Starting phenix.real_space_refine on Sat May 17 16:33:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz5_45053/05_2025/9bz5_45053_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz5_45053/05_2025/9bz5_45053.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bz5_45053/05_2025/9bz5_45053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz5_45053/05_2025/9bz5_45053.map" model { file = "/net/cci-nas-00/data/ceres_data/9bz5_45053/05_2025/9bz5_45053_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz5_45053/05_2025/9bz5_45053_neut.cif" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 9.45, per 1000 atoms: 0.59 Number of scatterers: 16038 At special positions: 0 Unit cell: (95.316, 134.862, 129.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.20 Conformation dependent library (CDL) restraints added in 2.0 seconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.104A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.985A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.954A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.664A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.693A 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: 3.627A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.120A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.960A 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: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.026A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.117A 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: 3.565A 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: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.876A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.360A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.479A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A 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: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.501A 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: 7.184A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.049A 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: 6.563A 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: 7.808A 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: 4.77 Time building geometry restraints manager: 4.87 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: 4788 1.34 - 1.46: 3077 1.46 - 1.58: 8340 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 2.39e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.038 1.20e-02 6.94e+03 1.02e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.574 -0.031 1.08e-02 8.57e+03 8.45e+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 7.55e+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 7.21e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21571 2.09 - 4.18: 521 4.18 - 6.27: 37 6.27 - 8.36: 1 8.36 - 10.45: 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 110.54 116.59 -6.05 1.36e+00 5.41e-01 1.98e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.10 -4.39 1.15e+00 7.56e-01 1.46e+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 1.24e+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 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.55 3.64 1.06e+00 8.90e-01 1.18e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 9470 35.81 - 71.61: 337 71.61 - 107.42: 37 107.42 - 143.23: 3 143.23 - 179.04: 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 -58.32 120.72 -179.04 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 301.68 151.17 150.51 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 31.92 148.05 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: 2141 0.094 - 0.187: 187 0.187 - 0.281: 28 0.281 - 0.374: 2 0.374 - 0.468: 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 5.47e+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 4.62e+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 2.95e+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 4.15e-02 2.76e+00 pdb=" N PRO D 75 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " 0.017 2.00e-02 2.50e+03 1.12e-02 2.18e+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 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 177 " 0.017 2.00e-02 2.50e+03 9.84e-03 1.94e+00 pdb=" CG TYR C 177 " -0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR C 177 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR C 177 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 177 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 177 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 177 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR C 177 " 0.010 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: 27042 3.70 - 4.30: 41544 4.30 - 4.90: 65416 Nonbonded interactions: 145687 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 1.961 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 145682 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 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: 0.550 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 35.910 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.080 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6562 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= 0.316 Angle : 0.740 10.451 22134 Z= 0.463 Chirality : 0.058 0.468 2360 Planarity : 0.003 0.042 2818 Dihedral : 17.953 179.036 6154 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.46 % Allowed : 15.21 % Favored : 83.33 % 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: 0.47 (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 0.021 0.002 TYR D 179 ARG 0.004 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.15420 ( 871) hydrogen bonds : angle 6.51762 ( 2571) covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74017 (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 1013 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 988 time to evaluate : 1.675 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: A 12 LEU cc_start: 0.8403 (mt) cc_final: 0.7792 (mp) REVERT: A 29 ASP cc_start: 0.8100 (t0) cc_final: 0.7899 (t0) REVERT: A 41 ILE cc_start: 0.8475 (mm) cc_final: 0.8014 (mm) REVERT: A 76 ASP cc_start: 0.8044 (m-30) cc_final: 0.7505 (m-30) REVERT: A 78 LYS cc_start: 0.8731 (tttt) cc_final: 0.8512 (ttmm) REVERT: A 121 ARG cc_start: 0.8688 (tpm-80) cc_final: 0.8409 (tpt170) REVERT: A 138 LYS cc_start: 0.8087 (mtpt) cc_final: 0.7862 (mtmm) REVERT: A 157 LEU cc_start: 0.9192 (tp) cc_final: 0.8626 (tp) REVERT: A 172 LEU cc_start: 0.9148 (mp) cc_final: 0.8757 (mp) REVERT: A 177 ASP cc_start: 0.8144 (t0) cc_final: 0.7588 (t0) REVERT: A 181 ASP cc_start: 0.7468 (m-30) cc_final: 0.7244 (m-30) REVERT: A 202 ASN cc_start: 0.8874 (t0) cc_final: 0.8304 (t0) REVERT: A 259 ASN cc_start: 0.7995 (m-40) cc_final: 0.7464 (m-40) REVERT: A 277 THR cc_start: 0.7734 (p) cc_final: 0.7406 (t) REVERT: A 300 VAL cc_start: 0.7802 (m) cc_final: 0.7536 (m) REVERT: A 319 MET cc_start: 0.7757 (tpp) cc_final: 0.7193 (tpp) REVERT: A 362 ASP cc_start: 0.6228 (m-30) cc_final: 0.5856 (m-30) REVERT: A 367 VAL cc_start: 0.9081 (m) cc_final: 0.8554 (t) REVERT: A 378 PHE cc_start: 0.8932 (p90) cc_final: 0.8609 (p90) REVERT: A 435 SER cc_start: 0.9482 (p) cc_final: 0.8719 (t) REVERT: A 531 TYR cc_start: 0.7795 (m-80) cc_final: 0.7470 (m-10) REVERT: A 550 MET cc_start: 0.7109 (mtm) cc_final: 0.6015 (mtp) REVERT: A 587 VAL cc_start: 0.8851 (t) cc_final: 0.8331 (t) REVERT: A 645 GLN cc_start: 0.7636 (tp40) cc_final: 0.7299 (tp40) REVERT: A 672 LEU cc_start: 0.8479 (mt) cc_final: 0.8184 (mt) REVERT: B 12 LEU cc_start: 0.8274 (mt) cc_final: 0.7823 (mt) REVERT: B 68 PHE cc_start: 0.8220 (p90) cc_final: 0.7749 (p90) REVERT: B 99 LYS cc_start: 0.8505 (mmtt) cc_final: 0.8075 (mmtt) REVERT: B 121 ARG cc_start: 0.8725 (tpm170) cc_final: 0.8291 (tpp-160) REVERT: B 155 THR cc_start: 0.8585 (m) cc_final: 0.8303 (m) REVERT: B 177 ASP cc_start: 0.8204 (t0) cc_final: 0.7522 (t70) REVERT: B 202 ASN cc_start: 0.8759 (t0) cc_final: 0.8276 (t0) REVERT: B 204 SER cc_start: 0.8837 (m) cc_final: 0.8227 (t) REVERT: B 206 LEU cc_start: 0.8459 (mt) cc_final: 0.8231 (mt) REVERT: B 234 PHE cc_start: 0.8865 (m-80) cc_final: 0.8489 (m-10) REVERT: B 236 TYR cc_start: 0.7837 (t80) cc_final: 0.7617 (t80) REVERT: B 286 ASP cc_start: 0.7121 (OUTLIER) cc_final: 0.6849 (m-30) REVERT: B 346 LEU cc_start: 0.8685 (mt) cc_final: 0.8462 (mt) REVERT: B 358 ILE cc_start: 0.9125 (mm) cc_final: 0.8893 (mm) REVERT: B 366 LYS cc_start: 0.8282 (ptpp) cc_final: 0.8069 (mtpt) REVERT: B 376 VAL cc_start: 0.9528 (t) cc_final: 0.9318 (m) REVERT: B 378 PHE cc_start: 0.8625 (p90) cc_final: 0.8395 (p90) REVERT: B 384 GLU cc_start: 0.9009 (pm20) cc_final: 0.8717 (pm20) REVERT: B 387 GLN cc_start: 0.7516 (mt0) cc_final: 0.7210 (mt0) REVERT: B 413 SER cc_start: 0.8525 (m) cc_final: 0.8273 (m) REVERT: B 442 THR cc_start: 0.8763 (p) cc_final: 0.8444 (m) REVERT: B 471 TYR cc_start: 0.8410 (t80) cc_final: 0.7495 (t80) REVERT: B 501 GLN cc_start: 0.7143 (tt0) cc_final: 0.6941 (tt0) REVERT: B 546 LEU cc_start: 0.8876 (mt) cc_final: 0.8347 (mt) REVERT: B 550 MET cc_start: 0.7858 (mtm) cc_final: 0.6477 (mtp) REVERT: B 576 LEU cc_start: 0.8646 (mt) cc_final: 0.8403 (mt) REVERT: B 612 TYR cc_start: 0.7481 (m-80) cc_final: 0.7171 (m-80) REVERT: C 56 MET cc_start: 0.1931 (mmm) cc_final: 0.1217 (ptm) REVERT: C 89 VAL cc_start: 0.5947 (t) cc_final: 0.4866 (t) REVERT: C 256 VAL cc_start: 0.5854 (t) cc_final: 0.5485 (p) REVERT: D 89 VAL cc_start: 0.7184 (t) cc_final: 0.6681 (t) outliers start: 25 outliers final: 5 residues processed: 998 average time/residue: 0.2970 time to fit residues: 424.3001 Evaluate side-chains 692 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 686 time to evaluate : 1.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 59 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 1.9990 chunk 145 optimal weight: 5.9990 chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 77 optimal weight: 0.9980 chunk 150 optimal weight: 4.9990 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 112 optimal weight: 0.7980 chunk 174 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 ASN A 304 HIS A 312 GLN A 313 HIS A 370 ASN A 387 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 62 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 329 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN B 676 HIS C 127 GLN C 249 GLN C 263 ASN C 265 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.150269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.108125 restraints weight = 34922.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.112140 restraints weight = 17441.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.114754 restraints weight = 10429.026| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3319 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3319 r_free = 0.3319 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16386 Z= 0.181 Angle : 0.704 11.516 22134 Z= 0.369 Chirality : 0.046 0.226 2360 Planarity : 0.004 0.037 2818 Dihedral : 11.425 166.844 2251 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.67 % Allowed : 22.96 % Favored : 73.37 % 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: 1.36 (0.18), residues: 1932 helix: 1.34 (0.15), residues: 1132 sheet: 0.11 (0.43), residues: 126 loop : 0.50 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 558 HIS 0.010 0.001 HIS C 201 PHE 0.029 0.002 PHE C 259 TYR 0.027 0.002 TYR C 162 ARG 0.006 0.001 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.04821 ( 871) hydrogen bonds : angle 5.16919 ( 2571) covalent geometry : bond 0.00391 (16386) covalent geometry : angle 0.70361 (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 781 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 718 time to evaluate : 1.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.9784 (mt) cc_final: 0.9481 (pp) REVERT: A 76 ASP cc_start: 0.9133 (m-30) cc_final: 0.8909 (m-30) REVERT: A 123 SER cc_start: 0.9634 (OUTLIER) cc_final: 0.9248 (p) REVERT: A 139 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8311 (mt-10) REVERT: A 157 LEU cc_start: 0.9617 (tp) cc_final: 0.9409 (tp) REVERT: A 191 GLN cc_start: 0.8959 (mm-40) cc_final: 0.8492 (mm-40) REVERT: A 202 ASN cc_start: 0.9508 (t0) cc_final: 0.9063 (t0) REVERT: A 218 ASN cc_start: 0.8874 (t0) cc_final: 0.8595 (t0) REVERT: A 221 LYS cc_start: 0.9192 (mmtp) cc_final: 0.8911 (mttt) REVERT: A 236 TYR cc_start: 0.9516 (t80) cc_final: 0.9298 (t80) REVERT: A 255 HIS cc_start: 0.8551 (t-90) cc_final: 0.8030 (t-90) REVERT: A 257 ASP cc_start: 0.9337 (m-30) cc_final: 0.8803 (m-30) REVERT: A 259 ASN cc_start: 0.8830 (m-40) cc_final: 0.8547 (m-40) REVERT: A 263 ASP cc_start: 0.8799 (m-30) cc_final: 0.8504 (m-30) REVERT: A 277 THR cc_start: 0.8863 (p) cc_final: 0.8522 (t) REVERT: A 286 ASP cc_start: 0.8396 (m-30) cc_final: 0.8107 (m-30) REVERT: A 322 MET cc_start: 0.8937 (mmm) cc_final: 0.8182 (mmm) REVERT: A 335 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7865 (mm-30) REVERT: A 348 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8547 (tmm) REVERT: A 362 ASP cc_start: 0.8303 (m-30) cc_final: 0.7305 (m-30) REVERT: A 379 SER cc_start: 0.9444 (t) cc_final: 0.9088 (t) REVERT: A 393 SER cc_start: 0.9375 (m) cc_final: 0.9090 (p) REVERT: A 402 GLU cc_start: 0.8032 (mp0) cc_final: 0.7651 (mp0) REVERT: A 501 GLN cc_start: 0.9148 (OUTLIER) cc_final: 0.8863 (tt0) REVERT: A 505 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8354 (mt-10) REVERT: A 550 MET cc_start: 0.6887 (mtm) cc_final: 0.6653 (mtm) REVERT: A 602 GLU cc_start: 0.7767 (pt0) cc_final: 0.7253 (pt0) REVERT: A 606 TYR cc_start: 0.7967 (m-80) cc_final: 0.7608 (m-80) REVERT: A 615 MET cc_start: 0.9027 (mmp) cc_final: 0.8548 (mmm) REVERT: A 618 LEU cc_start: 0.9371 (tp) cc_final: 0.9139 (tt) REVERT: A 639 ASP cc_start: 0.9027 (m-30) cc_final: 0.8278 (m-30) REVERT: B 31 GLU cc_start: 0.8720 (mp0) cc_final: 0.8498 (mp0) REVERT: B 65 GLU cc_start: 0.8503 (mm-30) cc_final: 0.7791 (mm-30) REVERT: B 68 PHE cc_start: 0.8979 (p90) cc_final: 0.8690 (p90) REVERT: B 119 GLU cc_start: 0.9135 (mp0) cc_final: 0.8598 (mp0) REVERT: B 121 ARG cc_start: 0.9404 (tpm170) cc_final: 0.9041 (tpp-160) REVERT: B 147 GLN cc_start: 0.9037 (mt0) cc_final: 0.8576 (mt0) REVERT: B 174 GLU cc_start: 0.8599 (tp30) cc_final: 0.8094 (tp30) REVERT: B 202 ASN cc_start: 0.9368 (t0) cc_final: 0.8966 (t0) REVERT: B 227 MET cc_start: 0.9237 (mtp) cc_final: 0.8932 (mtp) REVERT: B 236 TYR cc_start: 0.9022 (t80) cc_final: 0.8445 (t80) REVERT: B 251 LEU cc_start: 0.9179 (tp) cc_final: 0.8940 (tp) REVERT: B 257 ASP cc_start: 0.8728 (m-30) cc_final: 0.8207 (m-30) REVERT: B 270 ASP cc_start: 0.9214 (t70) cc_final: 0.8929 (t70) REVERT: B 279 SER cc_start: 0.8756 (m) cc_final: 0.8422 (t) REVERT: B 348 MET cc_start: 0.9129 (ptm) cc_final: 0.8479 (ptp) REVERT: B 386 LEU cc_start: 0.9575 (mt) cc_final: 0.9219 (mt) REVERT: B 393 SER cc_start: 0.9437 (m) cc_final: 0.9004 (p) REVERT: B 471 TYR cc_start: 0.9349 (t80) cc_final: 0.8519 (t80) REVERT: B 474 GLN cc_start: 0.8909 (mt0) cc_final: 0.8544 (mm-40) REVERT: B 475 ASN cc_start: 0.9247 (m-40) cc_final: 0.8539 (m-40) REVERT: B 515 ASP cc_start: 0.9098 (m-30) cc_final: 0.8814 (m-30) REVERT: B 546 LEU cc_start: 0.9591 (mt) cc_final: 0.9267 (mt) REVERT: B 558 TRP cc_start: 0.9417 (m100) cc_final: 0.8603 (m100) REVERT: B 589 SER cc_start: 0.9796 (m) cc_final: 0.9504 (p) REVERT: B 601 ILE cc_start: 0.9465 (mm) cc_final: 0.9056 (mm) REVERT: B 610 LYS cc_start: 0.8731 (ptmt) cc_final: 0.8440 (ptmm) REVERT: B 612 TYR cc_start: 0.9162 (m-80) cc_final: 0.8893 (m-80) REVERT: B 646 GLN cc_start: 0.9348 (OUTLIER) cc_final: 0.9004 (pt0) REVERT: B 650 GLN cc_start: 0.8413 (mt0) cc_final: 0.7999 (mm-40) REVERT: B 680 LYS cc_start: 0.9098 (mttt) cc_final: 0.8683 (mtmt) REVERT: B 683 TYR cc_start: 0.9089 (t80) cc_final: 0.8750 (t80) REVERT: C 149 ASP cc_start: 0.6785 (m-30) cc_final: 0.6512 (m-30) REVERT: C 154 PHE cc_start: 0.9033 (t80) cc_final: 0.8537 (t80) REVERT: C 157 MET cc_start: 0.8985 (mtt) cc_final: 0.8626 (mtt) REVERT: C 208 LEU cc_start: 0.7061 (mm) cc_final: 0.6790 (mm) REVERT: C 242 TYR cc_start: 0.8777 (t80) cc_final: 0.8546 (t80) REVERT: C 252 LEU cc_start: 0.7719 (mp) cc_final: 0.7309 (pp) REVERT: C 256 VAL cc_start: 0.8599 (t) cc_final: 0.8319 (t) REVERT: C 286 VAL cc_start: 0.7664 (OUTLIER) cc_final: 0.7390 (m) REVERT: C 288 ASN cc_start: 0.5178 (t0) cc_final: 0.4351 (m-40) REVERT: D 24 GLN cc_start: 0.9341 (tp-100) cc_final: 0.9126 (tp-100) REVERT: D 82 ASP cc_start: 0.8852 (m-30) cc_final: 0.8601 (t0) REVERT: D 154 PHE cc_start: 0.5614 (t80) cc_final: 0.5112 (t80) outliers start: 63 outliers final: 33 residues processed: 744 average time/residue: 0.2662 time to fit residues: 294.4617 Evaluate side-chains 704 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 666 time to evaluate : 1.777 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 646 GLN Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 230 ASP Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 191 optimal weight: 10.0000 chunk 57 optimal weight: 0.0670 chunk 52 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 189 optimal weight: 8.9990 chunk 141 optimal weight: 10.0000 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN B 11 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 338 ASN B 361 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 28 GLN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.140852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.099603 restraints weight = 37089.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.103297 restraints weight = 18356.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.105752 restraints weight = 11032.156| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16386 Z= 0.243 Angle : 0.698 11.059 22134 Z= 0.364 Chirality : 0.046 0.244 2360 Planarity : 0.004 0.039 2818 Dihedral : 11.270 167.649 2245 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 5.24 % Allowed : 22.03 % Favored : 72.73 % 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: 1.32 (0.19), residues: 1932 helix: 1.34 (0.15), residues: 1137 sheet: -0.14 (0.42), residues: 130 loop : 0.49 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 124 HIS 0.006 0.001 HIS C 101 PHE 0.047 0.002 PHE C 109 TYR 0.019 0.002 TYR C 169 ARG 0.007 0.001 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.04371 ( 871) hydrogen bonds : angle 5.13758 ( 2571) covalent geometry : bond 0.00525 (16386) covalent geometry : angle 0.69796 (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 765 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 675 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8733 (pm20) REVERT: A 55 LEU cc_start: 0.9807 (mt) cc_final: 0.9501 (pp) REVERT: A 99 LYS cc_start: 0.9497 (mmmm) cc_final: 0.9170 (mmtm) REVERT: A 123 SER cc_start: 0.9671 (OUTLIER) cc_final: 0.9302 (p) REVERT: A 139 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8344 (mt-10) REVERT: A 149 TYR cc_start: 0.9558 (t80) cc_final: 0.8922 (t80) REVERT: A 190 MET cc_start: 0.9364 (mtp) cc_final: 0.9067 (mtp) REVERT: A 191 GLN cc_start: 0.8994 (mm-40) cc_final: 0.8681 (mm-40) REVERT: A 202 ASN cc_start: 0.9517 (t0) cc_final: 0.9167 (t0) REVERT: A 218 ASN cc_start: 0.8936 (t0) cc_final: 0.8720 (t0) REVERT: A 221 LYS cc_start: 0.9198 (mmtp) cc_final: 0.8995 (mptt) REVERT: A 252 ASN cc_start: 0.9392 (t0) cc_final: 0.9149 (t0) REVERT: A 255 HIS cc_start: 0.8663 (t-90) cc_final: 0.8075 (t-90) REVERT: A 257 ASP cc_start: 0.9482 (m-30) cc_final: 0.8905 (m-30) REVERT: A 259 ASN cc_start: 0.8922 (m-40) cc_final: 0.8583 (m-40) REVERT: A 263 ASP cc_start: 0.8726 (m-30) cc_final: 0.8431 (m-30) REVERT: A 274 ARG cc_start: 0.8912 (ptm160) cc_final: 0.8646 (ptp-110) REVERT: A 277 THR cc_start: 0.8890 (p) cc_final: 0.8509 (t) REVERT: A 318 ASP cc_start: 0.9119 (t0) cc_final: 0.8910 (t0) REVERT: A 322 MET cc_start: 0.8797 (mmm) cc_final: 0.8526 (mmm) REVERT: A 335 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8078 (mm-30) REVERT: A 348 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8671 (tmm) REVERT: A 349 LEU cc_start: 0.9581 (OUTLIER) cc_final: 0.9351 (mp) REVERT: A 350 ARG cc_start: 0.9299 (mtp180) cc_final: 0.9001 (mtp180) REVERT: A 359 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8596 (ttp) REVERT: A 379 SER cc_start: 0.9407 (t) cc_final: 0.9002 (t) REVERT: A 393 SER cc_start: 0.9355 (m) cc_final: 0.9033 (p) REVERT: A 400 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8624 (mm-30) REVERT: A 402 GLU cc_start: 0.8102 (mp0) cc_final: 0.7761 (mp0) REVERT: A 426 GLU cc_start: 0.8364 (tm-30) cc_final: 0.8085 (tm-30) REVERT: A 501 GLN cc_start: 0.9301 (OUTLIER) cc_final: 0.8879 (tt0) REVERT: A 505 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8347 (mt-10) REVERT: A 515 ASP cc_start: 0.9098 (m-30) cc_final: 0.8685 (m-30) REVERT: A 548 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.8308 (mm-30) REVERT: A 590 SER cc_start: 0.9431 (t) cc_final: 0.9086 (p) REVERT: A 606 TYR cc_start: 0.8262 (m-80) cc_final: 0.7450 (m-80) REVERT: A 615 MET cc_start: 0.9221 (mmp) cc_final: 0.8777 (mmm) REVERT: A 639 ASP cc_start: 0.9035 (m-30) cc_final: 0.8268 (m-30) REVERT: B 8 LYS cc_start: 0.8839 (tppt) cc_final: 0.8579 (tppt) REVERT: B 65 GLU cc_start: 0.8547 (mm-30) cc_final: 0.8038 (mm-30) REVERT: B 95 MET cc_start: 0.9170 (tpp) cc_final: 0.8926 (tpp) REVERT: B 99 LYS cc_start: 0.9416 (mmtt) cc_final: 0.9140 (mmtt) REVERT: B 119 GLU cc_start: 0.9155 (mp0) cc_final: 0.8547 (mp0) REVERT: B 147 GLN cc_start: 0.9186 (mt0) cc_final: 0.8561 (mt0) REVERT: B 227 MET cc_start: 0.9309 (mtp) cc_final: 0.8970 (mtp) REVERT: B 236 TYR cc_start: 0.9175 (t80) cc_final: 0.8567 (t80) REVERT: B 246 SER cc_start: 0.7937 (m) cc_final: 0.7473 (p) REVERT: B 250 TYR cc_start: 0.9167 (m-80) cc_final: 0.8782 (m-80) REVERT: B 257 ASP cc_start: 0.8756 (m-30) cc_final: 0.8205 (m-30) REVERT: B 279 SER cc_start: 0.8921 (m) cc_final: 0.8630 (t) REVERT: B 317 MET cc_start: 0.8662 (pmm) cc_final: 0.8378 (pmm) REVERT: B 322 MET cc_start: 0.9303 (mmm) cc_final: 0.8783 (mmm) REVERT: B 370 ASN cc_start: 0.9364 (m-40) cc_final: 0.9159 (m-40) REVERT: B 378 PHE cc_start: 0.9091 (p90) cc_final: 0.8812 (p90) REVERT: B 393 SER cc_start: 0.9382 (m) cc_final: 0.8878 (p) REVERT: B 474 GLN cc_start: 0.8914 (mt0) cc_final: 0.8669 (mm-40) REVERT: B 475 ASN cc_start: 0.9347 (m-40) cc_final: 0.8968 (m110) REVERT: B 515 ASP cc_start: 0.9098 (m-30) cc_final: 0.8769 (m-30) REVERT: B 546 LEU cc_start: 0.9628 (mt) cc_final: 0.9380 (mt) REVERT: B 550 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7533 (mtp) REVERT: B 599 GLU cc_start: 0.8460 (pt0) cc_final: 0.8119 (pt0) REVERT: B 601 ILE cc_start: 0.9479 (mm) cc_final: 0.9148 (mm) REVERT: B 604 ARG cc_start: 0.8527 (mmt-90) cc_final: 0.7944 (mmt-90) REVERT: B 610 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8467 (ptmm) REVERT: B 612 TYR cc_start: 0.9197 (m-80) cc_final: 0.8778 (m-80) REVERT: B 648 ILE cc_start: 0.9489 (mm) cc_final: 0.9239 (mm) REVERT: B 677 ARG cc_start: 0.9321 (mmm-85) cc_final: 0.8907 (mmm160) REVERT: B 680 LYS cc_start: 0.8933 (mttt) cc_final: 0.8604 (mttt) REVERT: C 66 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.6616 (t0) REVERT: C 68 GLU cc_start: 0.9111 (mm-30) cc_final: 0.8898 (mm-30) REVERT: C 69 GLN cc_start: 0.9242 (tp40) cc_final: 0.8961 (pt0) REVERT: C 74 MET cc_start: 0.9322 (mmm) cc_final: 0.8639 (tpt) REVERT: C 149 ASP cc_start: 0.7033 (m-30) cc_final: 0.6694 (m-30) REVERT: C 154 PHE cc_start: 0.9192 (t80) cc_final: 0.8723 (t80) REVERT: C 157 MET cc_start: 0.9095 (mtt) cc_final: 0.8618 (mtt) REVERT: C 208 LEU cc_start: 0.7146 (mm) cc_final: 0.6833 (mm) REVERT: C 212 ILE cc_start: 0.7319 (mt) cc_final: 0.6106 (mt) REVERT: C 242 TYR cc_start: 0.9021 (t80) cc_final: 0.8753 (t80) REVERT: C 288 ASN cc_start: 0.5309 (t0) cc_final: 0.4411 (m-40) REVERT: D 82 ASP cc_start: 0.8795 (m-30) cc_final: 0.8582 (m-30) REVERT: D 97 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.6104 (mp0) REVERT: D 120 GLU cc_start: 0.9355 (mt-10) cc_final: 0.8890 (tp30) REVERT: D 316 LYS cc_start: 0.9296 (ttmm) cc_final: 0.9027 (ttpp) outliers start: 90 outliers final: 52 residues processed: 715 average time/residue: 0.2556 time to fit residues: 272.3028 Evaluate side-chains 686 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 624 time to evaluate : 1.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 312 GLN Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 191 GLN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 550 MET Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 89 VAL Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 97 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 240 LEU Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 180 optimal weight: 2.9990 chunk 99 optimal weight: 0.5980 chunk 1 optimal weight: 0.0670 chunk 39 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 69 optimal weight: 0.0170 chunk 71 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 overall best weight: 0.9358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 HIS A 501 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.141554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.101692 restraints weight = 36019.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.105271 restraints weight = 17734.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.107646 restraints weight = 10657.280| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.5754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16386 Z= 0.150 Angle : 0.688 14.907 22134 Z= 0.351 Chirality : 0.045 0.204 2360 Planarity : 0.004 0.043 2818 Dihedral : 10.878 162.482 2243 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.20 % Allowed : 25.64 % Favored : 70.16 % 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: 1.20 (0.18), residues: 1932 helix: 1.32 (0.15), residues: 1114 sheet: 0.20 (0.44), residues: 114 loop : 0.21 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 124 HIS 0.005 0.001 HIS C 201 PHE 0.052 0.002 PHE C 109 TYR 0.019 0.002 TYR B 683 ARG 0.005 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 871) hydrogen bonds : angle 5.07912 ( 2571) covalent geometry : bond 0.00341 (16386) covalent geometry : angle 0.68771 (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 740 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 668 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8978 (ttmm) cc_final: 0.8744 (ttpt) REVERT: A 31 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8811 (pm20) REVERT: A 51 LEU cc_start: 0.9322 (tp) cc_final: 0.9079 (tp) REVERT: A 55 LEU cc_start: 0.9805 (mt) cc_final: 0.9482 (pp) REVERT: A 99 LYS cc_start: 0.9519 (mmmm) cc_final: 0.9233 (mmtm) REVERT: A 123 SER cc_start: 0.9554 (OUTLIER) cc_final: 0.9300 (p) REVERT: A 139 GLU cc_start: 0.8701 (mt-10) cc_final: 0.8334 (mt-10) REVERT: A 149 TYR cc_start: 0.9570 (t80) cc_final: 0.8580 (t80) REVERT: A 150 GLN cc_start: 0.9411 (tp40) cc_final: 0.9012 (tm-30) REVERT: A 161 ARG cc_start: 0.8393 (ttm110) cc_final: 0.6967 (mtp85) REVERT: A 190 MET cc_start: 0.9353 (mtp) cc_final: 0.9083 (mtp) REVERT: A 202 ASN cc_start: 0.9473 (t0) cc_final: 0.9136 (t0) REVERT: A 218 ASN cc_start: 0.9073 (t0) cc_final: 0.8797 (t0) REVERT: A 221 LYS cc_start: 0.9137 (mmtp) cc_final: 0.8883 (mttp) REVERT: A 252 ASN cc_start: 0.9425 (t0) cc_final: 0.9153 (t0) REVERT: A 255 HIS cc_start: 0.8554 (t-90) cc_final: 0.7937 (t-90) REVERT: A 257 ASP cc_start: 0.9460 (m-30) cc_final: 0.8883 (m-30) REVERT: A 259 ASN cc_start: 0.8923 (m-40) cc_final: 0.8578 (m-40) REVERT: A 263 ASP cc_start: 0.8747 (m-30) cc_final: 0.8495 (m-30) REVERT: A 277 THR cc_start: 0.8812 (p) cc_final: 0.8409 (t) REVERT: A 286 ASP cc_start: 0.8567 (m-30) cc_final: 0.8156 (m-30) REVERT: A 321 GLU cc_start: 0.8220 (pp20) cc_final: 0.7996 (pp20) REVERT: A 322 MET cc_start: 0.8763 (mmm) cc_final: 0.8340 (mmm) REVERT: A 335 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8019 (mm-30) REVERT: A 362 ASP cc_start: 0.8294 (m-30) cc_final: 0.7743 (m-30) REVERT: A 393 SER cc_start: 0.9322 (m) cc_final: 0.9053 (p) REVERT: A 402 GLU cc_start: 0.8188 (mp0) cc_final: 0.7875 (mp0) REVERT: A 426 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8139 (tm-30) REVERT: A 479 TYR cc_start: 0.9146 (t80) cc_final: 0.8931 (t80) REVERT: A 505 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8288 (mt-10) REVERT: A 515 ASP cc_start: 0.9099 (m-30) cc_final: 0.8602 (m-30) REVERT: A 548 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8220 (mm-30) REVERT: A 550 MET cc_start: 0.7303 (mtm) cc_final: 0.7101 (mtm) REVERT: A 583 SER cc_start: 0.9251 (m) cc_final: 0.8592 (t) REVERT: A 588 GLN cc_start: 0.9397 (mm-40) cc_final: 0.9081 (mm-40) REVERT: A 606 TYR cc_start: 0.7970 (m-80) cc_final: 0.7129 (m-80) REVERT: A 615 MET cc_start: 0.9229 (mmp) cc_final: 0.8768 (mmp) REVERT: A 639 ASP cc_start: 0.8984 (m-30) cc_final: 0.8178 (m-30) REVERT: A 640 MET cc_start: 0.9400 (tpp) cc_final: 0.8367 (tpp) REVERT: B 8 LYS cc_start: 0.8814 (tppt) cc_final: 0.8546 (tppt) REVERT: B 43 GLN cc_start: 0.9334 (mp10) cc_final: 0.9087 (mp10) REVERT: B 65 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8056 (mm-30) REVERT: B 79 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8615 (pt0) REVERT: B 95 MET cc_start: 0.9120 (tpp) cc_final: 0.8776 (tpp) REVERT: B 99 LYS cc_start: 0.9373 (mmtt) cc_final: 0.9088 (mmtt) REVERT: B 119 GLU cc_start: 0.9028 (mp0) cc_final: 0.8420 (mp0) REVERT: B 127 LEU cc_start: 0.9710 (mm) cc_final: 0.9420 (mm) REVERT: B 147 GLN cc_start: 0.9173 (mt0) cc_final: 0.8552 (mt0) REVERT: B 149 TYR cc_start: 0.9334 (t80) cc_final: 0.9111 (t80) REVERT: B 191 GLN cc_start: 0.8607 (mm-40) cc_final: 0.8368 (mt0) REVERT: B 227 MET cc_start: 0.9274 (mtp) cc_final: 0.8991 (mtp) REVERT: B 228 LYS cc_start: 0.9374 (tttt) cc_final: 0.9168 (mmtm) REVERT: B 236 TYR cc_start: 0.9077 (t80) cc_final: 0.8537 (t80) REVERT: B 246 SER cc_start: 0.7934 (m) cc_final: 0.7542 (p) REVERT: B 250 TYR cc_start: 0.9203 (m-80) cc_final: 0.8727 (m-80) REVERT: B 256 ARG cc_start: 0.8976 (ttt-90) cc_final: 0.8468 (ttt90) REVERT: B 257 ASP cc_start: 0.8789 (m-30) cc_final: 0.8175 (m-30) REVERT: B 312 GLN cc_start: 0.8789 (mp10) cc_final: 0.8574 (pm20) REVERT: B 322 MET cc_start: 0.9149 (mmm) cc_final: 0.8615 (mmm) REVERT: B 344 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8609 (mt-10) REVERT: B 370 ASN cc_start: 0.9341 (m-40) cc_final: 0.9140 (m-40) REVERT: B 378 PHE cc_start: 0.8953 (p90) cc_final: 0.8721 (p90) REVERT: B 393 SER cc_start: 0.9410 (m) cc_final: 0.8968 (p) REVERT: B 396 ASP cc_start: 0.8575 (p0) cc_final: 0.8284 (p0) REVERT: B 441 GLU cc_start: 0.8505 (mt-10) cc_final: 0.8231 (mt-10) REVERT: B 467 ASN cc_start: 0.9341 (t0) cc_final: 0.9097 (m-40) REVERT: B 474 GLN cc_start: 0.8925 (mt0) cc_final: 0.8710 (mm110) REVERT: B 475 ASN cc_start: 0.9306 (m-40) cc_final: 0.8936 (m110) REVERT: B 492 PHE cc_start: 0.9529 (m-80) cc_final: 0.9144 (m-80) REVERT: B 515 ASP cc_start: 0.9067 (m-30) cc_final: 0.8643 (m-30) REVERT: B 516 GLN cc_start: 0.9255 (mt0) cc_final: 0.8975 (tp-100) REVERT: B 546 LEU cc_start: 0.9601 (mt) cc_final: 0.9378 (mt) REVERT: B 599 GLU cc_start: 0.8396 (pt0) cc_final: 0.8090 (pt0) REVERT: B 601 ILE cc_start: 0.9428 (mm) cc_final: 0.8952 (mm) REVERT: B 610 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8586 (ptmm) REVERT: B 612 TYR cc_start: 0.9181 (m-80) cc_final: 0.8793 (m-80) REVERT: B 632 MET cc_start: 0.8304 (mtt) cc_final: 0.7977 (mtm) REVERT: B 677 ARG cc_start: 0.9294 (mmm-85) cc_final: 0.8938 (mmm160) REVERT: B 683 TYR cc_start: 0.9052 (t80) cc_final: 0.8570 (t80) REVERT: B 684 TYR cc_start: 0.7991 (OUTLIER) cc_final: 0.7254 (m-80) REVERT: C 21 PHE cc_start: 0.8241 (m-80) cc_final: 0.7969 (m-80) REVERT: C 66 ASP cc_start: 0.7965 (OUTLIER) cc_final: 0.6677 (t0) REVERT: C 68 GLU cc_start: 0.9092 (mm-30) cc_final: 0.8830 (mm-30) REVERT: C 74 MET cc_start: 0.9273 (mmm) cc_final: 0.8653 (tpp) REVERT: C 122 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7764 (m-80) REVERT: C 154 PHE cc_start: 0.9170 (t80) cc_final: 0.8635 (t80) REVERT: C 157 MET cc_start: 0.9164 (mtt) cc_final: 0.8777 (mtt) REVERT: C 212 ILE cc_start: 0.7409 (mt) cc_final: 0.6348 (mt) REVERT: C 242 TYR cc_start: 0.8973 (t80) cc_final: 0.8712 (t80) REVERT: C 288 ASN cc_start: 0.5295 (t0) cc_final: 0.4423 (m-40) REVERT: D 21 PHE cc_start: 0.9248 (m-80) cc_final: 0.8754 (m-80) REVERT: D 82 ASP cc_start: 0.8764 (m-30) cc_final: 0.8533 (m-30) outliers start: 72 outliers final: 38 residues processed: 699 average time/residue: 0.2545 time to fit residues: 266.4546 Evaluate side-chains 656 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 612 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 122 PHE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 67 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 57 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 175 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 86 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN B 646 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN C 85 GLN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.141390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.100665 restraints weight = 36637.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.104335 restraints weight = 18178.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.106723 restraints weight = 10998.484| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.6162 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= 0.163 Angle : 0.700 15.597 22134 Z= 0.354 Chirality : 0.045 0.197 2360 Planarity : 0.004 0.035 2818 Dihedral : 10.753 163.001 2243 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.20 % Allowed : 27.16 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.19), residues: 1932 helix: 1.26 (0.15), residues: 1113 sheet: -0.68 (0.38), residues: 148 loop : 0.29 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 124 HIS 0.014 0.001 HIS A 647 PHE 0.054 0.002 PHE C 109 TYR 0.019 0.002 TYR D 236 ARG 0.007 0.001 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.04037 ( 871) hydrogen bonds : angle 5.04797 ( 2571) covalent geometry : bond 0.00369 (16386) covalent geometry : angle 0.70021 (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 700 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 628 time to evaluate : 1.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8966 (ttmm) cc_final: 0.8712 (ttpt) REVERT: A 31 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8759 (mp0) REVERT: A 51 LEU cc_start: 0.9305 (tp) cc_final: 0.9046 (tp) REVERT: A 55 LEU cc_start: 0.9816 (mt) cc_final: 0.9490 (pp) REVERT: A 99 LYS cc_start: 0.9522 (mmmm) cc_final: 0.9250 (mmtm) REVERT: A 107 LYS cc_start: 0.9170 (mmtt) cc_final: 0.8812 (mmmm) REVERT: A 123 SER cc_start: 0.9524 (OUTLIER) cc_final: 0.9212 (p) REVERT: A 139 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8514 (mt-10) REVERT: A 149 TYR cc_start: 0.9559 (t80) cc_final: 0.8585 (t80) REVERT: A 150 GLN cc_start: 0.9421 (tp40) cc_final: 0.9023 (tm-30) REVERT: A 180 ASN cc_start: 0.8697 (OUTLIER) cc_final: 0.8412 (m-40) REVERT: A 190 MET cc_start: 0.9343 (mtp) cc_final: 0.9087 (mtp) REVERT: A 202 ASN cc_start: 0.9372 (t0) cc_final: 0.8944 (t0) REVERT: A 218 ASN cc_start: 0.9291 (t0) cc_final: 0.8992 (t0) REVERT: A 221 LYS cc_start: 0.9148 (mmtp) cc_final: 0.8926 (mttp) REVERT: A 252 ASN cc_start: 0.9383 (t0) cc_final: 0.8992 (t0) REVERT: A 255 HIS cc_start: 0.8555 (t-90) cc_final: 0.7989 (t-90) REVERT: A 257 ASP cc_start: 0.9461 (m-30) cc_final: 0.8787 (m-30) REVERT: A 263 ASP cc_start: 0.8777 (m-30) cc_final: 0.8520 (m-30) REVERT: A 277 THR cc_start: 0.8799 (p) cc_final: 0.8381 (t) REVERT: A 286 ASP cc_start: 0.8597 (m-30) cc_final: 0.8280 (m-30) REVERT: A 322 MET cc_start: 0.8782 (mmm) cc_final: 0.8515 (mmm) REVERT: A 335 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8095 (mm-30) REVERT: A 348 MET cc_start: 0.8900 (OUTLIER) cc_final: 0.8511 (tmm) REVERT: A 362 ASP cc_start: 0.8226 (m-30) cc_final: 0.7517 (m-30) REVERT: A 384 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.7805 (pm20) REVERT: A 393 SER cc_start: 0.9313 (m) cc_final: 0.9053 (p) REVERT: A 402 GLU cc_start: 0.8270 (mp0) cc_final: 0.7917 (mp0) REVERT: A 426 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8203 (tm-30) REVERT: A 479 TYR cc_start: 0.9106 (t80) cc_final: 0.8700 (t80) REVERT: A 493 MET cc_start: 0.9114 (tmm) cc_final: 0.8718 (tmm) REVERT: A 505 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8426 (mt-10) REVERT: A 515 ASP cc_start: 0.9137 (m-30) cc_final: 0.8669 (m-30) REVERT: A 528 PHE cc_start: 0.9056 (m-80) cc_final: 0.8616 (m-80) REVERT: A 548 GLU cc_start: 0.8507 (OUTLIER) cc_final: 0.8168 (mm-30) REVERT: A 588 GLN cc_start: 0.9397 (mm-40) cc_final: 0.9091 (mm-40) REVERT: A 606 TYR cc_start: 0.7930 (m-80) cc_final: 0.7131 (m-80) REVERT: A 615 MET cc_start: 0.9293 (mmp) cc_final: 0.8823 (mmp) REVERT: A 621 ASN cc_start: 0.9498 (OUTLIER) cc_final: 0.9267 (p0) REVERT: A 640 MET cc_start: 0.9422 (tpp) cc_final: 0.8363 (tpp) REVERT: B 8 LYS cc_start: 0.8933 (tppt) cc_final: 0.8681 (tppt) REVERT: B 17 MET cc_start: 0.8757 (mmm) cc_final: 0.8450 (mmm) REVERT: B 65 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8273 (mm-30) REVERT: B 79 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8594 (pt0) REVERT: B 95 MET cc_start: 0.9128 (tpp) cc_final: 0.8805 (tpp) REVERT: B 99 LYS cc_start: 0.9390 (mmtt) cc_final: 0.9104 (mmtt) REVERT: B 111 LYS cc_start: 0.9548 (mmtp) cc_final: 0.9287 (mmtm) REVERT: B 117 ARG cc_start: 0.8882 (mtp85) cc_final: 0.8577 (mtp85) REVERT: B 119 GLU cc_start: 0.9010 (mp0) cc_final: 0.8250 (mp0) REVERT: B 147 GLN cc_start: 0.9234 (mt0) cc_final: 0.8639 (mt0) REVERT: B 149 TYR cc_start: 0.9382 (t80) cc_final: 0.9021 (t80) REVERT: B 211 GLU cc_start: 0.8075 (mm-30) cc_final: 0.7638 (mm-30) REVERT: B 227 MET cc_start: 0.9218 (mtp) cc_final: 0.8951 (mtp) REVERT: B 235 ARG cc_start: 0.9111 (ttm-80) cc_final: 0.8797 (mtt-85) REVERT: B 236 TYR cc_start: 0.9059 (t80) cc_final: 0.8496 (t80) REVERT: B 246 SER cc_start: 0.7817 (m) cc_final: 0.7511 (p) REVERT: B 250 TYR cc_start: 0.9228 (m-80) cc_final: 0.8535 (m-80) REVERT: B 257 ASP cc_start: 0.8791 (m-30) cc_final: 0.8328 (m-30) REVERT: B 263 ASP cc_start: 0.9301 (m-30) cc_final: 0.9095 (m-30) REVERT: B 279 SER cc_start: 0.8752 (m) cc_final: 0.8434 (t) REVERT: B 322 MET cc_start: 0.9400 (mmm) cc_final: 0.8909 (mmm) REVERT: B 370 ASN cc_start: 0.9370 (m-40) cc_final: 0.9128 (m-40) REVERT: B 375 LYS cc_start: 0.9420 (mttm) cc_final: 0.9212 (mttp) REVERT: B 393 SER cc_start: 0.9384 (m) cc_final: 0.9005 (p) REVERT: B 467 ASN cc_start: 0.9409 (t0) cc_final: 0.9153 (m-40) REVERT: B 475 ASN cc_start: 0.9333 (m-40) cc_final: 0.8962 (m110) REVERT: B 515 ASP cc_start: 0.9065 (m-30) cc_final: 0.8686 (m-30) REVERT: B 546 LEU cc_start: 0.9599 (mt) cc_final: 0.9375 (mt) REVERT: B 599 GLU cc_start: 0.8420 (pt0) cc_final: 0.8116 (pt0) REVERT: B 601 ILE cc_start: 0.9405 (mm) cc_final: 0.8976 (mm) REVERT: B 604 ARG cc_start: 0.8592 (mmp80) cc_final: 0.8352 (mmp80) REVERT: B 610 LYS cc_start: 0.8887 (ptmt) cc_final: 0.8642 (ptmm) REVERT: B 612 TYR cc_start: 0.9173 (m-80) cc_final: 0.8741 (m-80) REVERT: B 640 MET cc_start: 0.9222 (tpp) cc_final: 0.8964 (tpp) REVERT: B 680 LYS cc_start: 0.8901 (mttt) cc_final: 0.8642 (mttt) REVERT: B 683 TYR cc_start: 0.9074 (t80) cc_final: 0.8625 (t80) REVERT: B 684 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.7351 (m-80) REVERT: C 66 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.6963 (t0) REVERT: C 68 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8864 (mm-30) REVERT: C 74 MET cc_start: 0.9257 (mmm) cc_final: 0.8783 (tpp) REVERT: C 127 GLN cc_start: 0.8500 (mm110) cc_final: 0.7389 (pp30) REVERT: C 154 PHE cc_start: 0.9188 (t80) cc_final: 0.8664 (t80) REVERT: C 157 MET cc_start: 0.9179 (mtt) cc_final: 0.8895 (mtt) REVERT: C 185 MET cc_start: -0.3794 (mpp) cc_final: -0.4085 (mmm) REVERT: C 212 ILE cc_start: 0.7361 (mt) cc_final: 0.6263 (mt) REVERT: C 242 TYR cc_start: 0.9200 (t80) cc_final: 0.8932 (t80) REVERT: C 269 MET cc_start: 0.8525 (ptp) cc_final: 0.8059 (ptp) REVERT: C 286 VAL cc_start: 0.7678 (OUTLIER) cc_final: 0.7476 (m) REVERT: C 288 ASN cc_start: 0.5271 (t0) cc_final: 0.4365 (m-40) REVERT: D 21 PHE cc_start: 0.9176 (m-80) cc_final: 0.8734 (m-80) REVERT: D 82 ASP cc_start: 0.8802 (m-30) cc_final: 0.8589 (m-30) outliers start: 72 outliers final: 47 residues processed: 660 average time/residue: 0.2730 time to fit residues: 271.9366 Evaluate side-chains 644 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 588 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 570 MET Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain D residue 55 TYR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 31 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 62 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 156 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 113 optimal weight: 9.9990 chunk 177 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN A 676 HIS ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 71 ASN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.141780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.101784 restraints weight = 36508.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.105455 restraints weight = 18157.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.107789 restraints weight = 10894.867| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.6492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16386 Z= 0.157 Angle : 0.695 14.871 22134 Z= 0.352 Chirality : 0.046 0.186 2360 Planarity : 0.004 0.041 2818 Dihedral : 10.656 166.321 2243 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.25 % Allowed : 27.21 % Favored : 68.53 % 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: 0.87 (0.18), residues: 1932 helix: 1.13 (0.15), residues: 1119 sheet: -0.73 (0.38), residues: 148 loop : 0.14 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP D 44 HIS 0.006 0.001 HIS A 647 PHE 0.058 0.002 PHE C 109 TYR 0.021 0.001 TYR D 236 ARG 0.008 0.001 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.04001 ( 871) hydrogen bonds : angle 5.02305 ( 2571) covalent geometry : bond 0.00356 (16386) covalent geometry : angle 0.69484 (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 689 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 616 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.8991 (ttmm) cc_final: 0.8773 (ttpt) REVERT: A 31 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8735 (mp0) REVERT: A 55 LEU cc_start: 0.9810 (mt) cc_final: 0.9483 (pp) REVERT: A 99 LYS cc_start: 0.9493 (mmmm) cc_final: 0.9280 (tppt) REVERT: A 107 LYS cc_start: 0.9218 (mmtt) cc_final: 0.8797 (mmmm) REVERT: A 123 SER cc_start: 0.9494 (OUTLIER) cc_final: 0.9184 (p) REVERT: A 139 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8492 (mt-10) REVERT: A 149 TYR cc_start: 0.9584 (t80) cc_final: 0.8557 (t80) REVERT: A 150 GLN cc_start: 0.9430 (tp40) cc_final: 0.9079 (tm-30) REVERT: A 180 ASN cc_start: 0.8627 (m110) cc_final: 0.8244 (m-40) REVERT: A 190 MET cc_start: 0.9324 (mtp) cc_final: 0.9085 (mtp) REVERT: A 202 ASN cc_start: 0.9362 (t0) cc_final: 0.8897 (t0) REVERT: A 218 ASN cc_start: 0.9325 (t0) cc_final: 0.9079 (t0) REVERT: A 221 LYS cc_start: 0.9157 (mmtp) cc_final: 0.8939 (mttp) REVERT: A 252 ASN cc_start: 0.9422 (t0) cc_final: 0.9155 (t0) REVERT: A 255 HIS cc_start: 0.8618 (t-90) cc_final: 0.8401 (t-90) REVERT: A 263 ASP cc_start: 0.8768 (m-30) cc_final: 0.8457 (m-30) REVERT: A 277 THR cc_start: 0.8750 (p) cc_final: 0.8333 (t) REVERT: A 286 ASP cc_start: 0.8587 (m-30) cc_final: 0.8262 (m-30) REVERT: A 290 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8542 (tm-30) REVERT: A 335 GLU cc_start: 0.8328 (mm-30) cc_final: 0.8031 (mm-30) REVERT: A 348 MET cc_start: 0.8926 (OUTLIER) cc_final: 0.8595 (tmm) REVERT: A 362 ASP cc_start: 0.8189 (m-30) cc_final: 0.7374 (m-30) REVERT: A 384 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.7772 (pm20) REVERT: A 393 SER cc_start: 0.9288 (m) cc_final: 0.9059 (p) REVERT: A 402 GLU cc_start: 0.8330 (mp0) cc_final: 0.7962 (mp0) REVERT: A 420 MET cc_start: 0.9221 (mmm) cc_final: 0.8980 (tpt) REVERT: A 426 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8192 (tm-30) REVERT: A 446 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7450 (mmm160) REVERT: A 452 ARG cc_start: 0.9301 (OUTLIER) cc_final: 0.8870 (ttt-90) REVERT: A 505 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8366 (mt-10) REVERT: A 515 ASP cc_start: 0.9145 (m-30) cc_final: 0.8760 (m-30) REVERT: A 548 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.8191 (mm-30) REVERT: A 588 GLN cc_start: 0.9371 (mm-40) cc_final: 0.9100 (mm-40) REVERT: A 606 TYR cc_start: 0.7950 (m-80) cc_final: 0.7080 (m-80) REVERT: A 615 MET cc_start: 0.9331 (mmp) cc_final: 0.8841 (mmp) REVERT: A 621 ASN cc_start: 0.9497 (OUTLIER) cc_final: 0.9282 (p0) REVERT: A 640 MET cc_start: 0.9426 (tpp) cc_final: 0.8371 (tpp) REVERT: B 8 LYS cc_start: 0.8934 (tppt) cc_final: 0.8686 (tppt) REVERT: B 16 ILE cc_start: 0.9575 (mm) cc_final: 0.8758 (mm) REVERT: B 17 MET cc_start: 0.8739 (mmm) cc_final: 0.8318 (mmm) REVERT: B 65 GLU cc_start: 0.8603 (mm-30) cc_final: 0.8262 (mm-30) REVERT: B 79 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8591 (pt0) REVERT: B 87 LYS cc_start: 0.9397 (mmmt) cc_final: 0.9063 (tptm) REVERT: B 95 MET cc_start: 0.9100 (tpp) cc_final: 0.8683 (tpp) REVERT: B 99 LYS cc_start: 0.9385 (mmtt) cc_final: 0.9110 (mmtt) REVERT: B 107 LYS cc_start: 0.9174 (mtpp) cc_final: 0.8630 (mtpp) REVERT: B 111 LYS cc_start: 0.9530 (mmtp) cc_final: 0.9292 (mmtm) REVERT: B 119 GLU cc_start: 0.9001 (mp0) cc_final: 0.8271 (mp0) REVERT: B 147 GLN cc_start: 0.9249 (mt0) cc_final: 0.8670 (mt0) REVERT: B 149 TYR cc_start: 0.9421 (t80) cc_final: 0.8847 (t80) REVERT: B 236 TYR cc_start: 0.9005 (t80) cc_final: 0.8447 (t80) REVERT: B 246 SER cc_start: 0.7784 (m) cc_final: 0.7579 (p) REVERT: B 250 TYR cc_start: 0.9318 (m-80) cc_final: 0.8628 (m-80) REVERT: B 257 ASP cc_start: 0.8812 (m-30) cc_final: 0.8319 (m-30) REVERT: B 263 ASP cc_start: 0.9251 (m-30) cc_final: 0.9011 (m-30) REVERT: B 333 LYS cc_start: 0.9241 (tptp) cc_final: 0.8980 (ttmm) REVERT: B 375 LYS cc_start: 0.9411 (mttm) cc_final: 0.9204 (mttp) REVERT: B 393 SER cc_start: 0.9359 (m) cc_final: 0.9000 (p) REVERT: B 467 ASN cc_start: 0.9318 (t0) cc_final: 0.9114 (m-40) REVERT: B 475 ASN cc_start: 0.9265 (m-40) cc_final: 0.9005 (m110) REVERT: B 492 PHE cc_start: 0.9524 (m-80) cc_final: 0.9294 (m-10) REVERT: B 515 ASP cc_start: 0.9024 (m-30) cc_final: 0.8643 (m-30) REVERT: B 576 LEU cc_start: 0.9494 (mt) cc_final: 0.9211 (mt) REVERT: B 586 TYR cc_start: 0.9138 (m-80) cc_final: 0.8885 (m-80) REVERT: B 601 ILE cc_start: 0.9431 (mm) cc_final: 0.8974 (mm) REVERT: B 604 ARG cc_start: 0.8657 (mmp80) cc_final: 0.8195 (mmp80) REVERT: B 610 LYS cc_start: 0.8837 (ptmt) cc_final: 0.8554 (ptmt) REVERT: B 612 TYR cc_start: 0.9135 (m-80) cc_final: 0.8867 (m-80) REVERT: B 680 LYS cc_start: 0.8863 (mttt) cc_final: 0.8597 (mttt) REVERT: B 683 TYR cc_start: 0.9079 (t80) cc_final: 0.8765 (t80) REVERT: B 684 TYR cc_start: 0.8080 (OUTLIER) cc_final: 0.7564 (m-80) REVERT: C 21 PHE cc_start: 0.8334 (m-80) cc_final: 0.8082 (m-80) REVERT: C 68 GLU cc_start: 0.9154 (mm-30) cc_final: 0.8880 (mm-30) REVERT: C 74 MET cc_start: 0.9195 (mmm) cc_final: 0.8809 (tpp) REVERT: C 127 GLN cc_start: 0.8565 (mm110) cc_final: 0.7531 (pp30) REVERT: C 154 PHE cc_start: 0.9143 (t80) cc_final: 0.8737 (t80) REVERT: C 157 MET cc_start: 0.9261 (mtt) cc_final: 0.8969 (mtt) REVERT: C 177 TYR cc_start: 0.7689 (OUTLIER) cc_final: 0.7307 (t80) REVERT: C 212 ILE cc_start: 0.7416 (mt) cc_final: 0.6286 (mt) REVERT: C 242 TYR cc_start: 0.9200 (t80) cc_final: 0.8987 (t80) REVERT: C 269 MET cc_start: 0.8715 (ptp) cc_final: 0.8452 (ptt) REVERT: C 283 ASN cc_start: 0.5907 (t0) cc_final: 0.5473 (t0) REVERT: D 21 PHE cc_start: 0.8989 (m-80) cc_final: 0.8486 (m-80) REVERT: D 313 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8409 (tm-30) outliers start: 73 outliers final: 47 residues processed: 649 average time/residue: 0.2634 time to fit residues: 257.3595 Evaluate side-chains 644 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 588 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 148 GLU 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 183 SER Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 55 TYR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 39 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 161 optimal weight: 20.0000 chunk 23 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 chunk 184 optimal weight: 7.9990 chunk 119 optimal weight: 0.5980 chunk 175 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 474 GLN B 645 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.143159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.101933 restraints weight = 37159.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.105709 restraints weight = 18545.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.108019 restraints weight = 11238.700| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.6765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16386 Z= 0.150 Angle : 0.712 15.680 22134 Z= 0.358 Chirality : 0.045 0.224 2360 Planarity : 0.004 0.040 2818 Dihedral : 10.525 167.168 2243 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.08 % Allowed : 29.60 % Favored : 66.32 % 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: 0.86 (0.18), residues: 1932 helix: 1.12 (0.15), residues: 1119 sheet: 0.02 (0.45), residues: 104 loop : -0.08 (0.22), residues: 709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 124 HIS 0.007 0.001 HIS C 201 PHE 0.056 0.002 PHE C 109 TYR 0.018 0.001 TYR A 531 ARG 0.006 0.001 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 871) hydrogen bonds : angle 5.04869 ( 2571) covalent geometry : bond 0.00340 (16386) covalent geometry : angle 0.71226 (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 681 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 611 time to evaluate : 1.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9008 (ttmm) cc_final: 0.8768 (ttpt) REVERT: A 31 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8894 (mp0) REVERT: A 55 LEU cc_start: 0.9816 (mt) cc_final: 0.9493 (pp) REVERT: A 107 LYS cc_start: 0.9224 (mmtt) cc_final: 0.8809 (mmmm) REVERT: A 123 SER cc_start: 0.9418 (OUTLIER) cc_final: 0.9090 (p) REVERT: A 139 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8425 (mt-10) REVERT: A 149 TYR cc_start: 0.9605 (t80) cc_final: 0.8540 (t80) REVERT: A 150 GLN cc_start: 0.9444 (tp40) cc_final: 0.9091 (tm-30) REVERT: A 202 ASN cc_start: 0.9336 (t0) cc_final: 0.8891 (t0) REVERT: A 218 ASN cc_start: 0.9327 (t0) cc_final: 0.9055 (t0) REVERT: A 221 LYS cc_start: 0.9121 (mmtp) cc_final: 0.8792 (mttp) REVERT: A 252 ASN cc_start: 0.9444 (t0) cc_final: 0.9175 (t0) REVERT: A 255 HIS cc_start: 0.8589 (t-90) cc_final: 0.8006 (t-90) REVERT: A 263 ASP cc_start: 0.8759 (m-30) cc_final: 0.8406 (m-30) REVERT: A 277 THR cc_start: 0.8727 (p) cc_final: 0.8291 (t) REVERT: A 286 ASP cc_start: 0.8593 (m-30) cc_final: 0.8374 (m-30) REVERT: A 290 GLU cc_start: 0.8887 (tm-30) cc_final: 0.8535 (tm-30) REVERT: A 335 GLU cc_start: 0.8291 (mm-30) cc_final: 0.8034 (mm-30) REVERT: A 348 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8580 (tmm) REVERT: A 362 ASP cc_start: 0.8118 (m-30) cc_final: 0.7302 (m-30) REVERT: A 384 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.7788 (pm20) REVERT: A 393 SER cc_start: 0.9286 (m) cc_final: 0.9077 (p) REVERT: A 402 GLU cc_start: 0.8341 (mp0) cc_final: 0.7991 (mp0) REVERT: A 420 MET cc_start: 0.9216 (mmm) cc_final: 0.8958 (tpt) REVERT: A 426 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8188 (tm-30) REVERT: A 446 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7512 (mmm160) REVERT: A 475 ASN cc_start: 0.9132 (m-40) cc_final: 0.8870 (m-40) REVERT: A 479 TYR cc_start: 0.9005 (t80) cc_final: 0.8571 (t80) REVERT: A 505 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8408 (mt-10) REVERT: A 515 ASP cc_start: 0.9134 (m-30) cc_final: 0.8776 (m-30) REVERT: A 588 GLN cc_start: 0.9318 (mm-40) cc_final: 0.9103 (mm-40) REVERT: A 606 TYR cc_start: 0.7859 (m-80) cc_final: 0.7464 (m-80) REVERT: A 615 MET cc_start: 0.9317 (mmp) cc_final: 0.8794 (mmp) REVERT: A 640 MET cc_start: 0.9415 (tpp) cc_final: 0.8454 (tpp) REVERT: A 657 PHE cc_start: 0.8972 (m-80) cc_final: 0.8684 (m-80) REVERT: B 16 ILE cc_start: 0.9578 (mm) cc_final: 0.8773 (mm) REVERT: B 17 MET cc_start: 0.8774 (mmm) cc_final: 0.8337 (mmm) REVERT: B 65 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8263 (mm-30) REVERT: B 79 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8619 (pt0) REVERT: B 87 LYS cc_start: 0.9391 (mmmt) cc_final: 0.9108 (tppt) REVERT: B 95 MET cc_start: 0.9061 (tpp) cc_final: 0.8660 (tpp) REVERT: B 99 LYS cc_start: 0.9400 (mmtt) cc_final: 0.9130 (mmtt) REVERT: B 107 LYS cc_start: 0.9121 (mtpp) cc_final: 0.8612 (mtpp) REVERT: B 119 GLU cc_start: 0.8959 (mp0) cc_final: 0.8253 (mp0) REVERT: B 129 PHE cc_start: 0.8915 (m-10) cc_final: 0.8665 (m-10) REVERT: B 139 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8562 (mp0) REVERT: B 147 GLN cc_start: 0.9234 (mt0) cc_final: 0.8652 (mt0) REVERT: B 149 TYR cc_start: 0.9412 (t80) cc_final: 0.8741 (t80) REVERT: B 191 GLN cc_start: 0.8521 (mm-40) cc_final: 0.8040 (mt0) REVERT: B 232 ASN cc_start: 0.9204 (m110) cc_final: 0.8853 (m110) REVERT: B 235 ARG cc_start: 0.9080 (ttm-80) cc_final: 0.8819 (mmt90) REVERT: B 236 TYR cc_start: 0.8906 (t80) cc_final: 0.8451 (t80) REVERT: B 250 TYR cc_start: 0.9316 (m-80) cc_final: 0.8551 (m-80) REVERT: B 257 ASP cc_start: 0.8903 (m-30) cc_final: 0.8395 (m-30) REVERT: B 263 ASP cc_start: 0.9152 (m-30) cc_final: 0.8901 (m-30) REVERT: B 322 MET cc_start: 0.9279 (mmt) cc_final: 0.8994 (mmm) REVERT: B 333 LYS cc_start: 0.9266 (tptp) cc_final: 0.9024 (ttmm) REVERT: B 393 SER cc_start: 0.9329 (m) cc_final: 0.8984 (p) REVERT: B 467 ASN cc_start: 0.9345 (t0) cc_final: 0.9128 (m-40) REVERT: B 492 PHE cc_start: 0.9516 (m-80) cc_final: 0.8942 (m-10) REVERT: B 515 ASP cc_start: 0.8991 (m-30) cc_final: 0.8623 (m-30) REVERT: B 576 LEU cc_start: 0.9515 (mt) cc_final: 0.9231 (mt) REVERT: B 586 TYR cc_start: 0.9087 (m-80) cc_final: 0.8770 (m-80) REVERT: B 610 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8533 (ptmt) REVERT: B 612 TYR cc_start: 0.9097 (m-80) cc_final: 0.8831 (m-80) REVERT: B 636 LYS cc_start: 0.9486 (mmmt) cc_final: 0.9211 (mmmm) REVERT: B 680 LYS cc_start: 0.8871 (mttt) cc_final: 0.8627 (mttt) REVERT: B 683 TYR cc_start: 0.9047 (t80) cc_final: 0.8641 (t80) REVERT: B 684 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.7616 (m-80) REVERT: B 686 ARG cc_start: 0.8614 (mmt180) cc_final: 0.8345 (mmt90) REVERT: C 66 ASP cc_start: 0.7817 (OUTLIER) cc_final: 0.6938 (t0) REVERT: C 68 GLU cc_start: 0.9194 (mm-30) cc_final: 0.8865 (mm-30) REVERT: C 74 MET cc_start: 0.9227 (mmm) cc_final: 0.8822 (tpp) REVERT: C 127 GLN cc_start: 0.8654 (mm110) cc_final: 0.7687 (pp30) REVERT: C 154 PHE cc_start: 0.9159 (t80) cc_final: 0.8807 (t80) REVERT: C 212 ILE cc_start: 0.7360 (mt) cc_final: 0.6866 (mm) REVERT: C 242 TYR cc_start: 0.9259 (t80) cc_final: 0.8957 (t80) REVERT: C 269 MET cc_start: 0.8669 (ptp) cc_final: 0.8373 (ptt) REVERT: D 21 PHE cc_start: 0.8861 (m-80) cc_final: 0.8459 (m-80) outliers start: 70 outliers final: 47 residues processed: 646 average time/residue: 0.2586 time to fit residues: 251.5008 Evaluate side-chains 638 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 584 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 458 MET Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 159 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 183 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 180 optimal weight: 7.9990 chunk 108 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 475 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.147194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.107292 restraints weight = 36952.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.110893 restraints weight = 17981.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.113357 restraints weight = 10812.800| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.7027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16386 Z= 0.154 Angle : 0.746 18.138 22134 Z= 0.375 Chirality : 0.046 0.188 2360 Planarity : 0.004 0.039 2818 Dihedral : 10.479 165.805 2243 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.50 % Allowed : 31.47 % Favored : 65.03 % 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: 0.72 (0.18), residues: 1932 helix: 1.00 (0.15), residues: 1120 sheet: -0.08 (0.45), residues: 104 loop : -0.12 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 124 HIS 0.006 0.001 HIS C 201 PHE 0.061 0.002 PHE C 109 TYR 0.018 0.001 TYR C 105 ARG 0.013 0.001 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.04182 ( 871) hydrogen bonds : angle 5.19565 ( 2571) covalent geometry : bond 0.00349 (16386) covalent geometry : angle 0.74606 (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 662 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 602 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9049 (ttmm) cc_final: 0.8817 (ttpt) REVERT: A 31 GLU cc_start: 0.9138 (mt-10) cc_final: 0.8814 (mp0) REVERT: A 65 GLU cc_start: 0.8561 (mm-30) cc_final: 0.7731 (mp0) REVERT: A 123 SER cc_start: 0.9406 (OUTLIER) cc_final: 0.9082 (p) REVERT: A 139 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8384 (mt-10) REVERT: A 149 TYR cc_start: 0.9604 (t80) cc_final: 0.8493 (t80) REVERT: A 150 GLN cc_start: 0.9459 (tp40) cc_final: 0.9083 (tm-30) REVERT: A 202 ASN cc_start: 0.9336 (t0) cc_final: 0.8876 (t0) REVERT: A 218 ASN cc_start: 0.9348 (t0) cc_final: 0.9086 (t0) REVERT: A 221 LYS cc_start: 0.9121 (mmtp) cc_final: 0.8857 (mptt) REVERT: A 228 LYS cc_start: 0.9423 (mmtt) cc_final: 0.9193 (mmtm) REVERT: A 252 ASN cc_start: 0.9436 (t0) cc_final: 0.8953 (t0) REVERT: A 263 ASP cc_start: 0.8748 (m-30) cc_final: 0.8384 (m-30) REVERT: A 274 ARG cc_start: 0.8778 (ptp-110) cc_final: 0.8504 (ptp-110) REVERT: A 277 THR cc_start: 0.8718 (p) cc_final: 0.8294 (t) REVERT: A 286 ASP cc_start: 0.8649 (m-30) cc_final: 0.8391 (m-30) REVERT: A 290 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8534 (tm-30) REVERT: A 335 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8077 (mm-30) REVERT: A 362 ASP cc_start: 0.8165 (m-30) cc_final: 0.7313 (m-30) REVERT: A 384 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.7770 (pm20) REVERT: A 393 SER cc_start: 0.9256 (m) cc_final: 0.8917 (t) REVERT: A 402 GLU cc_start: 0.8320 (mp0) cc_final: 0.7526 (mp0) REVERT: A 420 MET cc_start: 0.9248 (mmm) cc_final: 0.8997 (tpt) REVERT: A 426 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8199 (tm-30) REVERT: A 447 ASN cc_start: 0.8102 (m-40) cc_final: 0.7149 (t0) REVERT: A 452 ARG cc_start: 0.9270 (OUTLIER) cc_final: 0.8687 (ptm160) REVERT: A 458 MET cc_start: 0.8732 (mmp) cc_final: 0.8409 (mmp) REVERT: A 475 ASN cc_start: 0.9138 (m-40) cc_final: 0.8807 (m110) REVERT: A 479 TYR cc_start: 0.9005 (t80) cc_final: 0.8565 (t80) REVERT: A 505 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8414 (mt-10) REVERT: A 515 ASP cc_start: 0.9155 (m-30) cc_final: 0.8878 (m-30) REVERT: A 606 TYR cc_start: 0.7848 (m-80) cc_final: 0.7595 (m-80) REVERT: A 615 MET cc_start: 0.9358 (mmp) cc_final: 0.8798 (mmp) REVERT: A 640 MET cc_start: 0.9406 (tpp) cc_final: 0.8449 (tpp) REVERT: B 16 ILE cc_start: 0.9576 (mm) cc_final: 0.8845 (mm) REVERT: B 17 MET cc_start: 0.8847 (mmm) cc_final: 0.8554 (mmm) REVERT: B 65 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8277 (mm-30) REVERT: B 79 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8645 (pt0) REVERT: B 87 LYS cc_start: 0.9406 (mmmt) cc_final: 0.9135 (tppt) REVERT: B 95 MET cc_start: 0.9100 (tpp) cc_final: 0.8713 (tpp) REVERT: B 99 LYS cc_start: 0.9392 (mmtt) cc_final: 0.9140 (mmtt) REVERT: B 107 LYS cc_start: 0.9126 (mtpp) cc_final: 0.8607 (mtpp) REVERT: B 119 GLU cc_start: 0.8933 (mp0) cc_final: 0.8234 (mp0) REVERT: B 127 LEU cc_start: 0.9744 (mm) cc_final: 0.9459 (mm) REVERT: B 129 PHE cc_start: 0.8969 (m-10) cc_final: 0.8709 (m-10) REVERT: B 147 GLN cc_start: 0.9233 (mt0) cc_final: 0.8690 (mt0) REVERT: B 149 TYR cc_start: 0.9435 (t80) cc_final: 0.8772 (t80) REVERT: B 191 GLN cc_start: 0.8542 (mm-40) cc_final: 0.8128 (mt0) REVERT: B 202 ASN cc_start: 0.9451 (t0) cc_final: 0.9090 (t0) REVERT: B 235 ARG cc_start: 0.9062 (ttm-80) cc_final: 0.8826 (mmt90) REVERT: B 236 TYR cc_start: 0.8844 (t80) cc_final: 0.8336 (t80) REVERT: B 250 TYR cc_start: 0.9358 (m-80) cc_final: 0.8668 (m-80) REVERT: B 257 ASP cc_start: 0.8898 (m-30) cc_final: 0.8421 (m-30) REVERT: B 263 ASP cc_start: 0.9136 (m-30) cc_final: 0.8880 (m-30) REVERT: B 279 SER cc_start: 0.8728 (m) cc_final: 0.8464 (t) REVERT: B 322 MET cc_start: 0.9283 (mmt) cc_final: 0.9006 (mmm) REVERT: B 333 LYS cc_start: 0.9267 (tptp) cc_final: 0.9027 (ttmm) REVERT: B 393 SER cc_start: 0.9306 (m) cc_final: 0.9078 (p) REVERT: B 394 TYR cc_start: 0.9266 (m-80) cc_final: 0.8932 (m-80) REVERT: B 396 ASP cc_start: 0.8472 (p0) cc_final: 0.8221 (p0) REVERT: B 413 SER cc_start: 0.9716 (OUTLIER) cc_final: 0.9321 (p) REVERT: B 492 PHE cc_start: 0.9504 (m-80) cc_final: 0.9275 (m-10) REVERT: B 515 ASP cc_start: 0.9001 (m-30) cc_final: 0.8620 (m-30) REVERT: B 576 LEU cc_start: 0.9512 (mt) cc_final: 0.9258 (mt) REVERT: B 586 TYR cc_start: 0.9067 (m-80) cc_final: 0.8697 (m-80) REVERT: B 612 TYR cc_start: 0.9097 (m-80) cc_final: 0.8547 (m-80) REVERT: B 636 LYS cc_start: 0.9459 (mmmt) cc_final: 0.9197 (mmmm) REVERT: B 640 MET cc_start: 0.9207 (tpp) cc_final: 0.8836 (tpp) REVERT: B 648 ILE cc_start: 0.9521 (mm) cc_final: 0.9285 (mm) REVERT: B 680 LYS cc_start: 0.8860 (mttt) cc_final: 0.8554 (mttt) REVERT: B 683 TYR cc_start: 0.9058 (t80) cc_final: 0.8728 (t80) REVERT: B 684 TYR cc_start: 0.8011 (OUTLIER) cc_final: 0.7534 (m-80) REVERT: C 58 VAL cc_start: 0.7684 (t) cc_final: 0.7341 (p) REVERT: C 68 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8552 (mm-30) REVERT: C 74 MET cc_start: 0.9183 (mmm) cc_final: 0.8887 (tpp) REVERT: C 127 GLN cc_start: 0.8585 (mm110) cc_final: 0.7648 (pp30) REVERT: C 130 TYR cc_start: 0.7429 (OUTLIER) cc_final: 0.6775 (m-80) REVERT: C 154 PHE cc_start: 0.9145 (t80) cc_final: 0.8769 (t80) REVERT: C 208 LEU cc_start: 0.6981 (mm) cc_final: 0.6753 (mt) REVERT: C 212 ILE cc_start: 0.7387 (mt) cc_final: 0.7167 (mm) REVERT: C 269 MET cc_start: 0.8671 (ptp) cc_final: 0.8345 (ptt) REVERT: D 236 TYR cc_start: 0.5557 (t80) cc_final: 0.5287 (t80) outliers start: 60 outliers final: 45 residues processed: 631 average time/residue: 0.2648 time to fit residues: 252.6347 Evaluate side-chains 624 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 573 time to evaluate : 1.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 93 MET Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 262 TYR Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 204 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 111 optimal weight: 6.9990 chunk 102 optimal weight: 0.7980 chunk 182 optimal weight: 2.9990 chunk 107 optimal weight: 0.1980 chunk 77 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 115 optimal weight: 0.0870 chunk 127 optimal weight: 0.9990 chunk 188 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 GLN A 676 HIS ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.144221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.103436 restraints weight = 37012.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.107115 restraints weight = 18426.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.109570 restraints weight = 11136.964| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3337 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3337 r_free = 0.3337 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3337 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.7267 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= 0.153 Angle : 0.796 22.026 22134 Z= 0.394 Chirality : 0.047 0.255 2360 Planarity : 0.004 0.039 2818 Dihedral : 10.260 154.841 2243 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.97 % Allowed : 32.81 % Favored : 64.22 % 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: 0.59 (0.18), residues: 1932 helix: 0.91 (0.15), residues: 1117 sheet: -0.07 (0.46), residues: 104 loop : -0.21 (0.22), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 44 HIS 0.007 0.001 HIS C 201 PHE 0.063 0.002 PHE C 109 TYR 0.019 0.001 TYR C 105 ARG 0.007 0.001 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.04252 ( 871) hydrogen bonds : angle 5.28792 ( 2571) covalent geometry : bond 0.00350 (16386) covalent geometry : angle 0.79571 (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 645 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 594 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9053 (ttmm) cc_final: 0.8799 (ttpt) REVERT: A 31 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8816 (mp0) REVERT: A 65 GLU cc_start: 0.8531 (mm-30) cc_final: 0.7681 (mp0) REVERT: A 139 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8371 (mt-10) REVERT: A 149 TYR cc_start: 0.9585 (t80) cc_final: 0.8441 (t80) REVERT: A 150 GLN cc_start: 0.9512 (tp40) cc_final: 0.9056 (tm-30) REVERT: A 202 ASN cc_start: 0.9315 (t0) cc_final: 0.8892 (t0) REVERT: A 218 ASN cc_start: 0.9358 (t0) cc_final: 0.9088 (t0) REVERT: A 221 LYS cc_start: 0.9127 (mmtp) cc_final: 0.8925 (mptt) REVERT: A 228 LYS cc_start: 0.9458 (mmtt) cc_final: 0.9233 (mmtm) REVERT: A 252 ASN cc_start: 0.9402 (t0) cc_final: 0.8885 (t0) REVERT: A 263 ASP cc_start: 0.8747 (m-30) cc_final: 0.8362 (m-30) REVERT: A 274 ARG cc_start: 0.8757 (ptp-110) cc_final: 0.8490 (ptp-110) REVERT: A 277 THR cc_start: 0.8690 (p) cc_final: 0.8268 (t) REVERT: A 286 ASP cc_start: 0.8636 (m-30) cc_final: 0.8400 (m-30) REVERT: A 290 GLU cc_start: 0.8909 (tm-30) cc_final: 0.8519 (tm-30) REVERT: A 335 GLU cc_start: 0.8289 (mm-30) cc_final: 0.8036 (mm-30) REVERT: A 362 ASP cc_start: 0.8167 (m-30) cc_final: 0.7305 (m-30) REVERT: A 384 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7745 (pm20) REVERT: A 393 SER cc_start: 0.9239 (m) cc_final: 0.8921 (t) REVERT: A 402 GLU cc_start: 0.8350 (mp0) cc_final: 0.7561 (mp0) REVERT: A 426 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8189 (tm-30) REVERT: A 452 ARG cc_start: 0.9273 (OUTLIER) cc_final: 0.9053 (ttt-90) REVERT: A 475 ASN cc_start: 0.9106 (m-40) cc_final: 0.8791 (m110) REVERT: A 505 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8415 (mt-10) REVERT: A 515 ASP cc_start: 0.9163 (m-30) cc_final: 0.8957 (m-30) REVERT: A 526 GLU cc_start: 0.8727 (mp0) cc_final: 0.8469 (mp0) REVERT: A 615 MET cc_start: 0.9355 (mmp) cc_final: 0.8784 (mmp) REVERT: A 640 MET cc_start: 0.9388 (tpp) cc_final: 0.8404 (tpp) REVERT: A 657 PHE cc_start: 0.8743 (m-80) cc_final: 0.8488 (m-80) REVERT: B 16 ILE cc_start: 0.9529 (mm) cc_final: 0.8813 (mm) REVERT: B 65 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8267 (mm-30) REVERT: B 79 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8661 (pt0) REVERT: B 87 LYS cc_start: 0.9407 (mmmt) cc_final: 0.9142 (tppt) REVERT: B 95 MET cc_start: 0.9085 (tpp) cc_final: 0.8651 (tpp) REVERT: B 99 LYS cc_start: 0.9350 (mmtt) cc_final: 0.9117 (mmtt) REVERT: B 107 LYS cc_start: 0.9054 (mtpp) cc_final: 0.8550 (mtpp) REVERT: B 119 GLU cc_start: 0.8923 (mp0) cc_final: 0.8264 (mp0) REVERT: B 127 LEU cc_start: 0.9728 (mm) cc_final: 0.9438 (mm) REVERT: B 147 GLN cc_start: 0.9288 (mt0) cc_final: 0.8760 (mt0) REVERT: B 149 TYR cc_start: 0.9425 (t80) cc_final: 0.8698 (t80) REVERT: B 191 GLN cc_start: 0.8466 (mm-40) cc_final: 0.8050 (mt0) REVERT: B 202 ASN cc_start: 0.9422 (t0) cc_final: 0.9078 (t0) REVERT: B 232 ASN cc_start: 0.9200 (m110) cc_final: 0.8881 (m110) REVERT: B 235 ARG cc_start: 0.9065 (ttm-80) cc_final: 0.8838 (mmt90) REVERT: B 236 TYR cc_start: 0.8856 (t80) cc_final: 0.8277 (t80) REVERT: B 250 TYR cc_start: 0.9312 (m-80) cc_final: 0.8517 (m-80) REVERT: B 257 ASP cc_start: 0.8928 (m-30) cc_final: 0.8428 (m-30) REVERT: B 333 LYS cc_start: 0.9267 (tptp) cc_final: 0.9031 (ttmm) REVERT: B 393 SER cc_start: 0.9378 (m) cc_final: 0.9098 (p) REVERT: B 394 TYR cc_start: 0.9218 (m-80) cc_final: 0.8949 (m-80) REVERT: B 399 GLU cc_start: 0.8351 (tp30) cc_final: 0.8093 (tp30) REVERT: B 413 SER cc_start: 0.9672 (m) cc_final: 0.9186 (p) REVERT: B 467 ASN cc_start: 0.9181 (OUTLIER) cc_final: 0.8912 (m-40) REVERT: B 492 PHE cc_start: 0.9447 (m-80) cc_final: 0.9242 (m-10) REVERT: B 494 MET cc_start: 0.9218 (mmt) cc_final: 0.8963 (mmt) REVERT: B 515 ASP cc_start: 0.8981 (m-30) cc_final: 0.8603 (m-30) REVERT: B 576 LEU cc_start: 0.9516 (mt) cc_final: 0.9255 (mt) REVERT: B 586 TYR cc_start: 0.9047 (m-80) cc_final: 0.8587 (m-80) REVERT: B 610 LYS cc_start: 0.8517 (ptmm) cc_final: 0.8118 (tttp) REVERT: B 612 TYR cc_start: 0.9125 (m-80) cc_final: 0.8532 (m-80) REVERT: B 633 ASP cc_start: 0.8653 (t0) cc_final: 0.8431 (t0) REVERT: B 640 MET cc_start: 0.9231 (tpp) cc_final: 0.8879 (tpp) REVERT: B 648 ILE cc_start: 0.9518 (mm) cc_final: 0.9268 (mm) REVERT: B 680 LYS cc_start: 0.8805 (mttt) cc_final: 0.8401 (mttt) REVERT: B 683 TYR cc_start: 0.9041 (t80) cc_final: 0.8777 (t80) REVERT: B 684 TYR cc_start: 0.8051 (OUTLIER) cc_final: 0.7714 (m-80) REVERT: B 686 ARG cc_start: 0.8638 (mmt180) cc_final: 0.8383 (mmt180) REVERT: C 68 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8604 (mm-30) REVERT: C 74 MET cc_start: 0.9235 (mmm) cc_final: 0.8960 (tpp) REVERT: C 130 TYR cc_start: 0.7448 (OUTLIER) cc_final: 0.6733 (m-80) REVERT: C 154 PHE cc_start: 0.9166 (t80) cc_final: 0.8851 (t80) REVERT: C 212 ILE cc_start: 0.7179 (mt) cc_final: 0.6748 (mm) REVERT: D 21 PHE cc_start: 0.8962 (m-80) cc_final: 0.8504 (t80) REVERT: D 137 MET cc_start: 0.0790 (mmt) cc_final: -0.0225 (mtm) outliers start: 51 outliers final: 38 residues processed: 620 average time/residue: 0.2560 time to fit residues: 239.4905 Evaluate side-chains 618 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 575 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 474 GLN Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 204 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 137 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 7.9990 chunk 160 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 chunk 120 optimal weight: 0.8980 chunk 135 optimal weight: 4.9990 chunk 148 optimal weight: 4.9990 chunk 127 optimal weight: 0.7980 chunk 68 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 GLN A 676 HIS ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 HIS ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 107 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 = 0.3849 r_free = 0.3849 target = 0.147786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.106949 restraints weight = 37510.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110687 restraints weight = 18594.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.113156 restraints weight = 11316.467| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.7525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16386 Z= 0.159 Angle : 0.850 20.741 22134 Z= 0.415 Chirality : 0.049 0.413 2360 Planarity : 0.004 0.040 2818 Dihedral : 10.046 146.719 2243 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.86 % Allowed : 33.16 % Favored : 63.99 % 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: 0.45 (0.18), residues: 1932 helix: 0.74 (0.15), residues: 1122 sheet: 0.03 (0.44), residues: 106 loop : -0.21 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP D 44 HIS 0.012 0.001 HIS C 101 PHE 0.063 0.002 PHE C 109 TYR 0.035 0.001 TYR D 55 ARG 0.009 0.001 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.04340 ( 871) hydrogen bonds : angle 5.40567 ( 2571) covalent geometry : bond 0.00365 (16386) covalent geometry : angle 0.84981 (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 645 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 596 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9068 (ttmm) cc_final: 0.8837 (ttpt) REVERT: A 31 GLU cc_start: 0.9095 (mt-10) cc_final: 0.8763 (mp0) REVERT: A 65 GLU cc_start: 0.8590 (mm-30) cc_final: 0.7781 (mp0) REVERT: A 139 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8367 (mt-10) REVERT: A 149 TYR cc_start: 0.9604 (t80) cc_final: 0.8533 (t80) REVERT: A 150 GLN cc_start: 0.9529 (tp40) cc_final: 0.8778 (tm-30) REVERT: A 161 ARG cc_start: 0.8380 (OUTLIER) cc_final: 0.7406 (mtm180) REVERT: A 180 ASN cc_start: 0.8638 (m110) cc_final: 0.7866 (m-40) REVERT: A 195 LEU cc_start: 0.9573 (mt) cc_final: 0.9240 (mt) REVERT: A 202 ASN cc_start: 0.9359 (t0) cc_final: 0.8928 (t0) REVERT: A 218 ASN cc_start: 0.9345 (t0) cc_final: 0.9089 (t0) REVERT: A 221 LYS cc_start: 0.9080 (mmtp) cc_final: 0.8756 (mptt) REVERT: A 228 LYS cc_start: 0.9449 (mmtt) cc_final: 0.9221 (mmtm) REVERT: A 252 ASN cc_start: 0.9378 (t0) cc_final: 0.9063 (t0) REVERT: A 263 ASP cc_start: 0.8713 (m-30) cc_final: 0.8324 (m-30) REVERT: A 274 ARG cc_start: 0.8780 (ptp-110) cc_final: 0.8512 (ptp-110) REVERT: A 277 THR cc_start: 0.8704 (p) cc_final: 0.8251 (t) REVERT: A 286 ASP cc_start: 0.8670 (m-30) cc_final: 0.8419 (m-30) REVERT: A 290 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8504 (tm-30) REVERT: A 335 GLU cc_start: 0.8297 (mm-30) cc_final: 0.8053 (mm-30) REVERT: A 348 MET cc_start: 0.8899 (OUTLIER) cc_final: 0.8606 (tmm) REVERT: A 362 ASP cc_start: 0.8134 (m-30) cc_final: 0.7279 (m-30) REVERT: A 384 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.7717 (pm20) REVERT: A 393 SER cc_start: 0.9259 (m) cc_final: 0.8937 (t) REVERT: A 402 GLU cc_start: 0.8387 (mp0) cc_final: 0.7616 (mp0) REVERT: A 426 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8099 (tm-30) REVERT: A 446 ARG cc_start: 0.7595 (OUTLIER) cc_final: 0.7340 (mtp85) REVERT: A 452 ARG cc_start: 0.9268 (OUTLIER) cc_final: 0.9051 (ttt-90) REVERT: A 475 ASN cc_start: 0.8950 (m-40) cc_final: 0.8448 (m110) REVERT: A 505 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8427 (mt-10) REVERT: A 515 ASP cc_start: 0.9198 (m-30) cc_final: 0.8944 (m-30) REVERT: A 584 ILE cc_start: 0.9416 (pt) cc_final: 0.8904 (pt) REVERT: A 615 MET cc_start: 0.9382 (mmp) cc_final: 0.8855 (mmp) REVERT: A 640 MET cc_start: 0.9398 (tpp) cc_final: 0.8289 (tpp) REVERT: B 65 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8261 (mm-30) REVERT: B 79 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8666 (pt0) REVERT: B 87 LYS cc_start: 0.9413 (mmmt) cc_final: 0.9087 (tptm) REVERT: B 95 MET cc_start: 0.9078 (tpp) cc_final: 0.8776 (tpp) REVERT: B 99 LYS cc_start: 0.9350 (mmtt) cc_final: 0.9131 (mmtt) REVERT: B 107 LYS cc_start: 0.9069 (mtpp) cc_final: 0.8585 (mtpp) REVERT: B 119 GLU cc_start: 0.8957 (mp0) cc_final: 0.8286 (mp0) REVERT: B 127 LEU cc_start: 0.9747 (mm) cc_final: 0.9443 (mm) REVERT: B 147 GLN cc_start: 0.9303 (mt0) cc_final: 0.8646 (mt0) REVERT: B 149 TYR cc_start: 0.9388 (t80) cc_final: 0.8788 (t80) REVERT: B 191 GLN cc_start: 0.8466 (mm-40) cc_final: 0.7669 (mt0) REVERT: B 202 ASN cc_start: 0.9422 (t0) cc_final: 0.9095 (t0) REVERT: B 235 ARG cc_start: 0.9078 (ttm-80) cc_final: 0.8841 (mmt90) REVERT: B 236 TYR cc_start: 0.8881 (t80) cc_final: 0.8243 (t80) REVERT: B 250 TYR cc_start: 0.9343 (m-80) cc_final: 0.8503 (m-80) REVERT: B 257 ASP cc_start: 0.8934 (m-30) cc_final: 0.8454 (m-30) REVERT: B 266 LYS cc_start: 0.9267 (ttmm) cc_final: 0.8756 (ttpt) REVERT: B 322 MET cc_start: 0.9272 (mmt) cc_final: 0.8701 (mmm) REVERT: B 333 LYS cc_start: 0.9277 (tptp) cc_final: 0.9051 (ttmm) REVERT: B 393 SER cc_start: 0.9244 (m) cc_final: 0.8889 (p) REVERT: B 399 GLU cc_start: 0.8349 (tp30) cc_final: 0.8083 (tp30) REVERT: B 413 SER cc_start: 0.9456 (m) cc_final: 0.9214 (p) REVERT: B 515 ASP cc_start: 0.8971 (m-30) cc_final: 0.8608 (m-30) REVERT: B 576 LEU cc_start: 0.9508 (mt) cc_final: 0.9271 (mt) REVERT: B 588 GLN cc_start: 0.9372 (mm-40) cc_final: 0.8897 (mm-40) REVERT: B 610 LYS cc_start: 0.8741 (ptmm) cc_final: 0.8372 (tttp) REVERT: B 612 TYR cc_start: 0.9062 (m-80) cc_final: 0.8280 (m-80) REVERT: B 627 LYS cc_start: 0.9209 (tttt) cc_final: 0.8850 (tttt) REVERT: B 632 MET cc_start: 0.8419 (mmm) cc_final: 0.7558 (mmm) REVERT: B 633 ASP cc_start: 0.8615 (t0) cc_final: 0.8335 (t0) REVERT: B 640 MET cc_start: 0.9233 (tpp) cc_final: 0.8913 (tpp) REVERT: B 648 ILE cc_start: 0.9498 (mm) cc_final: 0.9292 (mm) REVERT: B 680 LYS cc_start: 0.8781 (mttt) cc_final: 0.8524 (mttt) REVERT: B 683 TYR cc_start: 0.9046 (t80) cc_final: 0.8752 (t80) REVERT: B 684 TYR cc_start: 0.8041 (OUTLIER) cc_final: 0.7715 (m-80) REVERT: B 686 ARG cc_start: 0.8601 (mmt180) cc_final: 0.8353 (mmt180) REVERT: C 68 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8573 (mm-30) REVERT: C 74 MET cc_start: 0.9154 (mmm) cc_final: 0.8921 (tpp) REVERT: C 130 TYR cc_start: 0.7638 (OUTLIER) cc_final: 0.7002 (m-80) REVERT: C 154 PHE cc_start: 0.9155 (t80) cc_final: 0.8807 (t80) REVERT: C 212 ILE cc_start: 0.7103 (mt) cc_final: 0.6871 (mm) REVERT: C 274 ASP cc_start: 0.8237 (p0) cc_final: 0.7919 (p0) REVERT: C 318 ASP cc_start: 0.9141 (t0) cc_final: 0.8626 (t0) REVERT: D 21 PHE cc_start: 0.8965 (m-80) cc_final: 0.8310 (t80) REVERT: D 137 MET cc_start: 0.0742 (mmt) cc_final: -0.0199 (mtm) REVERT: D 246 LEU cc_start: 0.7225 (tp) cc_final: 0.6935 (tt) outliers start: 49 outliers final: 35 residues processed: 618 average time/residue: 0.2646 time to fit residues: 245.3387 Evaluate side-chains 609 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 567 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 161 ARG Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 279 SER Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 431 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 672 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 276 LYS Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 59 LEU Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 130 TYR Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 22 TYR Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 81 optimal weight: 0.9980 chunk 16 optimal weight: 0.0470 chunk 2 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 179 optimal weight: 5.9990 chunk 190 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 180 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS B 19 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 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 = 0.3858 r_free = 0.3858 target = 0.149732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.109023 restraints weight = 37497.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.112862 restraints weight = 18646.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.115322 restraints weight = 11316.586| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.7745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16386 Z= 0.155 Angle : 0.863 19.564 22134 Z= 0.424 Chirality : 0.049 0.339 2360 Planarity : 0.004 0.040 2818 Dihedral : 9.863 142.725 2243 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.56 % Allowed : 34.27 % Favored : 63.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.18), residues: 1932 helix: 0.68 (0.15), residues: 1118 sheet: 0.21 (0.46), residues: 104 loop : -0.26 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP D 44 HIS 0.008 0.001 HIS B 304 PHE 0.062 0.002 PHE C 109 TYR 0.041 0.001 TYR D 105 ARG 0.009 0.001 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.04348 ( 871) hydrogen bonds : angle 5.41916 ( 2571) covalent geometry : bond 0.00354 (16386) covalent geometry : angle 0.86270 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6570.39 seconds wall clock time: 115 minutes 28.98 seconds (6928.98 seconds total)