0.880 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: 0.010 Load rotamer database and sin/cos tables:3.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.670 ------------------------------------------------------------------------------- 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 : 1.756 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: A 28 LYS cc_start: 0.8512 (mmtm) cc_final: 0.8201 (mtpp) REVERT: A 76 ASP cc_start: 0.8314 (m-30) cc_final: 0.7591 (m-30) REVERT: A 172 LEU cc_start: 0.8973 (mp) cc_final: 0.8534 (mp) REVERT: A 177 ASP cc_start: 0.8139 (t0) cc_final: 0.7870 (t0) REVERT: A 188 ILE cc_start: 0.8410 (mt) cc_final: 0.8037 (mt) REVERT: A 191 GLN cc_start: 0.8224 (mm-40) cc_final: 0.8001 (mm-40) REVERT: A 192 LEU cc_start: 0.9026 (mt) cc_final: 0.8758 (mt) REVERT: A 202 ASN cc_start: 0.9096 (t0) cc_final: 0.8847 (t0) REVERT: A 258 ILE cc_start: 0.8947 (tp) cc_final: 0.8695 (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: 0.8386 (t) REVERT: A 391 VAL cc_start: 0.9431 (p) cc_final: 0.9208 (p) REVERT: A 407 ILE cc_start: 0.8631 (mt) cc_final: 0.8164 (mt) REVERT: A 420 MET cc_start: 0.7021 (mmm) cc_final: 0.6670 (mmm) REVERT: A 485 ARG cc_start: 0.7711 (mtm-85) cc_final: 0.7474 (mtm-85) REVERT: A 501 GLN cc_start: 0.8151 (tt0) cc_final: 0.7775 (tt0) REVERT: A 502 ARG cc_start: 0.7804 (tpt170) cc_final: 0.7595 (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: 0.6101 (mtm) REVERT: A 590 SER cc_start: 0.8929 (p) cc_final: 0.8280 (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: 0.8042 (mt) REVERT: B 118 TYR cc_start: 0.7321 (t80) cc_final: 0.7034 (t80) REVERT: B 191 GLN cc_start: 0.8443 (mm-40) cc_final: 0.8219 (mm-40) REVERT: B 192 LEU cc_start: 0.9085 (mt) cc_final: 0.8855 (mt) REVERT: B 204 SER cc_start: 0.8867 (m) cc_final: 0.8150 (t) REVERT: B 226 VAL cc_start: 0.8791 (t) cc_final: 0.8582 (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: 0.6428 (m-30) REVERT: B 315 ASP cc_start: 0.7898 (p0) cc_final: 0.7671 (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: 0.8721 (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: 0.8096 (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: 0.8282 (mt) REVERT: B 583 SER cc_start: 0.6929 (m) cc_final: 0.6561 (t) REVERT: B 645 GLN cc_start: 0.8234 (tp-100) cc_final: 0.7972 (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: 0.7354 (p) REVERT: C 95 MET cc_start: 0.5372 (tmm) cc_final: 0.4521 (tmm) REVERT: C 131 LEU cc_start: 0.5653 (OUTLIER) cc_final: 0.5426 (tp) REVERT: C 153 LEU cc_start: 0.6621 (tp) cc_final: 0.6000 (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: 0.3609 (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: 0.6897 (p) REVERT: D 89 VAL cc_start: 0.7381 (t) cc_final: 0.6656 (t) REVERT: D 178 PHE cc_start: 0.6753 (m-80) cc_final: 0.5554 (m-80) REVERT: D 265 ASN cc_start: 0.4532 (m-40) cc_final: 0.3776 (m110) outliers start: 23 outliers final: 7 residues processed: 1094 average time/residue: 0.3034 time to fit residues: 471.3080 Evaluate side-chains 722 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 712 time to evaluate : 1.664 ------------------------------------------------------------------------------- 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 25 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 = 0.3551 r_free = 0.3551 target = 0.115809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.085676 restraints weight = 40969.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.089144 restraints weight = 20984.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.091379 restraints weight = 12932.509| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3089 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3089 r_free = 0.3089 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3088 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 16386 Z= 0.233 Angle : 0.753 14.509 22134 Z= 0.395 Chirality : 0.047 0.193 2360 Planarity : 0.004 0.043 2818 Dihedral : 11.727 169.651 2258 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.78 % Allowed : 21.21 % Favored : 74.01 % 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: 1.26 (0.19), residues: 1932 helix: 1.24 (0.15), residues: 1128 sheet: 0.30 (0.43), residues: 126 loop : 0.46 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 30 HIS 0.012 0.002 HIS C 201 PHE 0.033 0.003 PHE D 172 TYR 0.021 0.002 TYR C 169 ARG 0.012 0.001 ARG D 261 Details of bonding type rmsd hydrogen bonds : bond 0.04988 ( 871) hydrogen bonds : angle 5.34152 ( 2571) covalent geometry : bond 0.00512 (16386) covalent geometry : angle 0.75272 (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 874 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 792 time to evaluate : 1.736 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: A 49 HIS cc_start: 0.8649 (t70) cc_final: 0.8409 (t70) REVERT: A 53 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8732 (mt-10) REVERT: A 76 ASP cc_start: 0.9058 (m-30) cc_final: 0.8647 (m-30) REVERT: A 107 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8239 (mmmm) REVERT: A 221 LYS cc_start: 0.8808 (mmtp) cc_final: 0.8595 (mttp) REVERT: A 232 ASN cc_start: 0.9388 (OUTLIER) cc_final: 0.9084 (m-40) REVERT: A 250 TYR cc_start: 0.8766 (m-80) cc_final: 0.8489 (m-80) REVERT: A 255 HIS cc_start: 0.8888 (t-90) cc_final: 0.7979 (t-90) REVERT: A 257 ASP cc_start: 0.9233 (m-30) cc_final: 0.8949 (m-30) REVERT: A 291 LEU cc_start: 0.9581 (mt) cc_final: 0.9291 (mt) REVERT: A 319 MET cc_start: 0.9032 (tpp) cc_final: 0.8619 (tpp) REVERT: A 335 GLU cc_start: 0.8366 (mt-10) cc_final: 0.8146 (mt-10) REVERT: A 378 PHE cc_start: 0.9018 (p90) cc_final: 0.8677 (p90) REVERT: A 415 ASN cc_start: 0.9270 (t0) cc_final: 0.9054 (t0) REVERT: A 435 SER cc_start: 0.9614 (p) cc_final: 0.9021 (t) REVERT: A 436 LEU cc_start: 0.9392 (mt) cc_final: 0.8843 (mt) REVERT: A 444 ASP cc_start: 0.7702 (t0) cc_final: 0.7020 (t70) REVERT: A 447 ASN cc_start: 0.8436 (m-40) cc_final: 0.7526 (t0) REVERT: A 471 TYR cc_start: 0.9027 (t80) cc_final: 0.8572 (t80) REVERT: A 515 ASP cc_start: 0.9143 (m-30) cc_final: 0.8774 (m-30) REVERT: A 528 PHE cc_start: 0.8870 (m-80) cc_final: 0.8628 (m-80) REVERT: A 546 LEU cc_start: 0.9762 (mt) cc_final: 0.9451 (mt) REVERT: A 550 MET cc_start: 0.6654 (mtm) cc_final: 0.5886 (mtm) REVERT: A 595 MET cc_start: 0.9344 (mmp) cc_final: 0.9046 (mmp) REVERT: A 615 MET cc_start: 0.9245 (mmt) cc_final: 0.8858 (mmm) REVERT: A 640 MET cc_start: 0.9211 (tpp) cc_final: 0.8908 (tpp) REVERT: A 645 GLN cc_start: 0.8897 (tp40) cc_final: 0.8377 (tp-100) REVERT: A 647 HIS cc_start: 0.8982 (m-70) cc_final: 0.8546 (m-70) REVERT: A 650 GLN cc_start: 0.8682 (mt0) cc_final: 0.8358 (mt0) REVERT: A 686 ARG cc_start: 0.8266 (ttm-80) cc_final: 0.8000 (ttm-80) REVERT: B 8 LYS cc_start: 0.9256 (tppt) cc_final: 0.8998 (tptm) REVERT: B 18 ILE cc_start: 0.9602 (mp) cc_final: 0.9271 (pt) REVERT: B 82 LYS cc_start: 0.9600 (mtpp) cc_final: 0.9269 (ptpp) REVERT: B 95 MET cc_start: 0.9100 (tpt) cc_final: 0.8783 (tpp) REVERT: B 99 LYS cc_start: 0.9305 (OUTLIER) cc_final: 0.8649 (tptp) REVERT: B 102 ASN cc_start: 0.9423 (m110) cc_final: 0.9112 (m110) REVERT: B 181 ASP cc_start: 0.8825 (m-30) cc_final: 0.8330 (m-30) REVERT: B 184 ARG cc_start: 0.9442 (tpp80) cc_final: 0.9187 (tpp80) REVERT: B 227 MET cc_start: 0.9263 (mtt) cc_final: 0.8994 (mtt) REVERT: B 235 ARG cc_start: 0.8789 (mtm110) cc_final: 0.8520 (mtm110) REVERT: B 250 TYR cc_start: 0.9050 (m-80) cc_final: 0.8808 (m-80) REVERT: B 257 ASP cc_start: 0.8744 (m-30) cc_final: 0.8463 (m-30) REVERT: B 341 LYS cc_start: 0.9615 (mmtm) cc_final: 0.9371 (mmmt) REVERT: B 348 MET cc_start: 0.8687 (tmm) cc_final: 0.8273 (tpt) REVERT: B 352 GLU cc_start: 0.8325 (mm-30) cc_final: 0.6029 (mm-30) REVERT: B 375 LYS cc_start: 0.9148 (mmmm) cc_final: 0.8902 (mmmm) REVERT: B 387 GLN cc_start: 0.9015 (mt0) cc_final: 0.8635 (mp10) REVERT: B 393 SER cc_start: 0.9247 (m) cc_final: 0.8641 (p) REVERT: B 402 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7536 (tm-30) REVERT: B 407 ILE cc_start: 0.9028 (mt) cc_final: 0.8827 (mt) REVERT: B 471 TYR cc_start: 0.9362 (t80) cc_final: 0.8499 (t80) REVERT: B 475 ASN cc_start: 0.9137 (m-40) cc_final: 0.8572 (m-40) REVERT: B 509 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8975 (tm-30) REVERT: B 515 ASP cc_start: 0.9275 (m-30) cc_final: 0.8801 (m-30) REVERT: B 570 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.7915 (mtm) REVERT: B 583 SER cc_start: 0.8996 (m) cc_final: 0.8457 (p) REVERT: B 620 SER cc_start: 0.9431 (OUTLIER) cc_final: 0.9168 (p) REVERT: B 632 MET cc_start: 0.8689 (mtm) cc_final: 0.8384 (mtm) REVERT: B 645 GLN cc_start: 0.9337 (tp-100) cc_final: 0.8867 (tp40) REVERT: C 21 PHE cc_start: 0.9406 (m-80) cc_final: 0.8752 (m-80) REVERT: C 30 TRP cc_start: 0.7614 (p-90) cc_final: 0.6982 (t60) REVERT: C 86 ARG cc_start: 0.4028 (mpt180) cc_final: 0.3636 (mpt180) REVERT: C 90 LEU cc_start: 0.9077 (mt) cc_final: 0.8809 (mt) REVERT: C 92 PHE cc_start: 0.9382 (t80) cc_final: 0.8432 (t80) REVERT: C 93 MET cc_start: 0.9472 (mtt) cc_final: 0.9137 (mtt) REVERT: C 95 MET cc_start: 0.9147 (tmm) cc_final: 0.8844 (tmm) REVERT: C 96 MET cc_start: 0.9156 (mmm) cc_final: 0.8178 (mmm) REVERT: C 101 HIS cc_start: 0.9139 (m170) cc_final: 0.8722 (m170) REVERT: C 109 PHE cc_start: 0.8431 (m-10) cc_final: 0.8201 (m-80) REVERT: C 130 TYR cc_start: 0.9666 (m-80) cc_final: 0.9371 (m-10) REVERT: C 145 ILE cc_start: 0.7691 (tp) cc_final: 0.7333 (tp) REVERT: C 155 LYS cc_start: 0.8752 (mttt) cc_final: 0.8351 (mmtt) REVERT: C 157 MET cc_start: 0.9294 (mtt) cc_final: 0.9054 (mtt) REVERT: C 173 TYR cc_start: 0.8408 (t80) cc_final: 0.7815 (t80) REVERT: C 174 TYR cc_start: 0.8843 (OUTLIER) cc_final: 0.7963 (t80) REVERT: C 197 ASP cc_start: 0.9489 (m-30) cc_final: 0.9180 (m-30) REVERT: C 198 GLU cc_start: 0.9676 (mm-30) cc_final: 0.9297 (mm-30) REVERT: C 216 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7570 (mp10) REVERT: C 241 GLU cc_start: 0.9614 (mp0) cc_final: 0.9198 (mp0) REVERT: C 242 TYR cc_start: 0.9376 (t80) cc_final: 0.8795 (t80) REVERT: C 259 PHE cc_start: 0.8953 (t80) cc_final: 0.8059 (t80) REVERT: C 263 ASN cc_start: 0.9583 (m110) cc_final: 0.8631 (p0) REVERT: C 268 LEU cc_start: 0.9558 (mt) cc_final: 0.9201 (mt) REVERT: C 273 PHE cc_start: 0.7222 (m-10) cc_final: 0.6449 (m-10) REVERT: D 30 TRP cc_start: 0.8082 (p-90) cc_final: 0.7486 (p-90) REVERT: D 50 ASN cc_start: 0.8984 (m-40) cc_final: 0.8484 (p0) REVERT: D 93 MET cc_start: 0.9318 (mtt) cc_final: 0.9077 (mtt) REVERT: D 96 MET cc_start: 0.8525 (mmm) cc_final: 0.8312 (mmt) REVERT: D 131 LEU cc_start: 0.8574 (tt) cc_final: 0.8297 (tp) REVERT: D 167 LEU cc_start: 0.9748 (mt) cc_final: 0.9319 (mt) REVERT: D 168 PHE cc_start: 0.8648 (m-80) cc_final: 0.7885 (m-80) REVERT: D 174 TYR cc_start: 0.8820 (t80) cc_final: 0.8006 (t80) REVERT: D 186 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7548 (mm-40) REVERT: D 198 GLU cc_start: 0.8677 (pp20) cc_final: 0.8348 (pp20) REVERT: D 242 TYR cc_start: 0.8833 (t80) cc_final: 0.8595 (t80) REVERT: D 254 HIS cc_start: 0.8995 (m90) cc_final: 0.8774 (m-70) outliers start: 82 outliers final: 46 residues processed: 825 average time/residue: 0.2705 time to fit residues: 329.1390 Evaluate side-chains 752 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 699 time to evaluate : 1.741 ------------------------------------------------------------------------------- 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 155 THR 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 509 GLU 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 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: 0.8980 chunk 168 optimal weight: 10.0000 chunk 175 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 47 optimal weight: 7.9990 chunk 191 optimal weight: 9.9990 chunk 57 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 189 optimal weight: 10.0000 chunk 141 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 239 GLN A 370 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 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 D 71 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.120069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.090294 restraints weight = 40714.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.093643 restraints weight = 20746.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.095902 restraints weight = 13055.281| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16386 Z= 0.158 Angle : 0.720 14.171 22134 Z= 0.368 Chirality : 0.047 0.265 2360 Planarity : 0.004 0.038 2818 Dihedral : 11.335 178.549 2252 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.08 % Allowed : 23.89 % Favored : 72.03 % 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: 1.26 (0.19), residues: 1932 helix: 1.31 (0.15), residues: 1107 sheet: 0.96 (0.49), residues: 104 loop : 0.23 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 44 HIS 0.010 0.001 HIS D 201 PHE 0.041 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 0.04519 ( 871) hydrogen bonds : angle 5.19189 ( 2571) covalent geometry : bond 0.00357 (16386) covalent geometry : angle 0.71979 (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 854 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 784 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 LYS cc_start: 0.9200 (mmtt) cc_final: 0.8969 (mmtp) REVERT: A 147 GLN cc_start: 0.9123 (mt0) cc_final: 0.8562 (mt0) REVERT: A 161 ARG cc_start: 0.8610 (ttm110) cc_final: 0.8164 (ptm160) REVERT: A 211 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7953 (mm-30) REVERT: A 221 LYS cc_start: 0.8809 (mmtp) cc_final: 0.8563 (mttp) REVERT: A 250 TYR cc_start: 0.8806 (m-80) cc_final: 0.8572 (m-80) REVERT: A 257 ASP cc_start: 0.9005 (m-30) cc_final: 0.8777 (m-30) REVERT: A 325 LYS cc_start: 0.9549 (mmmt) cc_final: 0.9092 (mmtp) REVERT: A 335 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8025 (mt-10) REVERT: A 383 SER cc_start: 0.8922 (p) cc_final: 0.8710 (p) REVERT: A 396 ASP cc_start: 0.8228 (p0) cc_final: 0.8025 (p0) REVERT: A 402 GLU cc_start: 0.8182 (tp30) cc_final: 0.7979 (tp30) REVERT: A 447 ASN cc_start: 0.7994 (m-40) cc_final: 0.7427 (t0) REVERT: A 459 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.9020 (mtmm) REVERT: A 471 TYR cc_start: 0.8980 (t80) cc_final: 0.8594 (t80) REVERT: A 515 ASP cc_start: 0.9179 (m-30) cc_final: 0.8885 (m-30) REVERT: A 526 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8657 (mp0) REVERT: A 528 PHE cc_start: 0.8879 (m-80) cc_final: 0.8643 (m-80) REVERT: A 546 LEU cc_start: 0.9750 (mt) cc_final: 0.9506 (mt) REVERT: A 590 SER cc_start: 0.9634 (t) cc_final: 0.8942 (p) REVERT: A 595 MET cc_start: 0.9302 (mmp) cc_final: 0.8931 (mmp) REVERT: A 615 MET cc_start: 0.9237 (mmt) cc_final: 0.8944 (mmm) REVERT: A 645 GLN cc_start: 0.8996 (tp40) cc_final: 0.8336 (tp-100) REVERT: A 647 HIS cc_start: 0.8790 (m-70) cc_final: 0.8094 (m90) REVERT: A 669 ARG cc_start: 0.9243 (tpp-160) cc_final: 0.8945 (tpp-160) REVERT: A 686 ARG cc_start: 0.8340 (ttm-80) cc_final: 0.8123 (ttm-80) REVERT: B 8 LYS cc_start: 0.9298 (tppt) cc_final: 0.9084 (tptm) REVERT: B 18 ILE cc_start: 0.9583 (mp) cc_final: 0.9280 (pt) REVERT: B 54 LYS cc_start: 0.9656 (tttt) cc_final: 0.9306 (tttt) REVERT: B 82 LYS cc_start: 0.9616 (mtpp) cc_final: 0.9247 (ptpp) REVERT: B 95 MET cc_start: 0.9098 (tpt) cc_final: 0.8685 (tpp) REVERT: B 99 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.8560 (tptp) REVERT: B 102 ASN cc_start: 0.9453 (m110) cc_final: 0.9202 (m110) REVERT: B 107 LYS cc_start: 0.9253 (mmmm) cc_final: 0.8866 (mmmm) REVERT: B 111 LYS cc_start: 0.9620 (mmtp) cc_final: 0.9417 (mmtm) REVERT: B 112 LYS cc_start: 0.9262 (pptt) cc_final: 0.9013 (pttm) REVERT: B 181 ASP cc_start: 0.8808 (m-30) cc_final: 0.8573 (m-30) REVERT: B 184 ARG cc_start: 0.9453 (tpp80) cc_final: 0.9204 (tpp80) REVERT: B 266 LYS cc_start: 0.9118 (mtpp) cc_final: 0.8773 (ptpp) REVERT: B 272 ASP cc_start: 0.8764 (p0) cc_final: 0.8426 (p0) REVERT: B 333 LYS cc_start: 0.9005 (tttm) cc_final: 0.8630 (tttm) REVERT: B 335 GLU cc_start: 0.8232 (mm-30) cc_final: 0.8031 (mp0) REVERT: B 341 LYS cc_start: 0.9626 (mmtm) cc_final: 0.8988 (mmmm) REVERT: B 348 MET cc_start: 0.8782 (tmm) cc_final: 0.8384 (tpt) REVERT: B 362 ASP cc_start: 0.8654 (m-30) cc_final: 0.8250 (m-30) REVERT: B 375 LYS cc_start: 0.9162 (mmmm) cc_final: 0.8903 (mmmm) REVERT: B 393 SER cc_start: 0.9318 (m) cc_final: 0.8875 (p) REVERT: B 402 GLU cc_start: 0.8163 (tm-30) cc_final: 0.7498 (tm-30) REVERT: B 431 LEU cc_start: 0.9472 (mm) cc_final: 0.9248 (mm) REVERT: B 471 TYR cc_start: 0.9194 (t80) cc_final: 0.8983 (t80) REVERT: B 475 ASN cc_start: 0.9194 (m-40) cc_final: 0.8747 (m110) REVERT: B 515 ASP cc_start: 0.9281 (m-30) cc_final: 0.8746 (m-30) REVERT: B 522 TYR cc_start: 0.8939 (m-10) cc_final: 0.8683 (m-10) REVERT: B 548 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7689 (mm-30) REVERT: B 558 TRP cc_start: 0.9489 (m100) cc_final: 0.8766 (m100) REVERT: B 583 SER cc_start: 0.8965 (m) cc_final: 0.8399 (p) REVERT: B 588 GLN cc_start: 0.9394 (mm110) cc_final: 0.9100 (mm110) REVERT: B 595 MET cc_start: 0.9355 (mmp) cc_final: 0.9091 (mmm) REVERT: B 599 GLU cc_start: 0.9027 (pm20) cc_final: 0.8754 (pm20) REVERT: B 620 SER cc_start: 0.9323 (OUTLIER) cc_final: 0.9101 (p) REVERT: B 632 MET cc_start: 0.8513 (mtm) cc_final: 0.8190 (mtm) REVERT: B 645 GLN cc_start: 0.9316 (tp-100) cc_final: 0.8884 (tp40) REVERT: B 668 ASN cc_start: 0.8988 (m110) cc_final: 0.8490 (m-40) REVERT: C 21 PHE cc_start: 0.9375 (m-80) cc_final: 0.9047 (m-80) REVERT: C 90 LEU cc_start: 0.9122 (mt) cc_final: 0.8817 (mt) REVERT: C 92 PHE cc_start: 0.9527 (t80) cc_final: 0.9225 (t80) REVERT: C 95 MET cc_start: 0.9108 (tmm) cc_final: 0.8891 (tmm) REVERT: C 109 PHE cc_start: 0.8378 (m-10) cc_final: 0.8146 (m-10) REVERT: C 133 LYS cc_start: 0.9330 (tptt) cc_final: 0.9108 (tppt) REVERT: C 153 LEU cc_start: 0.9493 (mt) cc_final: 0.9206 (mt) REVERT: C 155 LYS cc_start: 0.8826 (mttt) cc_final: 0.8493 (mmtt) REVERT: C 174 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.7692 (t80) REVERT: C 197 ASP cc_start: 0.9597 (m-30) cc_final: 0.9087 (m-30) REVERT: C 236 TYR cc_start: 0.9397 (t80) cc_final: 0.9144 (t80) REVERT: C 237 GLU cc_start: 0.9248 (pp20) cc_final: 0.9017 (pp20) REVERT: C 242 TYR cc_start: 0.9478 (t80) cc_final: 0.8563 (t80) REVERT: C 259 PHE cc_start: 0.9029 (t80) cc_final: 0.8283 (t80) REVERT: C 263 ASN cc_start: 0.9596 (m-40) cc_final: 0.8533 (p0) REVERT: C 314 PRO cc_start: 0.9130 (Cg_exo) cc_final: 0.8698 (Cg_endo) REVERT: D 30 TRP cc_start: 0.8289 (p-90) cc_final: 0.8008 (p-90) REVERT: D 46 TYR cc_start: 0.9316 (m-80) cc_final: 0.8779 (m-10) REVERT: D 50 ASN cc_start: 0.8977 (m-40) cc_final: 0.8650 (p0) REVERT: D 96 MET cc_start: 0.8161 (mmm) cc_final: 0.7798 (mmm) REVERT: D 131 LEU cc_start: 0.8672 (tt) cc_final: 0.8337 (tp) REVERT: D 168 PHE cc_start: 0.8445 (m-80) cc_final: 0.7881 (m-80) REVERT: D 172 PHE cc_start: 0.8882 (m-80) cc_final: 0.8218 (m-80) REVERT: D 174 TYR cc_start: 0.8357 (t80) cc_final: 0.7810 (t80) REVERT: D 185 MET cc_start: 0.6459 (mmm) cc_final: 0.6124 (mmm) REVERT: D 242 TYR cc_start: 0.8816 (t80) cc_final: 0.8528 (t80) REVERT: D 254 HIS cc_start: 0.9008 (m90) cc_final: 0.8795 (m-70) REVERT: D 268 LEU cc_start: 0.8896 (mm) cc_final: 0.8674 (mt) outliers start: 70 outliers final: 36 residues processed: 809 average time/residue: 0.2752 time to fit residues: 327.7959 Evaluate side-chains 759 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 719 time to evaluate : 1.778 ------------------------------------------------------------------------------- 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 194 LYS 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 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 232 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 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 25 ASN Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 210 GLN Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 180 optimal weight: 0.0470 chunk 99 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 69 optimal weight: 0.1980 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 148 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 8.9990 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 GLN A 232 ASN A 239 GLN A 304 HIS A 313 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** C 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 216 GLN C 270 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.092110 restraints weight = 40383.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.095341 restraints weight = 20724.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.097608 restraints weight = 13001.941| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3149 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.6115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16386 Z= 0.146 Angle : 0.738 13.620 22134 Z= 0.373 Chirality : 0.048 0.218 2360 Planarity : 0.004 0.049 2818 Dihedral : 10.933 163.215 2246 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.96 % Allowed : 26.05 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.19), residues: 1932 helix: 1.15 (0.15), residues: 1104 sheet: -0.39 (0.38), residues: 162 loop : 0.31 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 558 HIS 0.009 0.001 HIS D 201 PHE 0.040 0.002 PHE C 168 TYR 0.033 0.002 TYR D 142 ARG 0.011 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04335 ( 871) hydrogen bonds : angle 5.20620 ( 2571) covalent geometry : bond 0.00322 (16386) covalent geometry : angle 0.73758 (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 807 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 739 time to evaluate : 1.825 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: A 31 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8755 (pm20) REVERT: A 51 LEU cc_start: 0.9148 (tp) cc_final: 0.8934 (mp) REVERT: A 82 LYS cc_start: 0.9498 (mttm) cc_final: 0.9260 (mmtt) REVERT: A 117 ARG cc_start: 0.8734 (mmm-85) cc_final: 0.8228 (mmm-85) REVERT: A 138 LYS cc_start: 0.9263 (mmtt) cc_final: 0.9023 (mmtp) REVERT: A 147 GLN cc_start: 0.9049 (mt0) cc_final: 0.8499 (mt0) REVERT: A 161 ARG cc_start: 0.8353 (ttm110) cc_final: 0.7741 (ptp-170) REVERT: A 209 LYS cc_start: 0.8867 (tptt) cc_final: 0.8615 (tppt) REVERT: A 294 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8785 (mm-30) REVERT: A 301 PHE cc_start: 0.8795 (m-10) cc_final: 0.8527 (m-10) REVERT: A 325 LYS cc_start: 0.9570 (mmmt) cc_final: 0.9349 (mmtp) REVERT: A 383 SER cc_start: 0.8839 (p) cc_final: 0.8635 (p) REVERT: A 402 GLU cc_start: 0.8026 (tp30) cc_final: 0.7797 (tp30) REVERT: A 403 ILE cc_start: 0.9171 (mm) cc_final: 0.8820 (mm) REVERT: A 456 LYS cc_start: 0.9275 (ptpp) cc_final: 0.8998 (ptpp) REVERT: A 459 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.8771 (mtmm) REVERT: A 471 TYR cc_start: 0.9051 (t80) cc_final: 0.8586 (t80) REVERT: A 515 ASP cc_start: 0.9101 (m-30) cc_final: 0.8775 (m-30) REVERT: A 546 LEU cc_start: 0.9668 (mt) cc_final: 0.9400 (mt) REVERT: A 590 SER cc_start: 0.9588 (t) cc_final: 0.9072 (p) REVERT: A 595 MET cc_start: 0.9194 (mmp) cc_final: 0.8780 (mmp) REVERT: A 600 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8301 (mtt-85) REVERT: A 639 ASP cc_start: 0.8583 (m-30) cc_final: 0.8203 (m-30) REVERT: A 640 MET cc_start: 0.9232 (tpp) cc_final: 0.8910 (tpp) REVERT: A 645 GLN cc_start: 0.8953 (tp40) cc_final: 0.8463 (tp-100) REVERT: A 647 HIS cc_start: 0.8638 (m-70) cc_final: 0.8042 (m90) REVERT: A 650 GLN cc_start: 0.8899 (mt0) cc_final: 0.8634 (mt0) REVERT: A 665 ARG cc_start: 0.9206 (OUTLIER) cc_final: 0.8297 (ttt-90) REVERT: A 669 ARG cc_start: 0.9277 (tpp-160) cc_final: 0.9029 (tpp-160) REVERT: B 82 LYS cc_start: 0.9593 (mtpp) cc_final: 0.9132 (ptpp) REVERT: B 95 MET cc_start: 0.9048 (tpt) cc_final: 0.8503 (tpp) REVERT: B 99 LYS cc_start: 0.9358 (OUTLIER) cc_final: 0.8694 (tptp) REVERT: B 102 ASN cc_start: 0.9458 (m110) cc_final: 0.9198 (m110) REVERT: B 106 LEU cc_start: 0.9065 (tt) cc_final: 0.8639 (tt) REVERT: B 161 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8644 (mtt-85) REVERT: B 181 ASP cc_start: 0.8774 (m-30) cc_final: 0.8474 (m-30) REVERT: B 184 ARG cc_start: 0.9491 (tpp80) cc_final: 0.9273 (tpp80) REVERT: B 235 ARG cc_start: 0.8976 (mtm110) cc_final: 0.8623 (ptp-110) REVERT: B 236 TYR cc_start: 0.9235 (t80) cc_final: 0.8375 (t80) REVERT: B 266 LYS cc_start: 0.9062 (mtpp) cc_final: 0.8766 (ptpp) REVERT: B 322 MET cc_start: 0.9035 (mmt) cc_final: 0.8783 (mmm) REVERT: B 333 LYS cc_start: 0.9036 (tttm) cc_final: 0.8665 (tttm) REVERT: B 341 LYS cc_start: 0.9275 (mmtm) cc_final: 0.9030 (mmmt) REVERT: B 348 MET cc_start: 0.8797 (tmm) cc_final: 0.8312 (tpt) REVERT: B 362 ASP cc_start: 0.8537 (m-30) cc_final: 0.8159 (m-30) REVERT: B 375 LYS cc_start: 0.9208 (mmmm) cc_final: 0.8909 (mmmm) REVERT: B 393 SER cc_start: 0.9352 (m) cc_final: 0.8948 (p) REVERT: B 402 GLU cc_start: 0.8264 (tm-30) cc_final: 0.7677 (tm-30) REVERT: B 475 ASN cc_start: 0.9169 (m-40) cc_final: 0.8889 (m110) REVERT: B 483 GLU cc_start: 0.9473 (mp0) cc_final: 0.9125 (mp0) REVERT: B 515 ASP cc_start: 0.9224 (m-30) cc_final: 0.8684 (m-30) REVERT: B 526 GLU cc_start: 0.8837 (mp0) cc_final: 0.8634 (mm-30) REVERT: B 548 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7589 (mm-30) REVERT: B 558 TRP cc_start: 0.9482 (m100) cc_final: 0.8791 (m100) REVERT: B 570 MET cc_start: 0.7006 (mtm) cc_final: 0.6729 (mtm) REVERT: B 573 SER cc_start: 0.9696 (OUTLIER) cc_final: 0.9324 (p) REVERT: B 583 SER cc_start: 0.8985 (m) cc_final: 0.8492 (p) REVERT: B 588 GLN cc_start: 0.9230 (mm110) cc_final: 0.9027 (mm-40) REVERT: B 595 MET cc_start: 0.9301 (OUTLIER) cc_final: 0.9092 (mmm) REVERT: B 602 GLU cc_start: 0.8389 (pt0) cc_final: 0.8045 (pt0) REVERT: B 645 GLN cc_start: 0.9348 (tp40) cc_final: 0.8862 (tp40) REVERT: B 668 ASN cc_start: 0.9082 (m110) cc_final: 0.8590 (m-40) REVERT: B 686 ARG cc_start: 0.8326 (ttm170) cc_final: 0.8022 (mpt-90) REVERT: C 20 MET cc_start: 0.9464 (tmm) cc_final: 0.9226 (tmm) REVERT: C 21 PHE cc_start: 0.9395 (m-80) cc_final: 0.8745 (m-80) REVERT: C 55 TYR cc_start: 0.8927 (t80) cc_final: 0.8415 (m-80) REVERT: C 74 MET cc_start: 0.8596 (mtt) cc_final: 0.8289 (mtm) REVERT: C 90 LEU cc_start: 0.9192 (mt) cc_final: 0.8575 (mt) REVERT: C 92 PHE cc_start: 0.9556 (t80) cc_final: 0.9259 (t80) REVERT: C 101 HIS cc_start: 0.8277 (m170) cc_final: 0.7950 (m170) REVERT: C 109 PHE cc_start: 0.8302 (m-10) cc_final: 0.8044 (m-10) REVERT: C 155 LYS cc_start: 0.9037 (mttt) cc_final: 0.8656 (mmtt) REVERT: C 174 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.7227 (t80) REVERT: C 178 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8574 (t80) REVERT: C 194 ILE cc_start: 0.9554 (mt) cc_final: 0.8931 (tp) REVERT: C 198 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8611 (mm-30) REVERT: C 242 TYR cc_start: 0.9406 (t80) cc_final: 0.8629 (t80) REVERT: C 246 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8720 (mm) REVERT: C 259 PHE cc_start: 0.9036 (t80) cc_final: 0.8337 (t80) REVERT: C 260 ILE cc_start: 0.8881 (pt) cc_final: 0.8465 (pp) REVERT: C 263 ASN cc_start: 0.9548 (m-40) cc_final: 0.9211 (p0) REVERT: C 266 LYS cc_start: 0.9449 (mttt) cc_final: 0.9101 (mmmt) REVERT: C 274 ASP cc_start: 0.8074 (p0) cc_final: 0.7440 (p0) REVERT: C 314 PRO cc_start: 0.9282 (Cg_exo) cc_final: 0.8722 (Cg_endo) REVERT: D 46 TYR cc_start: 0.9203 (m-80) cc_final: 0.8804 (m-10) REVERT: D 92 PHE cc_start: 0.7719 (t80) cc_final: 0.7458 (t80) REVERT: D 96 MET cc_start: 0.8302 (mmm) cc_final: 0.7901 (mmm) REVERT: D 129 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8956 (ptpp) REVERT: D 131 LEU cc_start: 0.8750 (tt) cc_final: 0.8399 (tp) REVERT: D 168 PHE cc_start: 0.8352 (m-80) cc_final: 0.7630 (m-80) REVERT: D 172 PHE cc_start: 0.8731 (m-80) cc_final: 0.7878 (m-80) REVERT: D 173 TYR cc_start: 0.7516 (t80) cc_final: 0.7233 (t80) REVERT: D 242 TYR cc_start: 0.8716 (t80) cc_final: 0.8476 (t80) REVERT: D 268 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8459 (mp) outliers start: 68 outliers final: 36 residues processed: 764 average time/residue: 0.2708 time to fit residues: 302.8932 Evaluate side-chains 750 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 701 time to evaluate : 1.647 ------------------------------------------------------------------------------- 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 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 436 LEU 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 600 ARG Chi-restraints excluded: chain A residue 660 ASP Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 392 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 573 SER Chi-restraints excluded: chain B residue 595 MET 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 178 PHE Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 79 GLU Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 67 optimal weight: 4.9990 chunk 41 optimal weight: 0.0670 chunk 57 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 51 optimal weight: 0.0050 chunk 175 optimal weight: 4.9990 chunk 182 optimal weight: 0.7980 chunk 96 optimal weight: 0.4980 chunk 86 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.4732 ------------------------------------------------------------------------------- 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 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN D 28 GLN D 210 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.121635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.092874 restraints weight = 41370.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.096269 restraints weight = 20896.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.098525 restraints weight = 12834.285| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.6513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16386 Z= 0.140 Angle : 0.732 13.779 22134 Z= 0.369 Chirality : 0.046 0.253 2360 Planarity : 0.004 0.038 2818 Dihedral : 10.470 159.457 2246 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.55 % Allowed : 28.03 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.89 (0.19), residues: 1932 helix: 1.05 (0.15), residues: 1109 sheet: -0.54 (0.39), residues: 154 loop : 0.30 (0.23), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 30 HIS 0.005 0.001 HIS A 438 PHE 0.043 0.002 PHE C 172 TYR 0.048 0.002 TYR D 142 ARG 0.008 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04205 ( 871) hydrogen bonds : angle 5.16210 ( 2571) covalent geometry : bond 0.00314 (16386) covalent geometry : angle 0.73197 (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 794 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 733 time to evaluate : 1.959 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: A 31 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8799 (pm20) REVERT: A 138 LYS cc_start: 0.9302 (mmtt) cc_final: 0.9025 (mmtt) REVERT: A 147 GLN cc_start: 0.9086 (mt0) cc_final: 0.8554 (mm-40) REVERT: A 161 ARG cc_start: 0.8506 (ttm110) cc_final: 0.8002 (ptp-170) REVERT: A 205 LYS cc_start: 0.8705 (mttm) cc_final: 0.8125 (mtpp) REVERT: A 250 TYR cc_start: 0.8678 (m-80) cc_final: 0.8478 (m-80) REVERT: A 255 HIS cc_start: 0.8685 (t-90) cc_final: 0.8197 (t-90) REVERT: A 266 LYS cc_start: 0.8611 (ptmm) cc_final: 0.8038 (ptmm) REVERT: A 290 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8580 (tm-30) REVERT: A 294 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8785 (mm-30) REVERT: A 325 LYS cc_start: 0.9651 (mmmt) cc_final: 0.9367 (mmtp) REVERT: A 362 ASP cc_start: 0.8280 (m-30) cc_final: 0.7998 (m-30) REVERT: A 383 SER cc_start: 0.8811 (p) cc_final: 0.8604 (p) REVERT: A 402 GLU cc_start: 0.8118 (tp30) cc_final: 0.7909 (tp30) REVERT: A 403 ILE cc_start: 0.9140 (mm) cc_final: 0.8736 (mm) REVERT: A 420 MET cc_start: 0.9090 (mmm) cc_final: 0.8669 (mmm) REVERT: A 456 LYS cc_start: 0.9264 (ptpp) cc_final: 0.9050 (ptpp) REVERT: A 459 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.8829 (mtmm) REVERT: A 471 TYR cc_start: 0.9018 (t80) cc_final: 0.8605 (t80) REVERT: A 505 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8422 (mt-10) REVERT: A 515 ASP cc_start: 0.9146 (m-30) cc_final: 0.8807 (m-30) REVERT: A 546 LEU cc_start: 0.9676 (mt) cc_final: 0.9421 (mt) REVERT: A 590 SER cc_start: 0.9512 (t) cc_final: 0.9001 (p) REVERT: A 595 MET cc_start: 0.9208 (mmp) cc_final: 0.8747 (mmp) REVERT: A 600 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8285 (mtt-85) REVERT: A 606 TYR cc_start: 0.8104 (m-80) cc_final: 0.7682 (m-80) REVERT: A 639 ASP cc_start: 0.8555 (m-30) cc_final: 0.8160 (m-30) REVERT: A 645 GLN cc_start: 0.8906 (tp40) cc_final: 0.8472 (tp-100) REVERT: A 647 HIS cc_start: 0.8692 (m-70) cc_final: 0.8040 (m90) REVERT: A 650 GLN cc_start: 0.8902 (mt0) cc_final: 0.8212 (mm-40) REVERT: B 82 LYS cc_start: 0.9595 (mtpp) cc_final: 0.9126 (ptpp) REVERT: B 95 MET cc_start: 0.9092 (tpt) cc_final: 0.8382 (tpp) REVERT: B 99 LYS cc_start: 0.9314 (tptp) cc_final: 0.8757 (tptp) REVERT: B 102 ASN cc_start: 0.9488 (m110) cc_final: 0.9283 (m110) REVERT: B 112 LYS cc_start: 0.9277 (pptt) cc_final: 0.9019 (pttm) REVERT: B 119 GLU cc_start: 0.8994 (mp0) cc_final: 0.8401 (mp0) REVERT: B 181 ASP cc_start: 0.8796 (m-30) cc_final: 0.8488 (m-30) REVERT: B 235 ARG cc_start: 0.9017 (mtm110) cc_final: 0.8675 (ptp-110) REVERT: B 236 TYR cc_start: 0.9237 (t80) cc_final: 0.8354 (t80) REVERT: B 256 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8281 (tpt90) REVERT: B 266 LYS cc_start: 0.9100 (mtpp) cc_final: 0.8411 (ptpp) REVERT: B 274 ARG cc_start: 0.8620 (ttm110) cc_final: 0.8236 (ttm170) REVERT: B 317 MET cc_start: 0.8666 (pmm) cc_final: 0.8425 (pmm) REVERT: B 322 MET cc_start: 0.9052 (mmt) cc_final: 0.8830 (mmm) REVERT: B 333 LYS cc_start: 0.9149 (tttm) cc_final: 0.8826 (tttm) REVERT: B 348 MET cc_start: 0.8832 (tmm) cc_final: 0.8423 (tpt) REVERT: B 362 ASP cc_start: 0.8703 (m-30) cc_final: 0.8282 (m-30) REVERT: B 375 LYS cc_start: 0.9197 (mmmm) cc_final: 0.8882 (mmmm) REVERT: B 393 SER cc_start: 0.9322 (m) cc_final: 0.8909 (p) REVERT: B 402 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7751 (tm-30) REVERT: B 475 ASN cc_start: 0.9186 (m-40) cc_final: 0.8769 (m-40) REVERT: B 483 GLU cc_start: 0.9517 (mp0) cc_final: 0.9196 (mp0) REVERT: B 515 ASP cc_start: 0.9237 (m-30) cc_final: 0.8712 (m-30) REVERT: B 548 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7750 (mm-30) REVERT: B 558 TRP cc_start: 0.9504 (m100) cc_final: 0.8811 (m100) REVERT: B 583 SER cc_start: 0.9054 (m) cc_final: 0.8492 (p) REVERT: B 586 TYR cc_start: 0.9242 (m-80) cc_final: 0.8729 (m-80) REVERT: B 602 GLU cc_start: 0.8670 (pt0) cc_final: 0.7074 (pt0) REVERT: B 610 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8586 (ptmm) REVERT: B 632 MET cc_start: 0.8050 (mtm) cc_final: 0.7590 (mtt) REVERT: B 645 GLN cc_start: 0.9337 (tp40) cc_final: 0.8931 (tp-100) REVERT: B 668 ASN cc_start: 0.9133 (m110) cc_final: 0.8568 (m110) REVERT: B 686 ARG cc_start: 0.8384 (ttm170) cc_final: 0.8072 (mpt-90) REVERT: C 20 MET cc_start: 0.9504 (tmm) cc_final: 0.9234 (tmm) REVERT: C 21 PHE cc_start: 0.9512 (m-80) cc_final: 0.8753 (m-80) REVERT: C 55 TYR cc_start: 0.8943 (t80) cc_final: 0.8404 (m-80) REVERT: C 58 VAL cc_start: 0.8561 (OUTLIER) cc_final: 0.8209 (t) REVERT: C 74 MET cc_start: 0.8694 (mtt) cc_final: 0.8412 (mtt) REVERT: C 90 LEU cc_start: 0.8887 (mt) cc_final: 0.8676 (mt) REVERT: C 92 PHE cc_start: 0.9540 (t80) cc_final: 0.8849 (t80) REVERT: C 96 MET cc_start: 0.9094 (mmm) cc_final: 0.8463 (mmm) REVERT: C 109 PHE cc_start: 0.8316 (m-10) cc_final: 0.8109 (m-10) REVERT: C 137 MET cc_start: 0.9415 (tpt) cc_final: 0.9198 (mmm) REVERT: C 143 LYS cc_start: 0.8550 (tptt) cc_final: 0.8271 (tptp) REVERT: C 155 LYS cc_start: 0.9164 (mttt) cc_final: 0.8834 (mmtt) REVERT: C 174 TYR cc_start: 0.8221 (OUTLIER) cc_final: 0.7366 (t80) REVERT: C 178 PHE cc_start: 0.8920 (OUTLIER) cc_final: 0.8490 (t80) REVERT: C 185 MET cc_start: 0.8375 (mmm) cc_final: 0.8150 (mmm) REVERT: C 194 ILE cc_start: 0.9546 (mt) cc_final: 0.8891 (tp) REVERT: C 198 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8473 (mm-30) REVERT: C 242 TYR cc_start: 0.9452 (t80) cc_final: 0.8903 (t80) REVERT: C 259 PHE cc_start: 0.9114 (t80) cc_final: 0.8399 (t80) REVERT: C 260 ILE cc_start: 0.8907 (pt) cc_final: 0.8384 (pp) REVERT: C 263 ASN cc_start: 0.9593 (m-40) cc_final: 0.9328 (p0) REVERT: C 269 MET cc_start: 0.9627 (ptt) cc_final: 0.9223 (ptt) REVERT: C 274 ASP cc_start: 0.7973 (p0) cc_final: 0.7479 (p0) REVERT: C 314 PRO cc_start: 0.9240 (Cg_exo) cc_final: 0.8682 (Cg_endo) REVERT: D 46 TYR cc_start: 0.9232 (m-80) cc_final: 0.8819 (m-10) REVERT: D 51 GLU cc_start: 0.7938 (mm-30) cc_final: 0.7673 (mm-30) REVERT: D 131 LEU cc_start: 0.8877 (tt) cc_final: 0.8541 (tp) REVERT: D 168 PHE cc_start: 0.8334 (m-80) cc_final: 0.7444 (m-80) REVERT: D 169 TYR cc_start: 0.7583 (m-80) cc_final: 0.7043 (m-80) REVERT: D 174 TYR cc_start: 0.8487 (t80) cc_final: 0.7895 (t80) REVERT: D 242 TYR cc_start: 0.8847 (t80) cc_final: 0.8545 (t80) REVERT: D 268 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8440 (mt) outliers start: 61 outliers final: 38 residues processed: 757 average time/residue: 0.2956 time to fit residues: 333.1800 Evaluate side-chains 724 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 677 time to evaluate : 1.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 141 VAL 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 231 ASP 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 411 LEU 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 600 ARG Chi-restraints excluded: chain A residue 632 MET Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 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 B residue 610 LYS Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 168 PHE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 178 PHE Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 210 GLN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 31 optimal weight: 5.9990 chunk 126 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 69 optimal weight: 0.0870 chunk 156 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 115 optimal weight: 0.5980 chunk 39 optimal weight: 7.9990 chunk 169 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 177 optimal weight: 0.5980 overall best weight: 0.8160 ------------------------------------------------------------------------------- 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** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 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 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN C 234 GLN ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** 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 = 0.3639 r_free = 0.3639 target = 0.119537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.091489 restraints weight = 41536.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.094835 restraints weight = 21044.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.097102 restraints weight = 12947.028| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 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 = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.6877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16386 Z= 0.148 Angle : 0.748 14.584 22134 Z= 0.375 Chirality : 0.047 0.280 2360 Planarity : 0.004 0.050 2818 Dihedral : 10.091 152.557 2246 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 3.67 % Allowed : 30.30 % Favored : 66.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.18), residues: 1932 helix: 1.01 (0.15), residues: 1123 sheet: -0.30 (0.40), residues: 146 loop : 0.20 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 30 HIS 0.007 0.001 HIS C 101 PHE 0.035 0.002 PHE C 172 TYR 0.030 0.002 TYR B 574 ARG 0.011 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.04173 ( 871) hydrogen bonds : angle 5.19783 ( 2571) covalent geometry : bond 0.00339 (16386) covalent geometry : angle 0.74833 (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 790 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 727 time to evaluate : 1.913 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: 0.9151 (mt-10) cc_final: 0.8783 (pm20) REVERT: A 56 ASP cc_start: 0.8994 (m-30) cc_final: 0.8585 (m-30) REVERT: A 138 LYS cc_start: 0.9316 (mmtt) cc_final: 0.9041 (mmtt) REVERT: A 147 GLN cc_start: 0.9158 (mt0) cc_final: 0.8560 (mm-40) REVERT: A 161 ARG cc_start: 0.8511 (ttm110) cc_final: 0.7850 (ptp-170) REVERT: A 172 LEU cc_start: 0.8827 (mt) cc_final: 0.8626 (mt) REVERT: A 184 ARG cc_start: 0.9151 (mmm-85) cc_final: 0.8944 (mmm-85) REVERT: A 205 LYS cc_start: 0.8646 (mttm) cc_final: 0.8065 (mtpp) REVERT: A 221 LYS cc_start: 0.8732 (mmtp) cc_final: 0.8528 (mttm) REVERT: A 250 TYR cc_start: 0.8745 (m-80) cc_final: 0.8519 (m-80) REVERT: A 266 LYS cc_start: 0.8615 (ptmm) cc_final: 0.8014 (ptmm) REVERT: A 290 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8652 (tm-30) REVERT: A 325 LYS cc_start: 0.9676 (mmmt) cc_final: 0.9414 (mmtp) REVERT: A 384 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8213 (pm20) REVERT: A 402 GLU cc_start: 0.8173 (tp30) cc_final: 0.7919 (tp30) REVERT: A 403 ILE cc_start: 0.9102 (mm) cc_final: 0.8704 (mm) REVERT: A 413 SER cc_start: 0.9489 (m) cc_final: 0.9113 (t) REVERT: A 420 MET cc_start: 0.9102 (mmm) cc_final: 0.8712 (mmm) REVERT: A 456 LYS cc_start: 0.9236 (ptpp) cc_final: 0.8974 (ptpp) REVERT: A 459 LYS cc_start: 0.9326 (OUTLIER) cc_final: 0.8861 (mtmm) REVERT: A 471 TYR cc_start: 0.9075 (t80) cc_final: 0.8739 (t80) REVERT: A 505 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8583 (mt-10) REVERT: A 515 ASP cc_start: 0.9114 (m-30) cc_final: 0.8805 (m-30) REVERT: A 546 LEU cc_start: 0.9667 (mt) cc_final: 0.9435 (mt) REVERT: A 590 SER cc_start: 0.9487 (t) cc_final: 0.8894 (p) REVERT: A 600 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.8115 (mtt180) REVERT: A 606 TYR cc_start: 0.8130 (m-80) cc_final: 0.7689 (m-80) REVERT: A 639 ASP cc_start: 0.8579 (m-30) cc_final: 0.8157 (m-30) REVERT: A 640 MET cc_start: 0.9425 (tpp) cc_final: 0.9052 (tpp) REVERT: A 645 GLN cc_start: 0.8949 (tp40) cc_final: 0.8708 (tp40) REVERT: A 650 GLN cc_start: 0.8717 (mt0) cc_final: 0.8292 (mm-40) REVERT: A 686 ARG cc_start: 0.8277 (ttm110) cc_final: 0.7503 (mtp-110) REVERT: B 8 LYS cc_start: 0.9210 (tptm) cc_final: 0.8982 (tptm) REVERT: B 82 LYS cc_start: 0.9581 (mtpp) cc_final: 0.9114 (ptpp) REVERT: B 95 MET cc_start: 0.9029 (tpt) cc_final: 0.8259 (tpp) REVERT: B 99 LYS cc_start: 0.9301 (tptp) cc_final: 0.8793 (tptp) REVERT: B 112 LYS cc_start: 0.9271 (pptt) cc_final: 0.8979 (pttm) REVERT: B 119 GLU cc_start: 0.8982 (mp0) cc_final: 0.8388 (mp0) REVERT: B 161 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.8808 (mtt-85) REVERT: B 168 VAL cc_start: 0.9331 (t) cc_final: 0.9081 (m) REVERT: B 181 ASP cc_start: 0.8913 (m-30) cc_final: 0.8161 (m-30) REVERT: B 234 PHE cc_start: 0.9420 (m-80) cc_final: 0.9162 (m-10) REVERT: B 235 ARG cc_start: 0.9014 (mtm110) cc_final: 0.8725 (ptp-110) REVERT: B 256 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8369 (tpt90) REVERT: B 266 LYS cc_start: 0.9126 (mtpp) cc_final: 0.8415 (ptpp) REVERT: B 274 ARG cc_start: 0.8609 (ttm110) cc_final: 0.8266 (ttm170) REVERT: B 317 MET cc_start: 0.8729 (pmm) cc_final: 0.8453 (pmm) REVERT: B 322 MET cc_start: 0.9120 (mmt) cc_final: 0.8845 (mmm) REVERT: B 333 LYS cc_start: 0.9138 (tttm) cc_final: 0.8831 (tttm) REVERT: B 348 MET cc_start: 0.8841 (tmm) cc_final: 0.8392 (tpt) REVERT: B 358 ILE cc_start: 0.9593 (mm) cc_final: 0.9162 (tp) REVERT: B 362 ASP cc_start: 0.8693 (m-30) cc_final: 0.8300 (m-30) REVERT: B 375 LYS cc_start: 0.9188 (mmmm) cc_final: 0.8895 (mmmm) REVERT: B 384 GLU cc_start: 0.8556 (pm20) cc_final: 0.8029 (pm20) REVERT: B 402 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8216 (tm-30) REVERT: B 475 ASN cc_start: 0.9206 (m-40) cc_final: 0.8877 (m-40) REVERT: B 483 GLU cc_start: 0.9522 (mp0) cc_final: 0.9213 (mp0) REVERT: B 515 ASP cc_start: 0.9222 (m-30) cc_final: 0.8722 (m-30) REVERT: B 548 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7682 (mm-30) REVERT: B 558 TRP cc_start: 0.9500 (m100) cc_final: 0.8755 (m100) REVERT: B 573 SER cc_start: 0.9213 (OUTLIER) cc_final: 0.8942 (p) REVERT: B 583 SER cc_start: 0.9035 (m) cc_final: 0.8518 (p) REVERT: B 586 TYR cc_start: 0.9213 (m-80) cc_final: 0.8653 (m-80) REVERT: B 645 GLN cc_start: 0.9338 (tp40) cc_final: 0.8938 (tp40) REVERT: B 668 ASN cc_start: 0.9118 (m110) cc_final: 0.8578 (m110) REVERT: B 683 TYR cc_start: 0.8844 (t80) cc_final: 0.8366 (t80) REVERT: B 686 ARG cc_start: 0.8414 (ttm170) cc_final: 0.8001 (mpt-90) REVERT: C 20 MET cc_start: 0.9528 (tmm) cc_final: 0.9249 (tmm) REVERT: C 21 PHE cc_start: 0.9542 (m-80) cc_final: 0.8812 (m-80) REVERT: C 74 MET cc_start: 0.8695 (mtt) cc_final: 0.8398 (mtt) REVERT: C 92 PHE cc_start: 0.9586 (t80) cc_final: 0.9056 (t80) REVERT: C 96 MET cc_start: 0.9027 (mmm) cc_final: 0.8487 (mmm) REVERT: C 109 PHE cc_start: 0.8342 (m-10) cc_final: 0.8062 (m-10) REVERT: C 143 LYS cc_start: 0.8610 (tptt) cc_final: 0.8334 (tptp) REVERT: C 155 LYS cc_start: 0.9224 (mttt) cc_final: 0.8912 (mmtt) REVERT: C 174 TYR cc_start: 0.8059 (OUTLIER) cc_final: 0.7674 (t80) REVERT: C 185 MET cc_start: 0.8545 (mmm) cc_final: 0.8341 (mmm) REVERT: C 198 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8470 (mm-30) REVERT: C 252 LEU cc_start: 0.7839 (mp) cc_final: 0.7089 (tt) REVERT: C 259 PHE cc_start: 0.9265 (t80) cc_final: 0.8598 (t80) REVERT: C 260 ILE cc_start: 0.8889 (pt) cc_final: 0.8344 (pp) REVERT: C 263 ASN cc_start: 0.9592 (m-40) cc_final: 0.9329 (p0) REVERT: C 269 MET cc_start: 0.9546 (ptt) cc_final: 0.9220 (mmt) REVERT: C 274 ASP cc_start: 0.8009 (p0) cc_final: 0.7546 (p0) REVERT: C 314 PRO cc_start: 0.9301 (Cg_exo) cc_final: 0.8765 (Cg_endo) REVERT: D 46 TYR cc_start: 0.9244 (m-80) cc_final: 0.8858 (m-10) REVERT: D 71 ASN cc_start: 0.9391 (m-40) cc_final: 0.9122 (m110) REVERT: D 131 LEU cc_start: 0.8936 (tt) cc_final: 0.8620 (tp) REVERT: D 168 PHE cc_start: 0.8453 (m-80) cc_final: 0.7433 (m-80) REVERT: D 169 TYR cc_start: 0.7923 (m-80) cc_final: 0.7467 (m-80) REVERT: D 174 TYR cc_start: 0.8739 (t80) cc_final: 0.8087 (t80) REVERT: D 242 TYR cc_start: 0.8904 (t80) cc_final: 0.8564 (t80) REVERT: D 268 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8365 (mt) outliers start: 63 outliers final: 43 residues processed: 754 average time/residue: 0.2814 time to fit residues: 312.1002 Evaluate side-chains 726 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 675 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 58 LEU 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 182 ILE 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 306 ILE 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 459 LYS Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 552 ILE 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 B residue 33 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 343 LEU 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 B residue 573 SER Chi-restraints excluded: chain B residue 591 THR 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 312 VAL Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 154 PHE 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 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: 3.9990 chunk 85 optimal weight: 4.9990 chunk 161 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 146 optimal weight: 6.9990 chunk 184 optimal weight: 0.9980 chunk 119 optimal weight: 0.9980 chunk 175 optimal weight: 0.7980 chunk 24 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 HIS B 102 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 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 ** 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 = 0.3596 r_free = 0.3596 target = 0.116231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.088526 restraints weight = 41645.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.091636 restraints weight = 21101.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.093897 restraints weight = 12994.797| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.7215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16386 Z= 0.175 Angle : 0.781 17.460 22134 Z= 0.392 Chirality : 0.048 0.265 2360 Planarity : 0.004 0.042 2818 Dihedral : 10.050 143.359 2246 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.20 % Allowed : 31.00 % Favored : 64.80 % 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: 0.72 (0.18), residues: 1932 helix: 0.96 (0.15), residues: 1110 sheet: -0.63 (0.41), residues: 136 loop : 0.12 (0.23), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 30 HIS 0.008 0.001 HIS C 101 PHE 0.034 0.002 PHE C 172 TYR 0.030 0.002 TYR B 574 ARG 0.011 0.001 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.04227 ( 871) hydrogen bonds : angle 5.26889 ( 2571) covalent geometry : bond 0.00396 (16386) covalent geometry : angle 0.78143 (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 781 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 709 time to evaluate : 1.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8776 (pm20) REVERT: A 56 ASP cc_start: 0.8928 (m-30) cc_final: 0.8464 (m-30) REVERT: A 147 GLN cc_start: 0.9221 (mt0) cc_final: 0.8663 (mt0) REVERT: A 150 GLN cc_start: 0.9415 (tp40) cc_final: 0.8899 (tp40) REVERT: A 161 ARG cc_start: 0.8559 (ttm110) cc_final: 0.7751 (ptp-170) REVERT: A 205 LYS cc_start: 0.8666 (mttm) cc_final: 0.8310 (mtpt) REVERT: A 250 TYR cc_start: 0.8742 (m-80) cc_final: 0.8512 (m-80) REVERT: A 255 HIS cc_start: 0.8714 (t-90) cc_final: 0.8381 (t-90) REVERT: A 290 GLU cc_start: 0.9018 (tm-30) cc_final: 0.8566 (tm-30) REVERT: A 325 LYS cc_start: 0.9663 (mmmt) cc_final: 0.9402 (mmtp) REVERT: A 384 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8293 (pm20) REVERT: A 403 ILE cc_start: 0.9107 (mm) cc_final: 0.8605 (mm) REVERT: A 413 SER cc_start: 0.9494 (OUTLIER) cc_final: 0.9072 (t) REVERT: A 446 ARG cc_start: 0.7297 (mmm-85) cc_final: 0.6983 (mmm-85) REVERT: A 459 LYS cc_start: 0.9367 (OUTLIER) cc_final: 0.8835 (mtmm) REVERT: A 471 TYR cc_start: 0.9179 (t80) cc_final: 0.8974 (t80) REVERT: A 505 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8320 (mt-10) REVERT: A 515 ASP cc_start: 0.9164 (m-30) cc_final: 0.8888 (m-30) REVERT: A 590 SER cc_start: 0.9462 (t) cc_final: 0.9035 (p) REVERT: A 606 TYR cc_start: 0.8080 (m-80) cc_final: 0.7773 (m-80) REVERT: A 639 ASP cc_start: 0.8568 (m-30) cc_final: 0.8162 (m-30) REVERT: A 640 MET cc_start: 0.9462 (tpp) cc_final: 0.8972 (tpp) REVERT: A 645 GLN cc_start: 0.9052 (tp40) cc_final: 0.8819 (tp40) REVERT: A 683 TYR cc_start: 0.8662 (t80) cc_final: 0.8313 (t80) REVERT: A 686 ARG cc_start: 0.8246 (ttm110) cc_final: 0.7586 (mtp-110) REVERT: B 8 LYS cc_start: 0.9224 (tptm) cc_final: 0.9009 (tptm) REVERT: B 79 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8869 (mm-30) REVERT: B 82 LYS cc_start: 0.9572 (mtpp) cc_final: 0.9226 (ptpp) REVERT: B 95 MET cc_start: 0.9059 (tpt) cc_final: 0.8204 (tpp) REVERT: B 99 LYS cc_start: 0.9344 (tptp) cc_final: 0.8878 (tptp) REVERT: B 119 GLU cc_start: 0.9074 (mp0) cc_final: 0.8516 (mp0) REVERT: B 128 PHE cc_start: 0.9729 (t80) cc_final: 0.9451 (t80) REVERT: B 161 ARG cc_start: 0.9108 (OUTLIER) cc_final: 0.8818 (mtt-85) REVERT: B 181 ASP cc_start: 0.8771 (m-30) cc_final: 0.8515 (m-30) REVERT: B 235 ARG cc_start: 0.9067 (mtm110) cc_final: 0.8814 (ptp-110) REVERT: B 256 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8504 (ttp80) REVERT: B 263 ASP cc_start: 0.9222 (m-30) cc_final: 0.8704 (p0) REVERT: B 266 LYS cc_start: 0.9185 (mtpp) cc_final: 0.8288 (ptpp) REVERT: B 274 ARG cc_start: 0.8593 (ttm110) cc_final: 0.8208 (ttm170) REVERT: B 317 MET cc_start: 0.8663 (pmm) cc_final: 0.8404 (pmm) REVERT: B 333 LYS cc_start: 0.9065 (tttm) cc_final: 0.8753 (tttm) REVERT: B 348 MET cc_start: 0.8890 (tmm) cc_final: 0.8510 (tpt) REVERT: B 350 ARG cc_start: 0.9002 (mtp85) cc_final: 0.8407 (mtp85) REVERT: B 358 ILE cc_start: 0.9604 (mm) cc_final: 0.9139 (tp) REVERT: B 362 ASP cc_start: 0.8679 (m-30) cc_final: 0.8242 (m-30) REVERT: B 375 LYS cc_start: 0.9215 (mmmm) cc_final: 0.8879 (mmmm) REVERT: B 394 TYR cc_start: 0.9148 (m-80) cc_final: 0.8918 (m-80) REVERT: B 402 GLU cc_start: 0.8623 (tm-30) cc_final: 0.8193 (tm-30) REVERT: B 483 GLU cc_start: 0.9487 (mp0) cc_final: 0.9157 (mp0) REVERT: B 515 ASP cc_start: 0.9223 (m-30) cc_final: 0.8723 (m-30) REVERT: B 548 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7870 (mm-30) REVERT: B 558 TRP cc_start: 0.9474 (m100) cc_final: 0.8859 (m100) REVERT: B 570 MET cc_start: 0.8191 (mtp) cc_final: 0.7945 (mtp) REVERT: B 583 SER cc_start: 0.9126 (m) cc_final: 0.8664 (p) REVERT: B 586 TYR cc_start: 0.9247 (m-80) cc_final: 0.8533 (m-80) REVERT: B 610 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8619 (ptmm) REVERT: B 632 MET cc_start: 0.7847 (mtm) cc_final: 0.7557 (mtt) REVERT: B 634 MET cc_start: 0.8851 (mmm) cc_final: 0.8588 (mmt) REVERT: B 645 GLN cc_start: 0.9394 (tp40) cc_final: 0.8944 (tp40) REVERT: B 668 ASN cc_start: 0.9092 (m110) cc_final: 0.8537 (m110) REVERT: C 20 MET cc_start: 0.9551 (tmm) cc_final: 0.9259 (tmm) REVERT: C 21 PHE cc_start: 0.9549 (m-80) cc_final: 0.8832 (m-80) REVERT: C 74 MET cc_start: 0.8707 (mtt) cc_final: 0.8478 (mtt) REVERT: C 92 PHE cc_start: 0.9624 (t80) cc_final: 0.9112 (t80) REVERT: C 96 MET cc_start: 0.9012 (mmm) cc_final: 0.8506 (mmm) REVERT: C 109 PHE cc_start: 0.8173 (m-10) cc_final: 0.7899 (m-10) REVERT: C 143 LYS cc_start: 0.8656 (tptt) cc_final: 0.8395 (tptt) REVERT: C 155 LYS cc_start: 0.9341 (mttt) cc_final: 0.9062 (mmtt) REVERT: C 174 TYR cc_start: 0.7935 (OUTLIER) cc_final: 0.7726 (t80) REVERT: C 198 GLU cc_start: 0.9360 (mm-30) cc_final: 0.8803 (mm-30) REVERT: C 252 LEU cc_start: 0.7982 (mp) cc_final: 0.7145 (tt) REVERT: C 259 PHE cc_start: 0.9250 (t80) cc_final: 0.8699 (t80) REVERT: C 260 ILE cc_start: 0.8790 (pt) cc_final: 0.8387 (pp) REVERT: C 269 MET cc_start: 0.9519 (OUTLIER) cc_final: 0.9205 (mmt) REVERT: C 274 ASP cc_start: 0.8069 (p0) cc_final: 0.7640 (p0) REVERT: C 314 PRO cc_start: 0.9329 (Cg_exo) cc_final: 0.8814 (Cg_endo) REVERT: D 30 TRP cc_start: 0.8041 (p-90) cc_final: 0.7598 (p-90) REVERT: D 46 TYR cc_start: 0.9244 (m-80) cc_final: 0.8804 (m-10) REVERT: D 71 ASN cc_start: 0.9426 (m-40) cc_final: 0.9110 (m110) REVERT: D 137 MET cc_start: 0.8509 (mmt) cc_final: 0.8001 (mpp) REVERT: D 168 PHE cc_start: 0.8539 (m-80) cc_final: 0.7405 (m-80) REVERT: D 174 TYR cc_start: 0.8774 (t80) cc_final: 0.8114 (t80) REVERT: D 242 TYR cc_start: 0.8877 (t80) cc_final: 0.8606 (t80) REVERT: D 268 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8349 (mt) outliers start: 72 outliers final: 49 residues processed: 735 average time/residue: 0.2676 time to fit residues: 292.0079 Evaluate side-chains 719 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 660 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP 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 125 VAL 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 306 ILE 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 413 SER Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 632 MET 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 161 ARG Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 591 THR 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 269 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 204 TYR 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 Chi-restraints excluded: chain D residue 318 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 159 optimal weight: 30.0000 chunk 72 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 183 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 180 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.115755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.087948 restraints weight = 41267.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.091120 restraints weight = 21483.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.093266 restraints weight = 13554.824| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3145 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3145 r_free = 0.3145 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 = 0.3145 r_free = 0.3145 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3145 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.7481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16386 Z= 0.160 Angle : 0.809 17.250 22134 Z= 0.404 Chirality : 0.049 0.273 2360 Planarity : 0.004 0.042 2818 Dihedral : 9.950 137.755 2246 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.73 % Allowed : 33.57 % Favored : 62.70 % 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: 0.48 (0.19), residues: 1932 helix: 0.75 (0.15), residues: 1133 sheet: -0.75 (0.42), residues: 148 loop : 0.06 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 124 HIS 0.008 0.001 HIS D 201 PHE 0.036 0.002 PHE C 172 TYR 0.026 0.002 TYR C 236 ARG 0.008 0.001 ARG B 164 Details of bonding type rmsd hydrogen bonds : bond 0.04299 ( 871) hydrogen bonds : angle 5.32816 ( 2571) covalent geometry : bond 0.00363 (16386) covalent geometry : angle 0.80863 (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 761 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 697 time to evaluate : 1.764 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: 0.9124 (OUTLIER) cc_final: 0.8739 (pm20) REVERT: A 54 LYS cc_start: 0.9409 (ttpp) cc_final: 0.9024 (ptmt) REVERT: A 56 ASP cc_start: 0.8869 (m-30) cc_final: 0.8353 (m-30) REVERT: A 144 MET cc_start: 0.8439 (mmp) cc_final: 0.8174 (mmp) REVERT: A 147 GLN cc_start: 0.9135 (mt0) cc_final: 0.8582 (mm-40) REVERT: A 161 ARG cc_start: 0.8475 (ttm110) cc_final: 0.7751 (ptp-170) REVERT: A 213 ILE cc_start: 0.9135 (mp) cc_final: 0.8684 (tp) REVERT: A 250 TYR cc_start: 0.8699 (m-80) cc_final: 0.8460 (m-80) REVERT: A 255 HIS cc_start: 0.8764 (t-90) cc_final: 0.8456 (t-90) REVERT: A 290 GLU cc_start: 0.9048 (tm-30) cc_final: 0.8643 (tm-30) REVERT: A 301 PHE cc_start: 0.8923 (m-10) cc_final: 0.8713 (m-10) REVERT: A 325 LYS cc_start: 0.9638 (mmmt) cc_final: 0.9403 (mmtp) REVERT: A 375 LYS cc_start: 0.8851 (mmtp) cc_final: 0.8059 (mmtm) REVERT: A 384 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8267 (pm20) REVERT: A 399 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8526 (tm-30) REVERT: A 413 SER cc_start: 0.9461 (m) cc_final: 0.9036 (t) REVERT: A 446 ARG cc_start: 0.7400 (mmm-85) cc_final: 0.7039 (mmm-85) REVERT: A 459 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.9142 (mtmm) REVERT: A 505 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8321 (mt-10) REVERT: A 515 ASP cc_start: 0.9174 (m-30) cc_final: 0.8941 (m-30) REVERT: A 546 LEU cc_start: 0.9625 (mp) cc_final: 0.9324 (mt) REVERT: A 590 SER cc_start: 0.9513 (t) cc_final: 0.9013 (p) REVERT: A 595 MET cc_start: 0.9072 (mmt) cc_final: 0.8838 (mmt) REVERT: A 606 TYR cc_start: 0.8234 (m-80) cc_final: 0.7893 (m-80) REVERT: A 639 ASP cc_start: 0.8499 (m-30) cc_final: 0.8068 (m-30) REVERT: A 640 MET cc_start: 0.9476 (tpp) cc_final: 0.9066 (tpp) REVERT: A 645 GLN cc_start: 0.9056 (tp40) cc_final: 0.8548 (tp-100) REVERT: A 683 TYR cc_start: 0.8624 (t80) cc_final: 0.8283 (t80) REVERT: A 686 ARG cc_start: 0.8254 (ttm110) cc_final: 0.7671 (mtp-110) REVERT: B 8 LYS cc_start: 0.9215 (tptm) cc_final: 0.9003 (tptm) REVERT: B 79 GLU cc_start: 0.9115 (mm-30) cc_final: 0.8814 (mm-30) REVERT: B 82 LYS cc_start: 0.9566 (mtpp) cc_final: 0.9204 (ptpp) REVERT: B 95 MET cc_start: 0.9000 (tpt) cc_final: 0.8098 (tpp) REVERT: B 99 LYS cc_start: 0.9327 (tptp) cc_final: 0.8915 (tptp) REVERT: B 119 GLU cc_start: 0.9069 (mp0) cc_final: 0.8496 (mp0) REVERT: B 128 PHE cc_start: 0.9718 (t80) cc_final: 0.9440 (t80) REVERT: B 161 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8858 (mtt-85) REVERT: B 168 VAL cc_start: 0.9350 (t) cc_final: 0.9119 (m) REVERT: B 181 ASP cc_start: 0.8758 (m-30) cc_final: 0.8483 (m-30) REVERT: B 191 GLN cc_start: 0.9065 (mm-40) cc_final: 0.8798 (mm-40) REVERT: B 235 ARG cc_start: 0.9119 (mtm110) cc_final: 0.8882 (ptp-110) REVERT: B 236 TYR cc_start: 0.9252 (t80) cc_final: 0.8231 (t80) REVERT: B 250 TYR cc_start: 0.8861 (m-10) cc_final: 0.8524 (m-10) REVERT: B 256 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8512 (ttp80) REVERT: B 266 LYS cc_start: 0.9200 (mtpp) cc_final: 0.8653 (ptpp) REVERT: B 274 ARG cc_start: 0.8606 (ttm110) cc_final: 0.8277 (ttm170) REVERT: B 317 MET cc_start: 0.8586 (OUTLIER) cc_final: 0.8325 (pmm) REVERT: B 333 LYS cc_start: 0.9053 (tttm) cc_final: 0.8737 (tttm) REVERT: B 348 MET cc_start: 0.8891 (tmm) cc_final: 0.8537 (tpt) REVERT: B 350 ARG cc_start: 0.9084 (mtp85) cc_final: 0.8503 (mtp85) REVERT: B 358 ILE cc_start: 0.9609 (mm) cc_final: 0.9275 (tp) REVERT: B 362 ASP cc_start: 0.8660 (m-30) cc_final: 0.8136 (m-30) REVERT: B 375 LYS cc_start: 0.9253 (mmmm) cc_final: 0.8913 (mmmm) REVERT: B 384 GLU cc_start: 0.8769 (pm20) cc_final: 0.8127 (pm20) REVERT: B 394 TYR cc_start: 0.9125 (m-80) cc_final: 0.8819 (m-80) REVERT: B 402 GLU cc_start: 0.8670 (tm-30) cc_final: 0.8221 (tm-30) REVERT: B 483 GLU cc_start: 0.9511 (mp0) cc_final: 0.9174 (mp0) REVERT: B 515 ASP cc_start: 0.9208 (m-30) cc_final: 0.8714 (m-30) REVERT: B 548 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7820 (mm-30) REVERT: B 558 TRP cc_start: 0.9469 (m100) cc_final: 0.8812 (m100) REVERT: B 583 SER cc_start: 0.9101 (m) cc_final: 0.8639 (p) REVERT: B 586 TYR cc_start: 0.9208 (m-80) cc_final: 0.8486 (m-80) REVERT: B 610 LYS cc_start: 0.8876 (OUTLIER) cc_final: 0.8594 (ptmm) REVERT: B 645 GLN cc_start: 0.9392 (tp40) cc_final: 0.8974 (tp40) REVERT: B 668 ASN cc_start: 0.9096 (m110) cc_final: 0.8499 (m110) REVERT: C 20 MET cc_start: 0.9557 (tmm) cc_final: 0.8979 (ppp) REVERT: C 21 PHE cc_start: 0.9546 (m-80) cc_final: 0.8329 (m-80) REVERT: C 74 MET cc_start: 0.8686 (mtt) cc_final: 0.8453 (mtt) REVERT: C 92 PHE cc_start: 0.9609 (t80) cc_final: 0.9110 (t80) REVERT: C 96 MET cc_start: 0.8982 (mmm) cc_final: 0.8544 (mmm) REVERT: C 143 LYS cc_start: 0.8637 (tptt) cc_final: 0.8321 (tptp) REVERT: C 155 LYS cc_start: 0.9365 (mttt) cc_final: 0.9015 (mmtm) REVERT: C 198 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8597 (mm-30) REVERT: C 227 PHE cc_start: 0.9236 (t80) cc_final: 0.9024 (t80) REVERT: C 259 PHE cc_start: 0.9341 (t80) cc_final: 0.8630 (t80) REVERT: C 269 MET cc_start: 0.9625 (OUTLIER) cc_final: 0.9165 (mmt) REVERT: C 274 ASP cc_start: 0.8034 (p0) cc_final: 0.7612 (p0) REVERT: C 314 PRO cc_start: 0.9324 (Cg_exo) cc_final: 0.8842 (Cg_endo) REVERT: D 46 TYR cc_start: 0.9242 (m-80) cc_final: 0.8801 (m-10) REVERT: D 71 ASN cc_start: 0.9414 (m-40) cc_final: 0.9073 (m110) REVERT: D 168 PHE cc_start: 0.8542 (m-80) cc_final: 0.7395 (m-80) REVERT: D 169 TYR cc_start: 0.7788 (m-80) cc_final: 0.7189 (m-80) REVERT: D 174 TYR cc_start: 0.8753 (t80) cc_final: 0.8057 (t80) REVERT: D 210 GLN cc_start: 0.9343 (pp30) cc_final: 0.9021 (tp-100) REVERT: D 242 TYR cc_start: 0.8834 (t80) cc_final: 0.8592 (t80) REVERT: D 268 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8203 (mt) outliers start: 64 outliers final: 46 residues processed: 721 average time/residue: 0.2714 time to fit residues: 290.5548 Evaluate side-chains 734 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 679 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP 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 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 194 LYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 306 ILE 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 405 LEU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 602 GLU 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 161 ARG 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 343 LEU 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 472 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain C residue 151 ILE 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 269 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 204 TYR 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: 3.9990 chunk 102 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 107 optimal weight: 0.3980 chunk 77 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 115 optimal weight: 0.5980 chunk 127 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN B 150 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.116957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.088757 restraints weight = 41356.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.091985 restraints weight = 21580.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.094182 restraints weight = 13550.960| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.7720 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= 0.156 Angle : 0.842 17.298 22134 Z= 0.418 Chirality : 0.049 0.308 2360 Planarity : 0.004 0.041 2818 Dihedral : 9.846 137.001 2243 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.73 % Allowed : 34.56 % 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: 0.36 (0.19), residues: 1932 helix: 0.70 (0.15), residues: 1122 sheet: -0.77 (0.42), residues: 148 loop : -0.07 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 124 HIS 0.010 0.001 HIS D 201 PHE 0.037 0.002 PHE C 29 TYR 0.026 0.002 TYR D 142 ARG 0.007 0.001 ARG B 117 Details of bonding type rmsd hydrogen bonds : bond 0.04292 ( 871) hydrogen bonds : angle 5.39623 ( 2571) covalent geometry : bond 0.00354 (16386) covalent geometry : angle 0.84199 (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 774 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 710 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9020 (tppt) cc_final: 0.8816 (tppt) REVERT: A 31 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8760 (pm20) REVERT: A 54 LYS cc_start: 0.9395 (ttpp) cc_final: 0.8918 (ptmt) REVERT: A 56 ASP cc_start: 0.8876 (m-30) cc_final: 0.8369 (m-30) REVERT: A 144 MET cc_start: 0.8454 (mmp) cc_final: 0.8222 (mmp) REVERT: A 147 GLN cc_start: 0.9124 (mt0) cc_final: 0.8569 (mm-40) REVERT: A 161 ARG cc_start: 0.8495 (ttm110) cc_final: 0.7855 (ptp-170) REVERT: A 209 LYS cc_start: 0.8866 (tptt) cc_final: 0.8573 (tppt) REVERT: A 213 ILE cc_start: 0.8953 (mp) cc_final: 0.8532 (tp) REVERT: A 290 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8655 (tm-30) REVERT: A 325 LYS cc_start: 0.9619 (mmmt) cc_final: 0.9405 (mmtp) REVERT: A 375 LYS cc_start: 0.8814 (mmtp) cc_final: 0.8026 (mmtm) REVERT: A 384 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8256 (pm20) REVERT: A 413 SER cc_start: 0.9472 (m) cc_final: 0.8996 (t) REVERT: A 446 ARG cc_start: 0.7456 (mmm-85) cc_final: 0.7084 (mmm-85) REVERT: A 456 LYS cc_start: 0.9239 (ptpp) cc_final: 0.8996 (ptpp) REVERT: A 459 LYS cc_start: 0.9416 (OUTLIER) cc_final: 0.9162 (mtmm) REVERT: A 493 MET cc_start: 0.8843 (tmm) cc_final: 0.8469 (tmm) REVERT: A 505 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8301 (mt-10) REVERT: A 515 ASP cc_start: 0.9207 (m-30) cc_final: 0.8964 (m-30) REVERT: A 590 SER cc_start: 0.9502 (t) cc_final: 0.8918 (p) REVERT: A 595 MET cc_start: 0.9004 (mmt) cc_final: 0.8776 (mmt) REVERT: A 606 TYR cc_start: 0.8256 (m-80) cc_final: 0.7799 (m-80) REVERT: A 636 LYS cc_start: 0.9436 (mttm) cc_final: 0.9005 (mmmm) REVERT: A 639 ASP cc_start: 0.8476 (m-30) cc_final: 0.8043 (m-30) REVERT: A 640 MET cc_start: 0.9495 (tpp) cc_final: 0.9045 (tpp) REVERT: A 645 GLN cc_start: 0.9022 (tp40) cc_final: 0.8542 (tp-100) REVERT: A 686 ARG cc_start: 0.8267 (ttm110) cc_final: 0.7685 (mtp-110) REVERT: B 8 LYS cc_start: 0.9232 (tptm) cc_final: 0.9022 (tptm) REVERT: B 79 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8770 (mm-30) REVERT: B 82 LYS cc_start: 0.9549 (mtpp) cc_final: 0.9152 (ptpp) REVERT: B 95 MET cc_start: 0.8971 (tpt) cc_final: 0.8122 (tpp) REVERT: B 99 LYS cc_start: 0.9248 (tptp) cc_final: 0.8867 (tptp) REVERT: B 119 GLU cc_start: 0.9081 (mp0) cc_final: 0.8480 (mp0) REVERT: B 168 VAL cc_start: 0.9326 (t) cc_final: 0.9048 (m) REVERT: B 181 ASP cc_start: 0.8740 (m-30) cc_final: 0.8430 (m-30) REVERT: B 234 PHE cc_start: 0.9418 (m-80) cc_final: 0.9186 (m-10) REVERT: B 235 ARG cc_start: 0.9192 (mtm110) cc_final: 0.8946 (mtm110) REVERT: B 236 TYR cc_start: 0.9183 (t80) cc_final: 0.8185 (t80) REVERT: B 250 TYR cc_start: 0.8924 (m-10) cc_final: 0.8402 (m-10) REVERT: B 256 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8492 (ttp80) REVERT: B 266 LYS cc_start: 0.9192 (mtpp) cc_final: 0.8599 (ptpp) REVERT: B 274 ARG cc_start: 0.8648 (ttm110) cc_final: 0.8294 (ttm170) REVERT: B 317 MET cc_start: 0.8521 (pmm) cc_final: 0.8235 (pmm) REVERT: B 333 LYS cc_start: 0.9054 (tttm) cc_final: 0.8732 (tttm) REVERT: B 348 MET cc_start: 0.8867 (tmm) cc_final: 0.8536 (tpt) REVERT: B 350 ARG cc_start: 0.9098 (mtp85) cc_final: 0.8558 (mtp85) REVERT: B 358 ILE cc_start: 0.9635 (mm) cc_final: 0.9305 (tp) REVERT: B 362 ASP cc_start: 0.8659 (m-30) cc_final: 0.8160 (m-30) REVERT: B 375 LYS cc_start: 0.9247 (mmmm) cc_final: 0.8634 (mmmm) REVERT: B 384 GLU cc_start: 0.8831 (pm20) cc_final: 0.8145 (pm20) REVERT: B 394 TYR cc_start: 0.9101 (m-80) cc_final: 0.8818 (m-80) REVERT: B 402 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8241 (tm-30) REVERT: B 483 GLU cc_start: 0.9479 (mp0) cc_final: 0.9165 (mp0) REVERT: B 515 ASP cc_start: 0.9184 (m-30) cc_final: 0.8689 (m-30) REVERT: B 548 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7718 (mm-30) REVERT: B 558 TRP cc_start: 0.9410 (m100) cc_final: 0.8736 (m100) REVERT: B 586 TYR cc_start: 0.9178 (m-80) cc_final: 0.8558 (m-80) REVERT: B 610 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8566 (ptmm) REVERT: B 613 TYR cc_start: 0.8992 (t80) cc_final: 0.8220 (t80) REVERT: B 645 GLN cc_start: 0.9352 (tp40) cc_final: 0.9004 (tp40) REVERT: B 668 ASN cc_start: 0.9084 (m110) cc_final: 0.8594 (m-40) REVERT: B 686 ARG cc_start: 0.8114 (mmt180) cc_final: 0.7904 (mmt180) REVERT: C 20 MET cc_start: 0.9560 (tmm) cc_final: 0.8974 (ppp) REVERT: C 21 PHE cc_start: 0.9558 (m-80) cc_final: 0.8352 (m-80) REVERT: C 74 MET cc_start: 0.8739 (mtt) cc_final: 0.8497 (mtt) REVERT: C 92 PHE cc_start: 0.9600 (t80) cc_final: 0.9127 (t80) REVERT: C 96 MET cc_start: 0.9004 (mmm) cc_final: 0.8527 (mmm) REVERT: C 143 LYS cc_start: 0.8613 (tptt) cc_final: 0.8339 (tptp) REVERT: C 155 LYS cc_start: 0.9395 (mttt) cc_final: 0.9108 (mmtm) REVERT: C 189 GLU cc_start: 0.8824 (mm-30) cc_final: 0.8385 (mm-30) REVERT: C 198 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8555 (mm-30) REVERT: C 259 PHE cc_start: 0.9322 (t80) cc_final: 0.8704 (t80) REVERT: C 266 LYS cc_start: 0.9282 (mtpt) cc_final: 0.8979 (ptpp) REVERT: C 269 MET cc_start: 0.9542 (OUTLIER) cc_final: 0.9145 (mmt) REVERT: C 274 ASP cc_start: 0.8122 (p0) cc_final: 0.7693 (p0) REVERT: C 314 PRO cc_start: 0.9353 (Cg_exo) cc_final: 0.8889 (Cg_endo) REVERT: D 46 TYR cc_start: 0.9226 (m-80) cc_final: 0.8800 (m-10) REVERT: D 50 ASN cc_start: 0.8976 (m-40) cc_final: 0.8651 (p0) REVERT: D 168 PHE cc_start: 0.8574 (m-80) cc_final: 0.7562 (m-80) REVERT: D 169 TYR cc_start: 0.7493 (m-80) cc_final: 0.7103 (m-80) REVERT: D 174 TYR cc_start: 0.8886 (t80) cc_final: 0.8249 (t80) REVERT: D 183 LYS cc_start: 0.7868 (ptpt) cc_final: 0.7648 (ptpp) REVERT: D 242 TYR cc_start: 0.8882 (t80) cc_final: 0.8590 (t80) REVERT: D 268 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8089 (mt) outliers start: 64 outliers final: 47 residues processed: 733 average time/residue: 0.2732 time to fit residues: 295.9177 Evaluate side-chains 730 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 677 time to evaluate : 1.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP 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 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 306 ILE 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 405 LEU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 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 256 ARG Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 565 VAL Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain C residue 151 ILE 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 269 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 287 LEU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 137 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 135 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 70 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 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** C 238 ASN ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN ** D 265 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 = 0.3581 r_free = 0.3581 target = 0.115953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.088282 restraints weight = 41583.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.091455 restraints weight = 21632.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.093615 restraints weight = 13570.876| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.7903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16386 Z= 0.169 Angle : 0.888 16.867 22134 Z= 0.445 Chirality : 0.051 0.249 2360 Planarity : 0.004 0.067 2818 Dihedral : 9.880 137.210 2243 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 22.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.15 % Allowed : 36.71 % Favored : 60.14 % 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: 0.31 (0.19), residues: 1932 helix: 0.64 (0.15), residues: 1117 sheet: -0.74 (0.42), residues: 144 loop : -0.09 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 124 HIS 0.011 0.001 HIS D 201 PHE 0.039 0.002 PHE C 178 TYR 0.037 0.002 TYR D 236 ARG 0.014 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.04387 ( 871) hydrogen bonds : angle 5.48680 ( 2571) covalent geometry : bond 0.00387 (16386) covalent geometry : angle 0.88825 (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 740 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 686 time to evaluate : 1.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8799 (pm20) REVERT: A 54 LYS cc_start: 0.9392 (ttpp) cc_final: 0.8916 (ptmt) REVERT: A 56 ASP cc_start: 0.8911 (m-30) cc_final: 0.8410 (m-30) REVERT: A 144 MET cc_start: 0.8500 (mmp) cc_final: 0.8193 (mmp) REVERT: A 147 GLN cc_start: 0.9145 (mt0) cc_final: 0.8584 (mm-40) REVERT: A 150 GLN cc_start: 0.9486 (tp40) cc_final: 0.9079 (tp40) REVERT: A 161 ARG cc_start: 0.8635 (ttm110) cc_final: 0.8045 (ptp-170) REVERT: A 213 ILE cc_start: 0.8901 (mp) cc_final: 0.8563 (tp) REVERT: A 266 LYS cc_start: 0.8730 (ptmm) cc_final: 0.8327 (ptmm) REVERT: A 290 GLU cc_start: 0.9075 (tm-30) cc_final: 0.8706 (tm-30) REVERT: A 325 LYS cc_start: 0.9604 (mmmt) cc_final: 0.9404 (mmtp) REVERT: A 375 LYS cc_start: 0.8781 (mmtp) cc_final: 0.8022 (mmtm) REVERT: A 384 GLU cc_start: 0.8531 (OUTLIER) cc_final: 0.8234 (pm20) REVERT: A 413 SER cc_start: 0.9473 (m) cc_final: 0.8966 (t) REVERT: A 459 LYS cc_start: 0.9407 (OUTLIER) cc_final: 0.9155 (mtmm) REVERT: A 493 MET cc_start: 0.8810 (tmm) cc_final: 0.8410 (tmm) REVERT: A 505 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8315 (mt-10) REVERT: A 515 ASP cc_start: 0.9227 (m-30) cc_final: 0.9008 (m-30) REVERT: A 590 SER cc_start: 0.9461 (t) cc_final: 0.8879 (p) REVERT: A 595 MET cc_start: 0.9038 (mmt) cc_final: 0.8805 (mmt) REVERT: A 606 TYR cc_start: 0.8269 (m-80) cc_final: 0.7806 (m-80) REVERT: A 636 LYS cc_start: 0.9439 (mttm) cc_final: 0.9008 (mmmm) REVERT: A 639 ASP cc_start: 0.8469 (m-30) cc_final: 0.8047 (m-30) REVERT: A 640 MET cc_start: 0.9497 (tpp) cc_final: 0.9048 (tpp) REVERT: A 645 GLN cc_start: 0.8991 (tp40) cc_final: 0.8598 (tp40) REVERT: A 686 ARG cc_start: 0.8321 (ttm110) cc_final: 0.7748 (mtp-110) REVERT: B 79 GLU cc_start: 0.9072 (mm-30) cc_final: 0.8749 (mm-30) REVERT: B 82 LYS cc_start: 0.9520 (mtpp) cc_final: 0.9073 (ptpp) REVERT: B 95 MET cc_start: 0.8993 (tpt) cc_final: 0.8287 (tpp) REVERT: B 99 LYS cc_start: 0.9218 (tptp) cc_final: 0.8876 (tptp) REVERT: B 119 GLU cc_start: 0.9093 (mp0) cc_final: 0.8511 (mp0) REVERT: B 234 PHE cc_start: 0.9419 (m-80) cc_final: 0.9156 (m-10) REVERT: B 235 ARG cc_start: 0.9230 (mtm110) cc_final: 0.8985 (mtm110) REVERT: B 250 TYR cc_start: 0.9017 (m-10) cc_final: 0.8344 (m-10) REVERT: B 256 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8477 (ttp80) REVERT: B 266 LYS cc_start: 0.9233 (mtpp) cc_final: 0.8640 (ptpp) REVERT: B 274 ARG cc_start: 0.8668 (ttm110) cc_final: 0.8325 (ttm170) REVERT: B 314 MET cc_start: 0.9331 (tmm) cc_final: 0.8435 (tmm) REVERT: B 317 MET cc_start: 0.8408 (pmm) cc_final: 0.8161 (pmm) REVERT: B 333 LYS cc_start: 0.9042 (tttm) cc_final: 0.8705 (tttm) REVERT: B 348 MET cc_start: 0.8880 (tmm) cc_final: 0.8556 (tpt) REVERT: B 350 ARG cc_start: 0.9104 (mtp85) cc_final: 0.8532 (mtp85) REVERT: B 358 ILE cc_start: 0.9597 (mm) cc_final: 0.9290 (tp) REVERT: B 362 ASP cc_start: 0.8714 (m-30) cc_final: 0.8280 (m-30) REVERT: B 375 LYS cc_start: 0.9239 (mmmm) cc_final: 0.8615 (mmmm) REVERT: B 384 GLU cc_start: 0.8797 (pm20) cc_final: 0.8148 (pm20) REVERT: B 402 GLU cc_start: 0.8734 (tm-30) cc_final: 0.8242 (tm-30) REVERT: B 483 GLU cc_start: 0.9486 (mp0) cc_final: 0.9170 (mp0) REVERT: B 515 ASP cc_start: 0.9179 (m-30) cc_final: 0.8697 (m-30) REVERT: B 546 LEU cc_start: 0.9596 (mm) cc_final: 0.9391 (tp) REVERT: B 548 GLU cc_start: 0.8352 (mm-30) cc_final: 0.7686 (mm-30) REVERT: B 558 TRP cc_start: 0.9410 (m100) cc_final: 0.8757 (m100) REVERT: B 583 SER cc_start: 0.9094 (m) cc_final: 0.8310 (t) REVERT: B 586 TYR cc_start: 0.9169 (m-80) cc_final: 0.8712 (m-80) REVERT: B 610 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8622 (ptmm) REVERT: B 645 GLN cc_start: 0.9372 (tp40) cc_final: 0.8974 (tp40) REVERT: B 668 ASN cc_start: 0.9103 (m110) cc_final: 0.8601 (m-40) REVERT: B 683 TYR cc_start: 0.8722 (t80) cc_final: 0.8319 (t80) REVERT: B 686 ARG cc_start: 0.8160 (mmt180) cc_final: 0.7898 (mmt-90) REVERT: C 20 MET cc_start: 0.9563 (tmm) cc_final: 0.8987 (ppp) REVERT: C 21 PHE cc_start: 0.9570 (m-80) cc_final: 0.8446 (m-80) REVERT: C 74 MET cc_start: 0.8795 (mtt) cc_final: 0.8309 (mtt) REVERT: C 85 GLN cc_start: 0.8414 (mt0) cc_final: 0.7864 (mm-40) REVERT: C 90 LEU cc_start: 0.9285 (tp) cc_final: 0.9027 (pp) REVERT: C 92 PHE cc_start: 0.9635 (t80) cc_final: 0.9215 (t80) REVERT: C 96 MET cc_start: 0.8998 (mmm) cc_final: 0.8519 (mmm) REVERT: C 143 LYS cc_start: 0.8674 (tptt) cc_final: 0.8309 (tptp) REVERT: C 146 GLN cc_start: 0.8579 (mm110) cc_final: 0.7912 (tp-100) REVERT: C 155 LYS cc_start: 0.9446 (mttt) cc_final: 0.9142 (mmtm) REVERT: C 189 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8179 (mm-30) REVERT: C 259 PHE cc_start: 0.9315 (t80) cc_final: 0.8737 (t80) REVERT: C 266 LYS cc_start: 0.9250 (mtpt) cc_final: 0.8985 (ptpp) REVERT: C 269 MET cc_start: 0.9497 (OUTLIER) cc_final: 0.9149 (mmt) REVERT: C 274 ASP cc_start: 0.8053 (p0) cc_final: 0.7611 (p0) REVERT: D 50 ASN cc_start: 0.8961 (m-40) cc_final: 0.8689 (p0) REVERT: D 55 TYR cc_start: 0.8773 (t80) cc_final: 0.8388 (t80) REVERT: D 68 GLU cc_start: 0.7264 (mm-30) cc_final: 0.6782 (mm-30) REVERT: D 137 MET cc_start: 0.8270 (mmt) cc_final: 0.7805 (mpp) REVERT: D 168 PHE cc_start: 0.8447 (m-80) cc_final: 0.7587 (m-80) REVERT: D 169 TYR cc_start: 0.7291 (m-80) cc_final: 0.7064 (m-80) REVERT: D 174 TYR cc_start: 0.8869 (t80) cc_final: 0.8292 (t80) REVERT: D 268 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8150 (mt) outliers start: 54 outliers final: 45 residues processed: 704 average time/residue: 0.2727 time to fit residues: 285.1999 Evaluate side-chains 712 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 661 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 348 MET 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 459 LYS Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 632 MET 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 256 ARG Chi-restraints excluded: chain B residue 267 ILE 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 565 VAL Chi-restraints excluded: chain B residue 591 THR Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 640 MET Chi-restraints excluded: chain C residue 151 ILE 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 269 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 214 ASN 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: 0.4980 chunk 2 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 190 optimal weight: 9.9990 chunk 58 optimal weight: 7.9990 chunk 180 optimal weight: 0.0070 chunk 108 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 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 80 HIS ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.116695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.088426 restraints weight = 41449.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.091657 restraints weight = 21905.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.093925 restraints weight = 13776.825| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.8124 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= 0.170 Angle : 0.892 16.334 22134 Z= 0.447 Chirality : 0.051 0.253 2360 Planarity : 0.004 0.064 2818 Dihedral : 9.796 137.405 2243 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.26 % Allowed : 37.00 % Favored : 59.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.20 (0.19), residues: 1932 helix: 0.51 (0.15), residues: 1128 sheet: -0.72 (0.42), residues: 144 loop : -0.08 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 124 HIS 0.010 0.001 HIS D 201 PHE 0.054 0.003 PHE D 172 TYR 0.036 0.002 TYR D 236 ARG 0.012 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.04440 ( 871) hydrogen bonds : angle 5.56606 ( 2571) covalent geometry : bond 0.00389 (16386) covalent geometry : angle 0.89204 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6835.27 seconds wall clock time: 120 minutes 10.76 seconds (7210.76 seconds total)