Starting phenix.real_space_refine on Sat Jun 14 07:05:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz5_45053/06_2025/9bz5_45053_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz5_45053/06_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_45053/06_2025/9bz5_45053.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz5_45053/06_2025/9bz5_45053.map" model { file = "/net/cci-nas-00/data/ceres_data/9bz5_45053/06_2025/9bz5_45053_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz5_45053/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 9.76, per 1000 atoms: 0.61 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: 4.01 Conformation dependent library (CDL) restraints added in 2.0 seconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.104A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.516A 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: 4.78 Time building geometry restraints manager: 4.71 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: 0.680 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: 0.640 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 36.390 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.510 ------------------------------------------------------------------------------- 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 : 1.771 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: 0.2957 time to fit residues: 422.7237 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 : 1.647 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.154087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.112663 restraints weight = 35171.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.116667 restraints weight = 17413.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.119256 restraints weight = 10353.809| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 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 = 0.3321 r_free = 0.3321 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3321 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 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 : 11.425 166.845 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 : 3.61 % Allowed : 23.02 % 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 5.16918 ( 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 780 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 718 time to evaluate : 1.808 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: 0.9787 (mt) cc_final: 0.9483 (pp) REVERT: A 76 ASP cc_start: 0.9132 (m-30) cc_final: 0.8909 (m-30) REVERT: A 123 SER cc_start: 0.9635 (OUTLIER) cc_final: 0.9246 (p) REVERT: A 139 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8308 (mt-10) REVERT: A 157 LEU cc_start: 0.9615 (tp) cc_final: 0.9408 (tp) REVERT: A 191 GLN cc_start: 0.8960 (mm-40) cc_final: 0.8492 (mm-40) REVERT: A 202 ASN cc_start: 0.9509 (t0) cc_final: 0.9065 (t0) REVERT: A 218 ASN cc_start: 0.8863 (t0) cc_final: 0.8585 (t0) REVERT: A 221 LYS cc_start: 0.9195 (mmtp) cc_final: 0.8914 (mttt) REVERT: A 236 TYR cc_start: 0.9519 (t80) cc_final: 0.9302 (t80) REVERT: A 255 HIS cc_start: 0.8545 (t-90) cc_final: 0.8020 (t-90) REVERT: A 257 ASP cc_start: 0.9340 (m-30) cc_final: 0.8803 (m-30) REVERT: A 259 ASN cc_start: 0.8829 (m-40) cc_final: 0.8545 (m-40) REVERT: A 263 ASP cc_start: 0.8797 (m-30) cc_final: 0.8502 (m-30) REVERT: A 277 THR cc_start: 0.8858 (p) cc_final: 0.8519 (t) REVERT: A 286 ASP cc_start: 0.8396 (m-30) cc_final: 0.8106 (m-30) REVERT: A 322 MET cc_start: 0.8938 (mmm) cc_final: 0.8181 (mmm) REVERT: A 335 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7878 (mm-30) REVERT: A 348 MET cc_start: 0.8921 (OUTLIER) cc_final: 0.8547 (tmm) REVERT: A 362 ASP cc_start: 0.8303 (m-30) cc_final: 0.7307 (m-30) REVERT: A 379 SER cc_start: 0.9444 (t) cc_final: 0.9088 (t) REVERT: A 393 SER cc_start: 0.9382 (m) cc_final: 0.9100 (p) REVERT: A 402 GLU cc_start: 0.8029 (mp0) cc_final: 0.7649 (mp0) REVERT: A 501 GLN cc_start: 0.9147 (OUTLIER) cc_final: 0.8861 (tt0) REVERT: A 505 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8353 (mt-10) REVERT: A 550 MET cc_start: 0.6884 (mtm) cc_final: 0.6647 (mtm) REVERT: A 602 GLU cc_start: 0.7759 (pt0) cc_final: 0.7245 (pt0) REVERT: A 606 TYR cc_start: 0.7961 (m-80) cc_final: 0.7602 (m-80) REVERT: A 615 MET cc_start: 0.9025 (mmp) cc_final: 0.8546 (mmm) REVERT: A 618 LEU cc_start: 0.9369 (tp) cc_final: 0.9137 (tt) REVERT: A 639 ASP cc_start: 0.9031 (m-30) cc_final: 0.8281 (m-30) REVERT: B 31 GLU cc_start: 0.8717 (mp0) cc_final: 0.8495 (mp0) REVERT: B 65 GLU cc_start: 0.8496 (mm-30) cc_final: 0.7782 (mm-30) REVERT: B 68 PHE cc_start: 0.8979 (p90) cc_final: 0.8691 (p90) REVERT: B 119 GLU cc_start: 0.9134 (mp0) cc_final: 0.8596 (mp0) REVERT: B 121 ARG cc_start: 0.9405 (tpm170) cc_final: 0.9041 (tpp-160) REVERT: B 147 GLN cc_start: 0.9037 (mt0) cc_final: 0.8577 (mt0) REVERT: B 174 GLU cc_start: 0.8596 (tp30) cc_final: 0.8094 (tp30) REVERT: B 202 ASN cc_start: 0.9364 (t0) cc_final: 0.8966 (t0) REVERT: B 227 MET cc_start: 0.9236 (mtp) cc_final: 0.8933 (mtp) REVERT: B 236 TYR cc_start: 0.9025 (t80) cc_final: 0.8453 (t80) REVERT: B 251 LEU cc_start: 0.9180 (tp) cc_final: 0.8942 (tp) REVERT: B 257 ASP cc_start: 0.8726 (m-30) cc_final: 0.8205 (m-30) REVERT: B 270 ASP cc_start: 0.9208 (t70) cc_final: 0.8923 (t70) REVERT: B 279 SER cc_start: 0.8753 (m) cc_final: 0.8416 (t) REVERT: B 348 MET cc_start: 0.9133 (ptm) cc_final: 0.8478 (ptp) REVERT: B 386 LEU cc_start: 0.9575 (mt) cc_final: 0.9218 (mt) REVERT: B 393 SER cc_start: 0.9439 (m) cc_final: 0.9006 (p) REVERT: B 471 TYR cc_start: 0.9352 (t80) cc_final: 0.8520 (t80) REVERT: B 474 GLN cc_start: 0.8912 (mt0) cc_final: 0.8545 (mm-40) REVERT: B 475 ASN cc_start: 0.9247 (m-40) cc_final: 0.8537 (m-40) REVERT: B 515 ASP cc_start: 0.9094 (m-30) cc_final: 0.8808 (m-30) REVERT: B 546 LEU cc_start: 0.9590 (mt) cc_final: 0.9267 (mt) REVERT: B 558 TRP cc_start: 0.9417 (m100) cc_final: 0.8604 (m100) REVERT: B 589 SER cc_start: 0.9797 (m) cc_final: 0.9502 (p) REVERT: B 601 ILE cc_start: 0.9463 (mm) cc_final: 0.9056 (mm) REVERT: B 610 LYS cc_start: 0.8729 (ptmt) cc_final: 0.8437 (ptmm) REVERT: B 612 TYR cc_start: 0.9155 (m-80) cc_final: 0.8885 (m-80) REVERT: B 646 GLN cc_start: 0.9348 (OUTLIER) cc_final: 0.9004 (pt0) REVERT: B 650 GLN cc_start: 0.8415 (mt0) cc_final: 0.7998 (mm-40) REVERT: B 680 LYS cc_start: 0.9096 (mttt) cc_final: 0.8682 (mtmt) REVERT: B 683 TYR cc_start: 0.9089 (t80) cc_final: 0.8752 (t80) REVERT: C 149 ASP cc_start: 0.6793 (m-30) cc_final: 0.6521 (m-30) REVERT: C 154 PHE cc_start: 0.9047 (t80) cc_final: 0.8548 (t80) REVERT: C 157 MET cc_start: 0.8989 (mtt) cc_final: 0.8625 (mtt) REVERT: C 208 LEU cc_start: 0.7056 (mm) cc_final: 0.6783 (mm) REVERT: C 242 TYR cc_start: 0.8790 (t80) cc_final: 0.8556 (t80) REVERT: C 252 LEU cc_start: 0.7712 (mp) cc_final: 0.7299 (pp) REVERT: C 256 VAL cc_start: 0.8611 (t) cc_final: 0.8332 (t) REVERT: C 286 VAL cc_start: 0.7671 (OUTLIER) cc_final: 0.7394 (m) REVERT: C 288 ASN cc_start: 0.5189 (t0) cc_final: 0.4370 (m-40) REVERT: D 24 GLN cc_start: 0.9339 (tp-100) cc_final: 0.9121 (tp-100) REVERT: D 82 ASP cc_start: 0.8847 (m-30) cc_final: 0.8595 (t0) REVERT: D 154 PHE cc_start: 0.5627 (t80) cc_final: 0.5125 (t80) outliers start: 62 outliers final: 32 residues processed: 744 average time/residue: 0.2709 time to fit residues: 299.7653 Evaluate side-chains 703 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 666 time to evaluate : 1.805 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 168 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 171 optimal weight: 5.9990 chunk 189 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- 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 645 GLN ** 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 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 28 GLN C 84 HIS ** 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 23 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 = 0.3774 r_free = 0.3774 target = 0.135892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.094439 restraints weight = 37163.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.098013 restraints weight = 18675.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.100343 restraints weight = 11394.470| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3188 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.5395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 16386 Z= 0.277 Angle : 0.720 9.878 22134 Z= 0.376 Chirality : 0.046 0.222 2360 Planarity : 0.004 0.041 2818 Dihedral : 11.372 168.693 2245 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 5.36 % Allowed : 21.97 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.18), residues: 1932 helix: 1.30 (0.15), residues: 1133 sheet: -0.25 (0.41), residues: 134 loop : 0.51 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP D 124 HIS 0.007 0.002 HIS C 101 PHE 0.048 0.002 PHE C 109 TYR 0.019 0.002 TYR C 169 ARG 0.007 0.001 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.04425 ( 871) hydrogen bonds : angle 5.19701 ( 2571) covalent geometry : bond 0.00596 (16386) covalent geometry : angle 0.71999 (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 754 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 662 time to evaluate : 1.925 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 29 ASP cc_start: 0.9245 (t70) cc_final: 0.8941 (t0) REVERT: A 31 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8784 (pm20) REVERT: A 55 LEU cc_start: 0.9810 (mt) cc_final: 0.9507 (pp) REVERT: A 123 SER cc_start: 0.9700 (OUTLIER) cc_final: 0.9293 (p) REVERT: A 139 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8363 (mt-10) REVERT: A 149 TYR cc_start: 0.9543 (t80) cc_final: 0.8960 (t80) REVERT: A 190 MET cc_start: 0.9381 (mtp) cc_final: 0.9016 (mtp) REVERT: A 191 GLN cc_start: 0.9019 (mm-40) cc_final: 0.8731 (mm-40) REVERT: A 193 SER cc_start: 0.9592 (m) cc_final: 0.9011 (p) REVERT: A 202 ASN cc_start: 0.9507 (t0) cc_final: 0.9186 (t0) REVERT: A 246 SER cc_start: 0.8028 (m) cc_final: 0.7696 (p) REVERT: A 252 ASN cc_start: 0.9440 (t0) cc_final: 0.9199 (t0) REVERT: A 255 HIS cc_start: 0.8691 (t-90) cc_final: 0.8105 (t-90) REVERT: A 257 ASP cc_start: 0.9503 (m-30) cc_final: 0.8951 (m-30) REVERT: A 259 ASN cc_start: 0.8900 (m-40) cc_final: 0.8570 (m-40) REVERT: A 263 ASP cc_start: 0.8725 (m-30) cc_final: 0.8436 (m-30) REVERT: A 274 ARG cc_start: 0.8962 (ptm160) cc_final: 0.8330 (ptp-110) REVERT: A 277 THR cc_start: 0.8904 (p) cc_final: 0.8547 (t) REVERT: A 322 MET cc_start: 0.8745 (mmm) cc_final: 0.8401 (mmm) REVERT: A 335 GLU cc_start: 0.8371 (mm-30) cc_final: 0.8117 (mm-30) REVERT: A 348 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8709 (tmm) REVERT: A 349 LEU cc_start: 0.9603 (OUTLIER) cc_final: 0.9366 (mp) REVERT: A 350 ARG cc_start: 0.9321 (mtp180) cc_final: 0.9025 (mtp180) REVERT: A 379 SER cc_start: 0.9375 (t) cc_final: 0.9065 (t) REVERT: A 387 GLN cc_start: 0.8848 (mt0) cc_final: 0.8476 (mt0) REVERT: A 393 SER cc_start: 0.9302 (m) cc_final: 0.8993 (p) REVERT: A 402 GLU cc_start: 0.8129 (mp0) cc_final: 0.7779 (mp0) REVERT: A 426 GLU cc_start: 0.8507 (tm-30) cc_final: 0.8263 (tm-30) REVERT: A 501 GLN cc_start: 0.9327 (OUTLIER) cc_final: 0.8992 (tt0) REVERT: A 505 GLU cc_start: 0.8855 (mt-10) cc_final: 0.8309 (mt-10) REVERT: A 515 ASP cc_start: 0.9150 (m-30) cc_final: 0.8896 (m-30) REVERT: A 548 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8331 (mm-30) REVERT: A 590 SER cc_start: 0.9383 (t) cc_final: 0.9099 (p) REVERT: A 606 TYR cc_start: 0.8364 (m-80) cc_final: 0.8117 (m-80) REVERT: A 615 MET cc_start: 0.9256 (mmp) cc_final: 0.8817 (mmm) REVERT: A 639 ASP cc_start: 0.9033 (m-30) cc_final: 0.8255 (m-30) REVERT: B 8 LYS cc_start: 0.8877 (tppt) cc_final: 0.8613 (tppt) REVERT: B 65 GLU cc_start: 0.8559 (mm-30) cc_final: 0.8148 (mm-30) REVERT: B 95 MET cc_start: 0.9204 (tpp) cc_final: 0.8971 (tpp) REVERT: B 99 LYS cc_start: 0.9407 (mmtt) cc_final: 0.9139 (mmtt) REVERT: B 104 TYR cc_start: 0.8905 (m-80) cc_final: 0.8608 (m-80) REVERT: B 119 GLU cc_start: 0.9199 (mp0) cc_final: 0.8615 (mp0) REVERT: B 147 GLN cc_start: 0.9211 (mt0) cc_final: 0.8587 (mt0) REVERT: B 172 LEU cc_start: 0.9419 (mp) cc_final: 0.9107 (mt) REVERT: B 227 MET cc_start: 0.9345 (mtp) cc_final: 0.9022 (mtp) REVERT: B 236 TYR cc_start: 0.9188 (t80) cc_final: 0.8689 (t80) REVERT: B 246 SER cc_start: 0.7986 (m) cc_final: 0.7610 (p) REVERT: B 250 TYR cc_start: 0.9180 (m-80) cc_final: 0.8758 (m-80) REVERT: B 257 ASP cc_start: 0.8712 (m-30) cc_final: 0.8207 (m-30) REVERT: B 279 SER cc_start: 0.8975 (OUTLIER) cc_final: 0.8712 (t) REVERT: B 317 MET cc_start: 0.8644 (pmm) cc_final: 0.8362 (pmm) REVERT: B 322 MET cc_start: 0.9315 (mmm) cc_final: 0.8763 (mmm) REVERT: B 393 SER cc_start: 0.9350 (m) cc_final: 0.8855 (p) REVERT: B 402 GLU cc_start: 0.8840 (tp30) cc_final: 0.8625 (tp30) REVERT: B 474 GLN cc_start: 0.8931 (mt0) cc_final: 0.8694 (mm-40) REVERT: B 475 ASN cc_start: 0.9368 (m-40) cc_final: 0.9008 (m110) REVERT: B 515 ASP cc_start: 0.9118 (m-30) cc_final: 0.8780 (m-30) REVERT: B 546 LEU cc_start: 0.9635 (mt) cc_final: 0.9393 (mt) REVERT: B 550 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7520 (mtp) REVERT: B 599 GLU cc_start: 0.8483 (pt0) cc_final: 0.8130 (pt0) REVERT: B 601 ILE cc_start: 0.9483 (mm) cc_final: 0.9110 (mm) REVERT: B 604 ARG cc_start: 0.8554 (mmt-90) cc_final: 0.7907 (mmt-90) REVERT: B 610 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8471 (ptmm) REVERT: B 612 TYR cc_start: 0.9247 (m-80) cc_final: 0.8838 (m-80) REVERT: B 615 MET cc_start: 0.9558 (mmp) cc_final: 0.9353 (mmp) REVERT: B 677 ARG cc_start: 0.9330 (mmm-85) cc_final: 0.8930 (mmm160) REVERT: C 66 ASP cc_start: 0.8293 (OUTLIER) cc_final: 0.6764 (t0) REVERT: C 68 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8941 (mm-30) REVERT: C 69 GLN cc_start: 0.9364 (tp40) cc_final: 0.8848 (pt0) REVERT: C 74 MET cc_start: 0.9377 (mmm) cc_final: 0.8673 (tpt) REVERT: C 149 ASP cc_start: 0.7074 (m-30) cc_final: 0.6737 (m-30) REVERT: C 154 PHE cc_start: 0.9209 (t80) cc_final: 0.8710 (t80) REVERT: C 157 MET cc_start: 0.9108 (mtt) cc_final: 0.8586 (mtt) REVERT: C 208 LEU cc_start: 0.7149 (mm) cc_final: 0.6832 (mm) REVERT: C 212 ILE cc_start: 0.7326 (mt) cc_final: 0.6115 (mt) REVERT: C 242 TYR cc_start: 0.9071 (t80) cc_final: 0.8797 (t80) REVERT: C 260 ILE cc_start: 0.5992 (pt) cc_final: 0.5656 (pt) REVERT: C 288 ASN cc_start: 0.5367 (t0) cc_final: 0.4453 (m-40) REVERT: D 25 ASN cc_start: 0.8651 (t0) cc_final: 0.8415 (t0) REVERT: D 97 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.6108 (mp0) outliers start: 92 outliers final: 58 residues processed: 701 average time/residue: 0.2624 time to fit residues: 276.0179 Evaluate side-chains 689 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 621 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 134 THR 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 216 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU 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 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 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 279 SER 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 472 LEU Chi-restraints excluded: chain B residue 495 VAL 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 B residue 637 VAL 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 163 LEU Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 230 ASP 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 Chi-restraints excluded: chain D residue 315 LEU 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: 0.9990 chunk 1 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 chunk 90 optimal weight: 0.7980 chunk 94 optimal weight: 9.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 469 HIS A 501 GLN ** B 150 GLN ** 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 646 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS C 85 GLN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** C 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.141046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.100764 restraints weight = 36069.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104357 restraints weight = 17781.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.106694 restraints weight = 10706.038| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.5823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16386 Z= 0.155 Angle : 0.680 9.093 22134 Z= 0.350 Chirality : 0.045 0.223 2360 Planarity : 0.004 0.039 2818 Dihedral : 11.016 172.807 2244 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.20 % Allowed : 25.99 % Favored : 69.81 % 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: 1.15 (0.18), residues: 1932 helix: 1.30 (0.15), residues: 1113 sheet: -0.43 (0.38), residues: 148 loop : 0.34 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 558 HIS 0.004 0.001 HIS A 438 PHE 0.054 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 0.04135 ( 871) hydrogen bonds : angle 5.10833 ( 2571) covalent geometry : bond 0.00347 (16386) covalent geometry : angle 0.68010 (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 738 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 666 time to evaluate : 1.853 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: 0.8951 (ttmm) cc_final: 0.8709 (ttpt) REVERT: A 31 GLU cc_start: 0.9116 (mt-10) cc_final: 0.8767 (mp0) REVERT: A 51 LEU cc_start: 0.9359 (tp) cc_final: 0.9091 (tp) REVERT: A 55 LEU cc_start: 0.9807 (mt) cc_final: 0.9489 (pp) REVERT: A 65 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8206 (mm-30) REVERT: A 95 MET cc_start: 0.9023 (mmm) cc_final: 0.8532 (tpp) REVERT: A 99 LYS cc_start: 0.9529 (mmmm) cc_final: 0.9159 (tppt) REVERT: A 123 SER cc_start: 0.9550 (OUTLIER) cc_final: 0.9205 (p) REVERT: A 139 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8358 (mt-10) REVERT: A 149 TYR cc_start: 0.9534 (t80) cc_final: 0.8613 (t80) REVERT: A 150 GLN cc_start: 0.9402 (tp40) cc_final: 0.9027 (tm-30) REVERT: A 161 ARG cc_start: 0.8402 (ttm110) cc_final: 0.6991 (mtp85) REVERT: A 190 MET cc_start: 0.9358 (mtp) cc_final: 0.9075 (mtp) REVERT: A 191 GLN cc_start: 0.8852 (mm-40) cc_final: 0.8557 (mm-40) REVERT: A 202 ASN cc_start: 0.9463 (t0) cc_final: 0.9112 (t0) REVERT: A 228 LYS cc_start: 0.9396 (mttp) cc_final: 0.9086 (mmtt) REVERT: A 255 HIS cc_start: 0.8568 (t-90) cc_final: 0.7895 (t-90) REVERT: A 257 ASP cc_start: 0.9466 (m-30) cc_final: 0.8902 (m-30) REVERT: A 259 ASN cc_start: 0.8920 (m-40) cc_final: 0.8585 (m-40) REVERT: A 263 ASP cc_start: 0.8743 (m-30) cc_final: 0.8491 (m-30) REVERT: A 277 THR cc_start: 0.8822 (p) cc_final: 0.8390 (t) REVERT: A 286 ASP cc_start: 0.8630 (m-30) cc_final: 0.8297 (m-30) REVERT: A 322 MET cc_start: 0.8791 (mmm) cc_final: 0.8376 (mmm) REVERT: A 335 GLU cc_start: 0.8325 (mm-30) cc_final: 0.8063 (mm-30) REVERT: A 350 ARG cc_start: 0.9321 (mtp180) cc_final: 0.9073 (mtp180) REVERT: A 362 ASP cc_start: 0.8302 (m-30) cc_final: 0.7723 (m-30) REVERT: A 393 SER cc_start: 0.9344 (m) cc_final: 0.9057 (p) REVERT: A 402 GLU cc_start: 0.8223 (mp0) cc_final: 0.7882 (mp0) REVERT: A 420 MET cc_start: 0.9240 (mmm) cc_final: 0.8985 (tpt) REVERT: A 426 GLU cc_start: 0.8503 (tm-30) cc_final: 0.8220 (tm-30) REVERT: A 435 SER cc_start: 0.9713 (OUTLIER) cc_final: 0.9411 (p) REVERT: A 453 ARG cc_start: 0.9349 (OUTLIER) cc_final: 0.9016 (ttt-90) REVERT: A 505 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8275 (mt-10) REVERT: A 515 ASP cc_start: 0.9153 (m-30) cc_final: 0.8886 (m-30) REVERT: A 548 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8230 (mm-30) REVERT: A 550 MET cc_start: 0.7309 (mtm) cc_final: 0.6978 (mtm) REVERT: A 583 SER cc_start: 0.9241 (m) cc_final: 0.8525 (t) REVERT: A 588 GLN cc_start: 0.9418 (mm-40) cc_final: 0.9102 (mm-40) REVERT: A 606 TYR cc_start: 0.8146 (m-80) cc_final: 0.7247 (m-80) REVERT: A 615 MET cc_start: 0.9236 (mmp) cc_final: 0.8784 (mmp) REVERT: A 639 ASP cc_start: 0.8984 (m-30) cc_final: 0.8162 (m-30) REVERT: A 640 MET cc_start: 0.9429 (tpp) cc_final: 0.8428 (tpp) REVERT: B 8 LYS cc_start: 0.8838 (tppt) cc_final: 0.8569 (tppt) REVERT: B 43 GLN cc_start: 0.9342 (mp10) cc_final: 0.9105 (mp10) REVERT: B 65 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8062 (mm-30) REVERT: B 79 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8588 (pt0) REVERT: B 95 MET cc_start: 0.9148 (tpp) cc_final: 0.8927 (tpp) REVERT: B 99 LYS cc_start: 0.9373 (mmtt) cc_final: 0.9147 (mmtt) REVERT: B 119 GLU cc_start: 0.9078 (mp0) cc_final: 0.8418 (mp0) REVERT: B 127 LEU cc_start: 0.9714 (mm) cc_final: 0.9406 (mm) REVERT: B 147 GLN cc_start: 0.9182 (mt0) cc_final: 0.8563 (mt0) REVERT: B 149 TYR cc_start: 0.9338 (t80) cc_final: 0.9132 (t80) REVERT: B 172 LEU cc_start: 0.9383 (mp) cc_final: 0.8559 (mt) REVERT: B 202 ASN cc_start: 0.9511 (t0) cc_final: 0.9301 (t0) REVERT: B 227 MET cc_start: 0.9302 (mtp) cc_final: 0.9002 (mtp) REVERT: B 236 TYR cc_start: 0.9082 (t80) cc_final: 0.8477 (t80) REVERT: B 246 SER cc_start: 0.7961 (m) cc_final: 0.7611 (p) REVERT: B 250 TYR cc_start: 0.9223 (m-80) cc_final: 0.8761 (m-80) REVERT: B 256 ARG cc_start: 0.9000 (ttt-90) cc_final: 0.8469 (ttt90) REVERT: B 257 ASP cc_start: 0.8768 (m-30) cc_final: 0.8171 (m-30) REVERT: B 312 GLN cc_start: 0.8807 (mp10) cc_final: 0.8599 (pm20) REVERT: B 393 SER cc_start: 0.9418 (m) cc_final: 0.8987 (p) REVERT: B 399 GLU cc_start: 0.8488 (tp30) cc_final: 0.8252 (tp30) REVERT: B 406 ASP cc_start: 0.8267 (m-30) cc_final: 0.7946 (t0) REVERT: B 467 ASN cc_start: 0.9412 (t0) cc_final: 0.9152 (m-40) REVERT: B 474 GLN cc_start: 0.8915 (mt0) cc_final: 0.8649 (mm110) REVERT: B 475 ASN cc_start: 0.9323 (m-40) cc_final: 0.8948 (m110) REVERT: B 515 ASP cc_start: 0.9077 (m-30) cc_final: 0.8659 (m-30) REVERT: B 516 GLN cc_start: 0.9243 (mt0) cc_final: 0.8919 (tp-100) REVERT: B 546 LEU cc_start: 0.9604 (mt) cc_final: 0.9367 (mt) REVERT: B 599 GLU cc_start: 0.8491 (pt0) cc_final: 0.8170 (pt0) REVERT: B 601 ILE cc_start: 0.9420 (mm) cc_final: 0.8942 (mm) REVERT: B 610 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8493 (ptmm) REVERT: B 612 TYR cc_start: 0.9194 (m-80) cc_final: 0.8835 (m-80) REVERT: B 615 MET cc_start: 0.9495 (mmp) cc_final: 0.9220 (mmp) REVERT: B 632 MET cc_start: 0.8342 (mtt) cc_final: 0.8124 (mtm) REVERT: B 666 ASP cc_start: 0.9175 (m-30) cc_final: 0.8970 (m-30) REVERT: B 683 TYR cc_start: 0.9102 (t80) cc_final: 0.8677 (t80) REVERT: B 684 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.7266 (m-80) REVERT: C 21 PHE cc_start: 0.8282 (m-80) cc_final: 0.8000 (m-80) REVERT: C 66 ASP cc_start: 0.8084 (OUTLIER) cc_final: 0.6741 (t0) REVERT: C 68 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8841 (mm-30) REVERT: C 69 GLN cc_start: 0.9205 (tp40) cc_final: 0.8946 (pt0) REVERT: C 74 MET cc_start: 0.9285 (mmm) cc_final: 0.8686 (tpp) REVERT: C 154 PHE cc_start: 0.9208 (t80) cc_final: 0.8641 (t80) REVERT: C 157 MET cc_start: 0.9149 (mtt) cc_final: 0.8669 (mtt) REVERT: C 162 TYR cc_start: 0.8720 (m-10) cc_final: 0.7787 (m-80) REVERT: C 212 ILE cc_start: 0.7441 (mt) cc_final: 0.6380 (mt) REVERT: C 242 TYR cc_start: 0.9032 (t80) cc_final: 0.8650 (t80) REVERT: C 260 ILE cc_start: 0.5912 (pt) cc_final: 0.5548 (pt) REVERT: C 288 ASN cc_start: 0.5333 (t0) cc_final: 0.4454 (m-40) REVERT: D 21 PHE cc_start: 0.9226 (m-80) cc_final: 0.8726 (m-80) outliers start: 72 outliers final: 41 residues processed: 696 average time/residue: 0.2623 time to fit residues: 272.9164 Evaluate side-chains 670 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 622 time to evaluate : 1.696 ------------------------------------------------------------------------------- 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 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 453 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 413 SER 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 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 41 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 67 optimal weight: 0.9990 chunk 41 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 73 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 chunk 182 optimal weight: 8.9990 chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 387 GLN A 469 HIS ** B 150 GLN ** 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 Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.146139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.105299 restraints weight = 36531.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.109077 restraints weight = 17830.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.111440 restraints weight = 10695.333| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3289 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3289 r_free = 0.3289 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3289 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.6202 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= 0.144 Angle : 0.683 9.383 22134 Z= 0.349 Chirality : 0.045 0.248 2360 Planarity : 0.004 0.039 2818 Dihedral : 10.778 174.603 2243 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.85 % Allowed : 27.51 % 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: 1.03 (0.18), residues: 1932 helix: 1.25 (0.15), residues: 1114 sheet: -0.69 (0.37), residues: 148 loop : 0.25 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 9 HIS 0.014 0.001 HIS A 647 PHE 0.055 0.002 PHE C 109 TYR 0.017 0.002 TYR D 236 ARG 0.011 0.001 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.04083 ( 871) hydrogen bonds : angle 5.07640 ( 2571) covalent geometry : bond 0.00324 (16386) covalent geometry : angle 0.68256 (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 718 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 652 time to evaluate : 1.799 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: 0.8987 (ttmm) cc_final: 0.8655 (ttpp) REVERT: A 31 GLU cc_start: 0.9151 (mt-10) cc_final: 0.8774 (mp0) REVERT: A 91 PHE cc_start: 0.9026 (m-80) cc_final: 0.8650 (m-10) REVERT: A 95 MET cc_start: 0.8992 (mmm) cc_final: 0.8613 (tpp) REVERT: A 99 LYS cc_start: 0.9482 (mmmm) cc_final: 0.9245 (tppt) REVERT: A 139 GLU cc_start: 0.8744 (mt-10) cc_final: 0.8372 (mt-10) REVERT: A 149 TYR cc_start: 0.9527 (t80) cc_final: 0.8398 (t80) REVERT: A 150 GLN cc_start: 0.9410 (tp40) cc_final: 0.9033 (tm-30) REVERT: A 190 MET cc_start: 0.9343 (mtp) cc_final: 0.9121 (mtp) REVERT: A 202 ASN cc_start: 0.9447 (t0) cc_final: 0.9076 (t0) REVERT: A 228 LYS cc_start: 0.9383 (mttp) cc_final: 0.9096 (mmtt) REVERT: A 255 HIS cc_start: 0.8604 (t-90) cc_final: 0.8024 (t-90) REVERT: A 257 ASP cc_start: 0.9452 (m-30) cc_final: 0.8918 (m-30) REVERT: A 263 ASP cc_start: 0.8790 (m-30) cc_final: 0.8506 (m-30) REVERT: A 277 THR cc_start: 0.8778 (p) cc_final: 0.8348 (t) REVERT: A 286 ASP cc_start: 0.8595 (m-30) cc_final: 0.8270 (m-30) REVERT: A 290 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8562 (tm-30) REVERT: A 322 MET cc_start: 0.8821 (mmm) cc_final: 0.8560 (mmm) REVERT: A 335 GLU cc_start: 0.8316 (mm-30) cc_final: 0.8037 (mm-30) REVERT: A 350 ARG cc_start: 0.9322 (mtp180) cc_final: 0.9052 (mtp180) REVERT: A 362 ASP cc_start: 0.8217 (m-30) cc_final: 0.7490 (m-30) REVERT: A 384 GLU cc_start: 0.8604 (OUTLIER) cc_final: 0.7657 (pm20) REVERT: A 393 SER cc_start: 0.9305 (m) cc_final: 0.9054 (p) REVERT: A 402 GLU cc_start: 0.8249 (mp0) cc_final: 0.7901 (mp0) REVERT: A 426 GLU cc_start: 0.8501 (tm-30) cc_final: 0.8142 (tm-30) REVERT: A 435 SER cc_start: 0.9718 (OUTLIER) cc_final: 0.9386 (p) REVERT: A 453 ARG cc_start: 0.9400 (OUTLIER) cc_final: 0.9070 (ttt-90) REVERT: A 505 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8432 (mt-10) REVERT: A 515 ASP cc_start: 0.9140 (m-30) cc_final: 0.8701 (m-30) REVERT: A 528 PHE cc_start: 0.9033 (m-80) cc_final: 0.8574 (m-80) REVERT: A 588 GLN cc_start: 0.9365 (mm-40) cc_final: 0.9072 (mm-40) REVERT: A 606 TYR cc_start: 0.8081 (m-80) cc_final: 0.7229 (m-80) REVERT: A 615 MET cc_start: 0.9295 (mmp) cc_final: 0.8822 (mmp) REVERT: A 640 MET cc_start: 0.9408 (tpp) cc_final: 0.8328 (tpp) REVERT: B 8 LYS cc_start: 0.8942 (tppt) cc_final: 0.8693 (tppt) REVERT: B 65 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8267 (mm-30) REVERT: B 79 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8547 (pt0) REVERT: B 95 MET cc_start: 0.9105 (tpp) cc_final: 0.8725 (tpp) REVERT: B 99 LYS cc_start: 0.9391 (mmtt) cc_final: 0.9103 (mmtt) REVERT: B 107 LYS cc_start: 0.9169 (mtpp) cc_final: 0.8582 (mtpp) REVERT: B 117 ARG cc_start: 0.8908 (mtp85) cc_final: 0.8603 (mtp85) REVERT: B 119 GLU cc_start: 0.8993 (mp0) cc_final: 0.8259 (mp0) REVERT: B 147 GLN cc_start: 0.9210 (mt0) cc_final: 0.8611 (mt0) REVERT: B 149 TYR cc_start: 0.9373 (t80) cc_final: 0.8824 (t80) REVERT: B 172 LEU cc_start: 0.9384 (mp) cc_final: 0.8561 (mt) REVERT: B 174 GLU cc_start: 0.8510 (tp30) cc_final: 0.8259 (tp30) REVERT: B 202 ASN cc_start: 0.9470 (t0) cc_final: 0.9117 (t0) REVERT: B 227 MET cc_start: 0.9200 (mtp) cc_final: 0.8931 (mtp) REVERT: B 235 ARG cc_start: 0.9145 (ttm-80) cc_final: 0.8805 (mtt-85) REVERT: B 236 TYR cc_start: 0.8974 (t80) cc_final: 0.8480 (t80) REVERT: B 246 SER cc_start: 0.7845 (m) cc_final: 0.7628 (p) REVERT: B 250 TYR cc_start: 0.9214 (m-80) cc_final: 0.8566 (m-80) REVERT: B 257 ASP cc_start: 0.8781 (m-30) cc_final: 0.8303 (m-30) REVERT: B 263 ASP cc_start: 0.9284 (m-30) cc_final: 0.9063 (m-30) REVERT: B 322 MET cc_start: 0.9374 (mmm) cc_final: 0.8813 (mmm) REVERT: B 375 LYS cc_start: 0.9429 (mttm) cc_final: 0.9221 (mttp) REVERT: B 387 GLN cc_start: 0.9126 (mt0) cc_final: 0.8673 (mt0) REVERT: B 393 SER cc_start: 0.9418 (m) cc_final: 0.9041 (p) REVERT: B 402 GLU cc_start: 0.8768 (tp30) cc_final: 0.8359 (tm-30) REVERT: B 406 ASP cc_start: 0.8243 (m-30) cc_final: 0.8008 (t0) REVERT: B 413 SER cc_start: 0.9705 (OUTLIER) cc_final: 0.9293 (p) REVERT: B 447 ASN cc_start: 0.8493 (m-40) cc_final: 0.7991 (m110) REVERT: B 467 ASN cc_start: 0.9411 (t0) cc_final: 0.9153 (m-40) REVERT: B 474 GLN cc_start: 0.8992 (mt0) cc_final: 0.8770 (mm110) REVERT: B 475 ASN cc_start: 0.9331 (m-40) cc_final: 0.8942 (m110) REVERT: B 492 PHE cc_start: 0.9532 (m-80) cc_final: 0.9059 (m-80) REVERT: B 515 ASP cc_start: 0.9052 (m-30) cc_final: 0.8809 (m-30) REVERT: B 516 GLN cc_start: 0.9220 (mt0) cc_final: 0.8937 (tp-100) REVERT: B 546 LEU cc_start: 0.9605 (mt) cc_final: 0.9385 (mt) REVERT: B 586 TYR cc_start: 0.9187 (m-80) cc_final: 0.8965 (m-80) REVERT: B 599 GLU cc_start: 0.8501 (pt0) cc_final: 0.8192 (pt0) REVERT: B 601 ILE cc_start: 0.9409 (mm) cc_final: 0.8976 (mm) REVERT: B 604 ARG cc_start: 0.8581 (mmp80) cc_final: 0.8341 (mmp80) REVERT: B 610 LYS cc_start: 0.8870 (ptmt) cc_final: 0.8604 (ptmt) REVERT: B 612 TYR cc_start: 0.9136 (m-80) cc_final: 0.8708 (m-80) REVERT: B 640 MET cc_start: 0.9223 (tpp) cc_final: 0.8942 (tpp) REVERT: B 677 ARG cc_start: 0.9314 (mmm-85) cc_final: 0.8917 (mmm160) REVERT: B 684 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.7299 (m-80) REVERT: C 21 PHE cc_start: 0.8300 (m-80) cc_final: 0.7975 (m-80) REVERT: C 66 ASP cc_start: 0.8098 (OUTLIER) cc_final: 0.6797 (t0) REVERT: C 74 MET cc_start: 0.9265 (mmm) cc_final: 0.8700 (tpp) REVERT: C 127 GLN cc_start: 0.8531 (mm110) cc_final: 0.7450 (pp30) REVERT: C 154 PHE cc_start: 0.9172 (t80) cc_final: 0.8668 (t80) REVERT: C 157 MET cc_start: 0.9165 (mtt) cc_final: 0.8901 (mtt) REVERT: C 208 LEU cc_start: 0.6969 (mm) cc_final: 0.6541 (mm) REVERT: C 212 ILE cc_start: 0.7367 (mt) cc_final: 0.6314 (mt) REVERT: C 242 TYR cc_start: 0.9097 (t80) cc_final: 0.8725 (t80) REVERT: C 260 ILE cc_start: 0.5863 (pt) cc_final: 0.5504 (pt) REVERT: C 288 ASN cc_start: 0.5216 (t0) cc_final: 0.4331 (m-40) REVERT: D 21 PHE cc_start: 0.9126 (m-80) cc_final: 0.8652 (m-80) REVERT: D 24 GLN cc_start: 0.9312 (tp-100) cc_final: 0.9087 (tm-30) outliers start: 66 outliers final: 43 residues processed: 681 average time/residue: 0.2630 time to fit residues: 268.7998 Evaluate side-chains 654 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 605 time to evaluate : 1.807 ------------------------------------------------------------------------------- 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 127 LEU 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 183 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 408 SER Chi-restraints excluded: chain A residue 411 LEU 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 453 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 178 SER 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 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 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 66 ASP Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 177 TYR 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: 1.9990 chunk 126 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 156 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 39 optimal weight: 9.9990 chunk 169 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 177 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 645 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.145260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.102743 restraints weight = 36157.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.106481 restraints weight = 18085.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.108857 restraints weight = 11082.314| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.6552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16386 Z= 0.150 Angle : 0.696 11.505 22134 Z= 0.352 Chirality : 0.046 0.252 2360 Planarity : 0.003 0.031 2818 Dihedral : 10.639 170.313 2243 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 16.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.96 % Allowed : 28.50 % Favored : 67.54 % 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: 0.88 (0.18), residues: 1932 helix: 1.15 (0.15), residues: 1122 sheet: -0.78 (0.38), residues: 148 loop : 0.13 (0.23), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 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 0.009 0.001 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.04007 ( 871) hydrogen bonds : angle 5.09052 ( 2571) covalent geometry : bond 0.00341 (16386) covalent geometry : angle 0.69618 (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 697 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 629 time to evaluate : 1.818 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: 0.9009 (ttmm) cc_final: 0.8785 (ttpt) REVERT: A 31 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8723 (mp0) REVERT: A 99 LYS cc_start: 0.9487 (mmmm) cc_final: 0.9276 (tppt) REVERT: A 123 SER cc_start: 0.9385 (OUTLIER) cc_final: 0.9178 (p) REVERT: A 139 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8392 (mt-10) REVERT: A 149 TYR cc_start: 0.9562 (t80) cc_final: 0.8613 (t80) REVERT: A 150 GLN cc_start: 0.9428 (tp40) cc_final: 0.9052 (tm-30) REVERT: A 202 ASN cc_start: 0.9335 (t0) cc_final: 0.8956 (t0) REVERT: A 228 LYS cc_start: 0.9465 (mttp) cc_final: 0.9203 (mmtt) REVERT: A 263 ASP cc_start: 0.8755 (m-30) cc_final: 0.8447 (m-30) REVERT: A 277 THR cc_start: 0.8742 (p) cc_final: 0.8307 (t) REVERT: A 286 ASP cc_start: 0.8570 (m-30) cc_final: 0.8238 (m-30) REVERT: A 290 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8449 (tm-30) REVERT: A 335 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8036 (mm-30) REVERT: A 362 ASP cc_start: 0.8207 (m-30) cc_final: 0.7382 (m-30) REVERT: A 384 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.7673 (pm20) REVERT: A 402 GLU cc_start: 0.8322 (mp0) cc_final: 0.7879 (mp0) REVERT: A 426 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8179 (tm-30) REVERT: A 435 SER cc_start: 0.9710 (OUTLIER) cc_final: 0.9375 (p) REVERT: A 446 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.7440 (mmm160) REVERT: A 453 ARG cc_start: 0.9424 (OUTLIER) cc_final: 0.8909 (ttp80) REVERT: A 458 MET cc_start: 0.8721 (mmp) cc_final: 0.8411 (mmp) REVERT: A 505 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8365 (mt-10) REVERT: A 515 ASP cc_start: 0.9123 (m-30) cc_final: 0.8726 (m-30) REVERT: A 588 GLN cc_start: 0.9376 (mm-40) cc_final: 0.9112 (mm-40) REVERT: A 606 TYR cc_start: 0.7958 (m-80) cc_final: 0.7101 (m-80) REVERT: A 615 MET cc_start: 0.9326 (mmp) cc_final: 0.8830 (mmp) REVERT: A 640 MET cc_start: 0.9388 (tpp) cc_final: 0.8344 (tpp) REVERT: B 8 LYS cc_start: 0.8971 (tppt) cc_final: 0.8728 (tppt) REVERT: B 16 ILE cc_start: 0.9567 (mm) cc_final: 0.9349 (mm) REVERT: B 65 GLU cc_start: 0.8638 (mm-30) cc_final: 0.8304 (mm-30) REVERT: B 79 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8608 (pt0) REVERT: B 87 LYS cc_start: 0.9390 (mmmt) cc_final: 0.9090 (tppt) REVERT: B 95 MET cc_start: 0.9123 (tpp) cc_final: 0.8782 (tpp) REVERT: B 99 LYS cc_start: 0.9377 (mmtt) cc_final: 0.9081 (mmtt) REVERT: B 104 TYR cc_start: 0.8857 (m-80) cc_final: 0.8432 (m-80) REVERT: B 107 LYS cc_start: 0.9158 (mtpp) cc_final: 0.8586 (mtpp) REVERT: B 111 LYS cc_start: 0.9526 (mmtp) cc_final: 0.9291 (mmtm) REVERT: B 117 ARG cc_start: 0.8916 (mtp85) cc_final: 0.8627 (mtp85) REVERT: B 119 GLU cc_start: 0.9003 (mp0) cc_final: 0.8277 (mp0) REVERT: B 129 PHE cc_start: 0.9040 (m-10) cc_final: 0.8808 (m-10) REVERT: B 147 GLN cc_start: 0.9237 (mt0) cc_final: 0.8639 (mt0) REVERT: B 149 TYR cc_start: 0.9400 (t80) cc_final: 0.8762 (t80) REVERT: B 174 GLU cc_start: 0.8532 (tp30) cc_final: 0.8173 (tp30) REVERT: B 202 ASN cc_start: 0.9497 (t0) cc_final: 0.8850 (t0) REVERT: B 235 ARG cc_start: 0.9139 (ttm-80) cc_final: 0.8823 (mmt90) REVERT: B 236 TYR cc_start: 0.9000 (t80) cc_final: 0.8665 (t80) REVERT: B 246 SER cc_start: 0.7865 (m) cc_final: 0.7634 (p) REVERT: B 250 TYR cc_start: 0.9309 (m-80) cc_final: 0.8629 (m-80) REVERT: B 257 ASP cc_start: 0.8805 (m-30) cc_final: 0.8309 (m-30) REVERT: B 263 ASP cc_start: 0.9232 (m-30) cc_final: 0.8971 (m-30) REVERT: B 317 MET cc_start: 0.8587 (pmm) cc_final: 0.8339 (pmm) REVERT: B 322 MET cc_start: 0.9361 (mmm) cc_final: 0.8803 (mmm) REVERT: B 333 LYS cc_start: 0.9243 (tptp) cc_final: 0.8971 (ttmm) REVERT: B 375 LYS cc_start: 0.9400 (mttm) cc_final: 0.9192 (mttp) REVERT: B 387 GLN cc_start: 0.9119 (mt0) cc_final: 0.8652 (mt0) REVERT: B 393 SER cc_start: 0.9359 (m) cc_final: 0.9000 (p) REVERT: B 413 SER cc_start: 0.9685 (OUTLIER) cc_final: 0.9303 (p) REVERT: B 467 ASN cc_start: 0.9356 (t0) cc_final: 0.9131 (m-40) REVERT: B 475 ASN cc_start: 0.9358 (m-40) cc_final: 0.8969 (m110) REVERT: B 515 ASP cc_start: 0.9054 (m-30) cc_final: 0.8600 (m-30) REVERT: B 516 GLN cc_start: 0.9257 (mt0) cc_final: 0.8939 (tp-100) REVERT: B 546 LEU cc_start: 0.9612 (mt) cc_final: 0.9400 (mt) REVERT: B 586 TYR cc_start: 0.9102 (m-80) cc_final: 0.8861 (m-80) REVERT: B 599 GLU cc_start: 0.8573 (pt0) cc_final: 0.8296 (pt0) REVERT: B 601 ILE cc_start: 0.9494 (mm) cc_final: 0.9041 (mm) REVERT: B 602 GLU cc_start: 0.8497 (pt0) cc_final: 0.7796 (pt0) REVERT: B 604 ARG cc_start: 0.8687 (mmp80) cc_final: 0.8319 (mmp80) REVERT: B 610 LYS cc_start: 0.8845 (ptmt) cc_final: 0.8555 (ptmt) REVERT: B 612 TYR cc_start: 0.9145 (m-80) cc_final: 0.8902 (m-80) REVERT: B 636 LYS cc_start: 0.9503 (mmmt) cc_final: 0.9235 (mmmm) REVERT: B 640 MET cc_start: 0.9210 (tpp) cc_final: 0.8934 (tpp) REVERT: B 683 TYR cc_start: 0.9053 (t80) cc_final: 0.8534 (t80) REVERT: B 684 TYR cc_start: 0.8119 (OUTLIER) cc_final: 0.7405 (m-80) REVERT: B 686 ARG cc_start: 0.8651 (mmt180) cc_final: 0.8398 (mmt90) REVERT: C 21 PHE cc_start: 0.8364 (m-80) cc_final: 0.8090 (m-80) REVERT: C 68 GLU cc_start: 0.9129 (mm-30) cc_final: 0.8872 (mm-30) REVERT: C 74 MET cc_start: 0.9244 (mmm) cc_final: 0.8793 (tpp) REVERT: C 127 GLN cc_start: 0.8564 (mm110) cc_final: 0.7525 (pp30) REVERT: C 154 PHE cc_start: 0.9159 (t80) cc_final: 0.8720 (t80) REVERT: C 157 MET cc_start: 0.9292 (mtt) cc_final: 0.9024 (mtt) REVERT: C 212 ILE cc_start: 0.7435 (mt) cc_final: 0.6309 (mt) REVERT: C 242 TYR cc_start: 0.9202 (t80) cc_final: 0.8784 (t80) REVERT: D 21 PHE cc_start: 0.8973 (m-80) cc_final: 0.8627 (m-80) outliers start: 68 outliers final: 43 residues processed: 659 average time/residue: 0.2892 time to fit residues: 287.8620 Evaluate side-chains 629 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 579 time to evaluate : 2.397 ------------------------------------------------------------------------------- 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 127 LEU 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 183 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 408 SER Chi-restraints excluded: chain A residue 411 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 453 ARG Chi-restraints excluded: chain A residue 552 ILE Chi-restraints excluded: chain A residue 583 SER 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 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 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 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 71 ASN Chi-restraints excluded: chain C residue 177 TYR 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 240 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 39 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 161 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 146 optimal weight: 0.8980 chunk 184 optimal weight: 0.9980 chunk 119 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 24 optimal weight: 0.0870 chunk 5 optimal weight: 0.8980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN A 304 HIS A 676 HIS ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 HIS B 313 HIS ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 85 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 23 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 = 0.3834 r_free = 0.3834 target = 0.146941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106462 restraints weight = 36949.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110216 restraints weight = 18073.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.112638 restraints weight = 10771.577| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.6853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16386 Z= 0.142 Angle : 0.733 13.983 22134 Z= 0.366 Chirality : 0.046 0.256 2360 Planarity : 0.003 0.035 2818 Dihedral : 10.537 172.885 2243 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.67 % Allowed : 30.54 % Favored : 65.79 % 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: 0.74 (0.18), residues: 1932 helix: 1.04 (0.15), residues: 1122 sheet: -0.80 (0.37), residues: 150 loop : 0.05 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 124 HIS 0.008 0.001 HIS C 201 PHE 0.059 0.002 PHE C 109 TYR 0.021 0.001 TYR D 236 ARG 0.008 0.001 ARG B 207 Details of bonding type rmsd hydrogen bonds : bond 0.04035 ( 871) hydrogen bonds : angle 5.10593 ( 2571) covalent geometry : bond 0.00323 (16386) covalent geometry : angle 0.73326 (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 668 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 605 time to evaluate : 1.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9034 (ttmm) cc_final: 0.8792 (ttpt) REVERT: A 31 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8790 (mp0) REVERT: A 123 SER cc_start: 0.9381 (OUTLIER) cc_final: 0.9142 (p) REVERT: A 128 PHE cc_start: 0.9431 (t80) cc_final: 0.9110 (t80) REVERT: A 139 GLU cc_start: 0.8790 (mt-10) cc_final: 0.8551 (mt-10) REVERT: A 149 TYR cc_start: 0.9545 (t80) cc_final: 0.8706 (t80) REVERT: A 202 ASN cc_start: 0.9321 (t0) cc_final: 0.8916 (t0) REVERT: A 252 ASN cc_start: 0.9345 (t0) cc_final: 0.8970 (t0) REVERT: A 263 ASP cc_start: 0.8776 (m-30) cc_final: 0.8409 (m-30) REVERT: A 277 THR cc_start: 0.8716 (p) cc_final: 0.8285 (t) REVERT: A 286 ASP cc_start: 0.8688 (m-30) cc_final: 0.8416 (m-30) REVERT: A 290 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8579 (tm-30) REVERT: A 335 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8084 (mm-30) REVERT: A 362 ASP cc_start: 0.8177 (m-30) cc_final: 0.7320 (m-30) REVERT: A 384 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7570 (pm20) REVERT: A 402 GLU cc_start: 0.8083 (mp0) cc_final: 0.7672 (mp0) REVERT: A 426 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8164 (tm-30) REVERT: A 435 SER cc_start: 0.9690 (OUTLIER) cc_final: 0.9370 (p) REVERT: A 446 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7145 (mtp85) REVERT: A 453 ARG cc_start: 0.9425 (OUTLIER) cc_final: 0.8948 (ttp80) REVERT: A 505 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8419 (mt-10) REVERT: A 515 ASP cc_start: 0.9156 (m-30) cc_final: 0.8758 (m-30) REVERT: A 588 GLN cc_start: 0.9331 (mm-40) cc_final: 0.9129 (mm-40) REVERT: A 598 MET cc_start: 0.8817 (tpp) cc_final: 0.8617 (mmt) REVERT: A 606 TYR cc_start: 0.7833 (m-80) cc_final: 0.7379 (m-80) REVERT: A 615 MET cc_start: 0.9307 (mmp) cc_final: 0.8767 (mmp) REVERT: A 640 MET cc_start: 0.9383 (tpp) cc_final: 0.8353 (tpp) REVERT: B 8 LYS cc_start: 0.8967 (tppt) cc_final: 0.8683 (tppt) REVERT: B 12 LEU cc_start: 0.9208 (mt) cc_final: 0.8987 (mt) REVERT: B 65 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8299 (mm-30) REVERT: B 87 LYS cc_start: 0.9395 (mmmt) cc_final: 0.9111 (tppt) REVERT: B 95 MET cc_start: 0.9124 (tpp) cc_final: 0.8759 (tpp) REVERT: B 99 LYS cc_start: 0.9384 (mmtt) cc_final: 0.9126 (mmtt) REVERT: B 107 LYS cc_start: 0.9124 (mtpp) cc_final: 0.8756 (mtpp) REVERT: B 111 LYS cc_start: 0.9546 (mmtp) cc_final: 0.9332 (mmtm) REVERT: B 119 GLU cc_start: 0.8953 (mp0) cc_final: 0.8226 (mp0) REVERT: B 127 LEU cc_start: 0.9737 (mm) cc_final: 0.9449 (mm) REVERT: B 129 PHE cc_start: 0.9075 (m-10) cc_final: 0.8811 (m-10) REVERT: B 139 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8554 (mp0) REVERT: B 147 GLN cc_start: 0.9215 (mt0) cc_final: 0.8655 (mt0) REVERT: B 149 TYR cc_start: 0.9408 (t80) cc_final: 0.8712 (t80) REVERT: B 207 ARG cc_start: 0.8424 (ptp-170) cc_final: 0.8066 (ptp-170) REVERT: B 235 ARG cc_start: 0.9113 (ttm-80) cc_final: 0.8799 (mmt90) REVERT: B 236 TYR cc_start: 0.8952 (t80) cc_final: 0.8666 (t80) REVERT: B 246 SER cc_start: 0.7841 (m) cc_final: 0.7627 (p) REVERT: B 257 ASP cc_start: 0.8932 (m-30) cc_final: 0.8415 (m-30) REVERT: B 263 ASP cc_start: 0.9153 (m-30) cc_final: 0.8890 (m-30) REVERT: B 274 ARG cc_start: 0.8007 (tpp80) cc_final: 0.7740 (tpp80) REVERT: B 322 MET cc_start: 0.9348 (mmm) cc_final: 0.8768 (mmm) REVERT: B 333 LYS cc_start: 0.9283 (tptp) cc_final: 0.9003 (ttmm) REVERT: B 375 LYS cc_start: 0.9371 (mttm) cc_final: 0.9158 (mttp) REVERT: B 393 SER cc_start: 0.9312 (m) cc_final: 0.9075 (p) REVERT: B 396 ASP cc_start: 0.8423 (p0) cc_final: 0.8169 (p0) REVERT: B 413 SER cc_start: 0.9674 (OUTLIER) cc_final: 0.9307 (p) REVERT: B 467 ASN cc_start: 0.9337 (t0) cc_final: 0.9118 (m-40) REVERT: B 475 ASN cc_start: 0.9329 (m-40) cc_final: 0.9009 (m110) REVERT: B 492 PHE cc_start: 0.9530 (m-80) cc_final: 0.9111 (m-10) REVERT: B 515 ASP cc_start: 0.9019 (m-30) cc_final: 0.8592 (m-30) REVERT: B 586 TYR cc_start: 0.9060 (m-80) cc_final: 0.8827 (m-80) REVERT: B 599 GLU cc_start: 0.8585 (pt0) cc_final: 0.8309 (pt0) REVERT: B 601 ILE cc_start: 0.9483 (mm) cc_final: 0.9007 (mm) REVERT: B 602 GLU cc_start: 0.8512 (pt0) cc_final: 0.7749 (pt0) REVERT: B 604 ARG cc_start: 0.8721 (mmp80) cc_final: 0.8461 (mmp80) REVERT: B 610 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8533 (ptmt) REVERT: B 612 TYR cc_start: 0.9076 (m-80) cc_final: 0.8765 (m-80) REVERT: B 634 MET cc_start: 0.8781 (mmm) cc_final: 0.8453 (tpt) REVERT: B 636 LYS cc_start: 0.9502 (mmmt) cc_final: 0.9231 (mmmm) REVERT: B 650 GLN cc_start: 0.8115 (mt0) cc_final: 0.7772 (mt0) REVERT: B 683 TYR cc_start: 0.9007 (t80) cc_final: 0.8555 (t80) REVERT: B 684 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.7419 (m-80) REVERT: C 68 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8689 (mm-30) REVERT: C 74 MET cc_start: 0.9196 (mmm) cc_final: 0.8755 (tpp) REVERT: C 127 GLN cc_start: 0.8642 (mm110) cc_final: 0.7655 (pp30) REVERT: C 154 PHE cc_start: 0.9130 (t80) cc_final: 0.8796 (t80) REVERT: C 204 TYR cc_start: 0.8514 (t80) cc_final: 0.8222 (t80) REVERT: C 212 ILE cc_start: 0.7410 (mt) cc_final: 0.6853 (mm) REVERT: D 21 PHE cc_start: 0.8829 (m-80) cc_final: 0.8472 (m-80) REVERT: D 25 ASN cc_start: 0.8245 (t0) cc_final: 0.8016 (t0) outliers start: 63 outliers final: 42 residues processed: 635 average time/residue: 0.2725 time to fit residues: 261.7591 Evaluate side-chains 619 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 569 time to evaluate : 1.920 ------------------------------------------------------------------------------- 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 127 LEU 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 183 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 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 453 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 178 SER Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 190 MET 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 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 605 THR Chi-restraints excluded: chain B residue 610 LYS Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 652 ILE 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 69 GLN Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 276 TYR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 55 TYR Chi-restraints excluded: chain D residue 115 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 159 optimal weight: 20.0000 chunk 72 optimal weight: 8.9990 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 52 optimal weight: 0.6980 chunk 180 optimal weight: 0.9990 chunk 108 optimal weight: 6.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS B 19 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 474 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.142871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.101911 restraints weight = 36927.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.105582 restraints weight = 18431.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.107982 restraints weight = 11155.578| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.7124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16386 Z= 0.150 Angle : 0.757 14.615 22134 Z= 0.378 Chirality : 0.047 0.259 2360 Planarity : 0.004 0.035 2818 Dihedral : 10.453 172.360 2243 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.96 % Allowed : 31.88 % Favored : 64.16 % 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: 0.64 (0.18), residues: 1932 helix: 0.96 (0.15), residues: 1118 sheet: -0.80 (0.38), residues: 150 loop : 0.02 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 124 HIS 0.012 0.001 HIS C 101 PHE 0.064 0.002 PHE C 92 TYR 0.042 0.001 TYR D 105 ARG 0.008 0.001 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 871) hydrogen bonds : angle 5.16201 ( 2571) covalent geometry : bond 0.00340 (16386) covalent geometry : angle 0.75743 (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 655 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 587 time to evaluate : 1.835 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: 0.9052 (ttmm) cc_final: 0.8802 (ttpt) REVERT: A 31 GLU cc_start: 0.9151 (mt-10) cc_final: 0.8818 (mp0) REVERT: A 65 GLU cc_start: 0.8579 (mm-30) cc_final: 0.7963 (mp0) REVERT: A 123 SER cc_start: 0.9300 (OUTLIER) cc_final: 0.9037 (p) REVERT: A 128 PHE cc_start: 0.9451 (t80) cc_final: 0.9098 (t80) REVERT: A 139 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8428 (mt-10) REVERT: A 149 TYR cc_start: 0.9495 (t80) cc_final: 0.8561 (t80) REVERT: A 150 GLN cc_start: 0.9418 (tp40) cc_final: 0.8907 (tm-30) REVERT: A 202 ASN cc_start: 0.9302 (t0) cc_final: 0.8881 (t0) REVERT: A 218 ASN cc_start: 0.9192 (t0) cc_final: 0.8972 (t0) REVERT: A 252 ASN cc_start: 0.9345 (t0) cc_final: 0.8974 (t0) REVERT: A 263 ASP cc_start: 0.8774 (m-30) cc_final: 0.8410 (m-30) REVERT: A 277 THR cc_start: 0.8733 (p) cc_final: 0.8302 (t) REVERT: A 286 ASP cc_start: 0.8705 (m-30) cc_final: 0.8443 (m-30) REVERT: A 290 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8510 (tm-30) REVERT: A 335 GLU cc_start: 0.8340 (mm-30) cc_final: 0.8064 (mm-30) REVERT: A 348 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8651 (tmm) REVERT: A 362 ASP cc_start: 0.8180 (m-30) cc_final: 0.7326 (m-30) REVERT: A 384 GLU cc_start: 0.8539 (OUTLIER) cc_final: 0.7737 (pm20) REVERT: A 402 GLU cc_start: 0.8105 (mp0) cc_final: 0.7683 (mp0) REVERT: A 426 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8119 (tm-30) REVERT: A 435 SER cc_start: 0.9702 (OUTLIER) cc_final: 0.9384 (p) REVERT: A 452 ARG cc_start: 0.9269 (OUTLIER) cc_final: 0.9000 (ptm-80) REVERT: A 453 ARG cc_start: 0.9424 (OUTLIER) cc_final: 0.8930 (ttp80) REVERT: A 493 MET cc_start: 0.8739 (tmm) cc_final: 0.8416 (tmm) REVERT: A 505 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8423 (mt-10) REVERT: A 515 ASP cc_start: 0.9163 (m-30) cc_final: 0.8937 (m-30) REVERT: A 598 MET cc_start: 0.8824 (tpp) cc_final: 0.8468 (mmt) REVERT: A 615 MET cc_start: 0.9296 (mmp) cc_final: 0.8717 (mmp) REVERT: A 640 MET cc_start: 0.9371 (tpp) cc_final: 0.8327 (tpp) REVERT: A 686 ARG cc_start: 0.8563 (tpp80) cc_final: 0.8160 (tpp-160) REVERT: B 8 LYS cc_start: 0.9002 (tppt) cc_final: 0.8685 (tppt) REVERT: B 12 LEU cc_start: 0.9207 (mt) cc_final: 0.8981 (mt) REVERT: B 65 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8324 (mm-30) REVERT: B 87 LYS cc_start: 0.9413 (mmmt) cc_final: 0.9067 (tptm) REVERT: B 95 MET cc_start: 0.9152 (tpp) cc_final: 0.8802 (tpp) REVERT: B 99 LYS cc_start: 0.9341 (mmtt) cc_final: 0.9112 (mmtt) REVERT: B 119 GLU cc_start: 0.8954 (mp0) cc_final: 0.8256 (mp0) REVERT: B 127 LEU cc_start: 0.9739 (mm) cc_final: 0.9470 (mm) REVERT: B 129 PHE cc_start: 0.9113 (m-10) cc_final: 0.8905 (m-10) REVERT: B 147 GLN cc_start: 0.9217 (mt0) cc_final: 0.8018 (mt0) REVERT: B 149 TYR cc_start: 0.9394 (t80) cc_final: 0.8673 (t80) REVERT: B 235 ARG cc_start: 0.9143 (ttm-80) cc_final: 0.8800 (mmt90) REVERT: B 236 TYR cc_start: 0.8906 (t80) cc_final: 0.8622 (t80) REVERT: B 246 SER cc_start: 0.7792 (m) cc_final: 0.7504 (p) REVERT: B 250 TYR cc_start: 0.9307 (m-80) cc_final: 0.8558 (m-80) REVERT: B 257 ASP cc_start: 0.8862 (m-30) cc_final: 0.8381 (m-30) REVERT: B 263 ASP cc_start: 0.9106 (m-30) cc_final: 0.8830 (m-30) REVERT: B 274 ARG cc_start: 0.8114 (tpp80) cc_final: 0.7901 (tpp80) REVERT: B 322 MET cc_start: 0.9306 (mmm) cc_final: 0.8740 (mmm) REVERT: B 333 LYS cc_start: 0.9265 (tptp) cc_final: 0.9020 (ttmm) REVERT: B 393 SER cc_start: 0.9391 (m) cc_final: 0.9088 (p) REVERT: B 413 SER cc_start: 0.9663 (OUTLIER) cc_final: 0.9326 (p) REVERT: B 480 GLU cc_start: 0.8862 (mp0) cc_final: 0.8606 (mp0) REVERT: B 492 PHE cc_start: 0.9518 (m-80) cc_final: 0.9104 (m-80) REVERT: B 515 ASP cc_start: 0.9019 (m-30) cc_final: 0.8568 (m-30) REVERT: B 570 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7304 (ptp) REVERT: B 586 TYR cc_start: 0.9017 (m-80) cc_final: 0.8753 (m-80) REVERT: B 588 GLN cc_start: 0.9415 (mm-40) cc_final: 0.8215 (mm-40) REVERT: B 599 GLU cc_start: 0.8617 (pt0) cc_final: 0.8322 (pt0) REVERT: B 601 ILE cc_start: 0.9486 (mm) cc_final: 0.8947 (mm) REVERT: B 602 GLU cc_start: 0.8479 (pt0) cc_final: 0.7687 (pt0) REVERT: B 604 ARG cc_start: 0.8734 (mmp80) cc_final: 0.8466 (mmp80) REVERT: B 610 LYS cc_start: 0.8820 (OUTLIER) cc_final: 0.8508 (ptmt) REVERT: B 612 TYR cc_start: 0.9019 (m-80) cc_final: 0.8589 (m-80) REVERT: B 636 LYS cc_start: 0.9465 (mmmt) cc_final: 0.9215 (mmmm) REVERT: B 640 MET cc_start: 0.9356 (tpp) cc_final: 0.9033 (tpp) REVERT: B 650 GLN cc_start: 0.8321 (mt0) cc_final: 0.7777 (mt0) REVERT: B 683 TYR cc_start: 0.9050 (t80) cc_final: 0.8713 (t80) REVERT: B 684 TYR cc_start: 0.8053 (OUTLIER) cc_final: 0.7518 (m-80) REVERT: C 68 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8798 (mm-30) REVERT: C 74 MET cc_start: 0.9246 (mmm) cc_final: 0.8764 (tpp) REVERT: C 154 PHE cc_start: 0.9178 (t80) cc_final: 0.8775 (t80) REVERT: C 204 TYR cc_start: 0.8654 (t80) cc_final: 0.8424 (t80) REVERT: C 212 ILE cc_start: 0.7231 (mt) cc_final: 0.7000 (mm) REVERT: C 242 TYR cc_start: 0.9089 (t80) cc_final: 0.8837 (t80) REVERT: D 157 MET cc_start: 0.1340 (ttp) cc_final: 0.1124 (ttp) REVERT: D 240 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7834 (mm) outliers start: 68 outliers final: 44 residues processed: 621 average time/residue: 0.2691 time to fit residues: 252.4337 Evaluate side-chains 626 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 571 time to evaluate : 1.913 ------------------------------------------------------------------------------- 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 127 LEU 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 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 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 453 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 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 411 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 570 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 B residue 652 ILE Chi-restraints excluded: chain B residue 660 ASP 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 93 MET Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 42 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 111 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 182 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 96 optimal weight: 0.8980 chunk 115 optimal weight: 3.9990 chunk 127 optimal weight: 0.7980 chunk 188 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 50 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 475 ASN B 588 GLN B 646 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.143332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.102126 restraints weight = 37254.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.105835 restraints weight = 18487.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.108256 restraints weight = 11243.434| |-----------------------------------------------------------------------------| r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.7401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16386 Z= 0.151 Angle : 0.801 17.762 22134 Z= 0.396 Chirality : 0.048 0.247 2360 Planarity : 0.004 0.040 2818 Dihedral : 10.299 169.760 2243 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.61 % Allowed : 32.81 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.18), residues: 1932 helix: 0.86 (0.15), residues: 1118 sheet: -0.79 (0.38), residues: 150 loop : -0.05 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP D 44 HIS 0.006 0.001 HIS C 201 PHE 0.063 0.002 PHE C 92 TYR 0.055 0.001 TYR D 105 ARG 0.007 0.001 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.04150 ( 871) hydrogen bonds : angle 5.20116 ( 2571) covalent geometry : bond 0.00344 (16386) covalent geometry : angle 0.80080 (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 639 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 577 time to evaluate : 1.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9066 (ttmm) cc_final: 0.8808 (ttpt) REVERT: A 31 GLU cc_start: 0.9136 (mt-10) cc_final: 0.8802 (mp0) REVERT: A 65 GLU cc_start: 0.8538 (mm-30) cc_final: 0.7736 (mp0) REVERT: A 123 SER cc_start: 0.9259 (OUTLIER) cc_final: 0.9000 (p) REVERT: A 128 PHE cc_start: 0.9462 (t80) cc_final: 0.9101 (t80) REVERT: A 139 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8430 (mt-10) REVERT: A 149 TYR cc_start: 0.9586 (t80) cc_final: 0.8428 (t80) REVERT: A 150 GLN cc_start: 0.9444 (tp40) cc_final: 0.8764 (tm-30) REVERT: A 202 ASN cc_start: 0.9299 (t0) cc_final: 0.8927 (t0) REVERT: A 218 ASN cc_start: 0.9144 (t0) cc_final: 0.8917 (t0) REVERT: A 263 ASP cc_start: 0.8734 (m-30) cc_final: 0.8349 (m-30) REVERT: A 277 THR cc_start: 0.8747 (p) cc_final: 0.8307 (t) REVERT: A 290 GLU cc_start: 0.8989 (tm-30) cc_final: 0.8540 (tm-30) REVERT: A 335 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8079 (mm-30) REVERT: A 362 ASP cc_start: 0.8146 (m-30) cc_final: 0.7283 (m-30) REVERT: A 384 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7726 (pm20) REVERT: A 402 GLU cc_start: 0.8171 (mp0) cc_final: 0.7751 (mp0) REVERT: A 426 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8141 (tm-30) REVERT: A 452 ARG cc_start: 0.9249 (OUTLIER) cc_final: 0.8681 (ttt-90) REVERT: A 453 ARG cc_start: 0.9442 (OUTLIER) cc_final: 0.8935 (ttp80) REVERT: A 505 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8426 (mt-10) REVERT: A 515 ASP cc_start: 0.9194 (m-30) cc_final: 0.8949 (m-30) REVERT: A 584 ILE cc_start: 0.9486 (pt) cc_final: 0.8888 (pt) REVERT: A 595 MET cc_start: 0.8967 (mmp) cc_final: 0.8544 (mmm) REVERT: A 598 MET cc_start: 0.8794 (OUTLIER) cc_final: 0.8375 (mmt) REVERT: A 615 MET cc_start: 0.9292 (mmp) cc_final: 0.8697 (mmp) REVERT: A 639 ASP cc_start: 0.9017 (t70) cc_final: 0.8762 (p0) REVERT: A 657 PHE cc_start: 0.8865 (m-80) cc_final: 0.8246 (m-80) REVERT: A 686 ARG cc_start: 0.8514 (tpp80) cc_final: 0.8176 (tpp-160) REVERT: B 8 LYS cc_start: 0.9019 (tppt) cc_final: 0.8702 (tppt) REVERT: B 12 LEU cc_start: 0.9210 (mt) cc_final: 0.8977 (mt) REVERT: B 27 ASP cc_start: 0.8367 (p0) cc_final: 0.8092 (p0) REVERT: B 65 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8348 (mm-30) REVERT: B 87 LYS cc_start: 0.9415 (mmmt) cc_final: 0.9068 (tptm) REVERT: B 99 LYS cc_start: 0.9335 (mmtt) cc_final: 0.9126 (mmtt) REVERT: B 119 GLU cc_start: 0.8970 (mp0) cc_final: 0.8289 (mp0) REVERT: B 127 LEU cc_start: 0.9745 (mm) cc_final: 0.9442 (mm) REVERT: B 129 PHE cc_start: 0.9151 (m-10) cc_final: 0.8852 (m-10) REVERT: B 147 GLN cc_start: 0.9285 (mt0) cc_final: 0.8438 (mt0) REVERT: B 149 TYR cc_start: 0.9380 (t80) cc_final: 0.8556 (t80) REVERT: B 235 ARG cc_start: 0.9125 (ttm-80) cc_final: 0.8790 (mmt90) REVERT: B 236 TYR cc_start: 0.8891 (t80) cc_final: 0.8578 (t80) REVERT: B 246 SER cc_start: 0.7748 (m) cc_final: 0.7502 (p) REVERT: B 257 ASP cc_start: 0.8854 (m-30) cc_final: 0.8455 (m-30) REVERT: B 274 ARG cc_start: 0.8199 (tpp80) cc_final: 0.7920 (tpp80) REVERT: B 322 MET cc_start: 0.9306 (mmm) cc_final: 0.8733 (mmm) REVERT: B 333 LYS cc_start: 0.9267 (tptp) cc_final: 0.9012 (ttmm) REVERT: B 393 SER cc_start: 0.9345 (m) cc_final: 0.9060 (p) REVERT: B 394 TYR cc_start: 0.9248 (m-80) cc_final: 0.8803 (m-80) REVERT: B 413 SER cc_start: 0.9598 (OUTLIER) cc_final: 0.9302 (p) REVERT: B 446 ARG cc_start: 0.8091 (mtp85) cc_final: 0.7679 (mtp85) REVERT: B 467 ASN cc_start: 0.9066 (OUTLIER) cc_final: 0.8838 (m-40) REVERT: B 480 GLU cc_start: 0.8849 (mp0) cc_final: 0.8491 (mp0) REVERT: B 492 PHE cc_start: 0.9531 (m-80) cc_final: 0.9159 (m-80) REVERT: B 494 MET cc_start: 0.9153 (mmt) cc_final: 0.8928 (mmm) REVERT: B 515 ASP cc_start: 0.9016 (m-30) cc_final: 0.8777 (m-30) REVERT: B 586 TYR cc_start: 0.8979 (m-80) cc_final: 0.8644 (m-80) REVERT: B 588 GLN cc_start: 0.9465 (mm110) cc_final: 0.8793 (mm110) REVERT: B 599 GLU cc_start: 0.8606 (pt0) cc_final: 0.8299 (pt0) REVERT: B 601 ILE cc_start: 0.9505 (mm) cc_final: 0.8927 (mm) REVERT: B 602 GLU cc_start: 0.8466 (pt0) cc_final: 0.7504 (pt0) REVERT: B 604 ARG cc_start: 0.8797 (mmp80) cc_final: 0.8467 (mmp80) REVERT: B 610 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8723 (ptmt) REVERT: B 612 TYR cc_start: 0.8986 (m-80) cc_final: 0.8082 (m-80) REVERT: B 632 MET cc_start: 0.8403 (mtp) cc_final: 0.7660 (mtp) REVERT: B 636 LYS cc_start: 0.9470 (mmmt) cc_final: 0.9207 (mmmm) REVERT: B 640 MET cc_start: 0.9335 (tpp) cc_final: 0.9016 (tpp) REVERT: B 650 GLN cc_start: 0.8291 (mt0) cc_final: 0.8025 (mm-40) REVERT: B 683 TYR cc_start: 0.9086 (t80) cc_final: 0.8732 (t80) REVERT: B 684 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.7545 (m-80) REVERT: B 686 ARG cc_start: 0.8634 (mmt180) cc_final: 0.8321 (mmt180) REVERT: C 68 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8813 (mm-30) REVERT: C 74 MET cc_start: 0.9206 (mmm) cc_final: 0.8770 (tpp) REVERT: C 154 PHE cc_start: 0.9172 (t80) cc_final: 0.8738 (t80) REVERT: C 162 TYR cc_start: 0.8776 (m-80) cc_final: 0.8511 (m-80) REVERT: C 204 TYR cc_start: 0.8616 (t80) cc_final: 0.8394 (t80) REVERT: C 212 ILE cc_start: 0.7181 (mt) cc_final: 0.6946 (mm) REVERT: C 316 LYS cc_start: 0.8991 (mmtt) cc_final: 0.8496 (mmtm) REVERT: D 21 PHE cc_start: 0.8974 (m-80) cc_final: 0.8562 (t80) REVERT: D 137 MET cc_start: 0.0797 (mmt) cc_final: -0.0170 (mtm) REVERT: D 157 MET cc_start: 0.1271 (ttp) cc_final: 0.1041 (ttp) REVERT: D 240 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7994 (mm) outliers start: 62 outliers final: 41 residues processed: 604 average time/residue: 0.2658 time to fit residues: 241.7664 Evaluate side-chains 606 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 555 time to evaluate : 1.778 ------------------------------------------------------------------------------- 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 127 LEU 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 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 598 MET 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 190 MET 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 314 MET Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 460 SER 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 610 LYS 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 C residue 54 THR Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 72 THR 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 Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 137 optimal weight: 6.9990 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 160 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 120 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 148 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.140265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.100436 restraints weight = 37986.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.103961 restraints weight = 18362.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.106285 restraints weight = 11104.092| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.7543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16386 Z= 0.241 Angle : 0.833 13.372 22134 Z= 0.421 Chirality : 0.050 0.255 2360 Planarity : 0.004 0.049 2818 Dihedral : 10.403 160.597 2243 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 19.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.44 % Allowed : 33.74 % Favored : 62.82 % 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: 0.50 (0.19), residues: 1932 helix: 0.83 (0.15), residues: 1129 sheet: -0.74 (0.39), residues: 150 loop : -0.05 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP D 44 HIS 0.008 0.002 HIS A 469 PHE 0.067 0.003 PHE C 109 TYR 0.060 0.002 TYR D 105 ARG 0.008 0.001 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.04333 ( 871) hydrogen bonds : angle 5.39272 ( 2571) covalent geometry : bond 0.00539 (16386) covalent geometry : angle 0.83350 (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 631 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 572 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9115 (ttmm) cc_final: 0.8896 (ttpt) REVERT: A 31 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8736 (mp0) REVERT: A 65 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8236 (mm-30) REVERT: A 123 SER cc_start: 0.9391 (OUTLIER) cc_final: 0.9029 (p) REVERT: A 128 PHE cc_start: 0.9572 (t80) cc_final: 0.9255 (t80) REVERT: A 139 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8411 (mt-10) REVERT: A 149 TYR cc_start: 0.9537 (t80) cc_final: 0.8639 (t80) REVERT: A 150 GLN cc_start: 0.9454 (tp40) cc_final: 0.8587 (tm-30) REVERT: A 195 LEU cc_start: 0.9629 (mt) cc_final: 0.9366 (mt) REVERT: A 202 ASN cc_start: 0.9466 (t0) cc_final: 0.9066 (t0) REVERT: A 263 ASP cc_start: 0.8760 (m-30) cc_final: 0.8391 (m-30) REVERT: A 277 THR cc_start: 0.8816 (p) cc_final: 0.8336 (t) REVERT: A 286 ASP cc_start: 0.8697 (m-30) cc_final: 0.8450 (m-30) REVERT: A 290 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8579 (tm-30) REVERT: A 335 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8086 (mm-30) REVERT: A 348 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8650 (tmm) REVERT: A 362 ASP cc_start: 0.8256 (m-30) cc_final: 0.7888 (m-30) REVERT: A 384 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.7872 (pm20) REVERT: A 402 GLU cc_start: 0.8230 (mp0) cc_final: 0.7786 (mp0) REVERT: A 426 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8300 (tm-30) REVERT: A 452 ARG cc_start: 0.9245 (OUTLIER) cc_final: 0.8929 (ptm-80) REVERT: A 453 ARG cc_start: 0.9481 (OUTLIER) cc_final: 0.8445 (ttp80) REVERT: A 493 MET cc_start: 0.8808 (tmm) cc_final: 0.8607 (tmm) REVERT: A 505 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8288 (mt-10) REVERT: A 515 ASP cc_start: 0.9199 (m-30) cc_final: 0.8963 (m-30) REVERT: A 584 ILE cc_start: 0.9529 (pt) cc_final: 0.8974 (pt) REVERT: A 595 MET cc_start: 0.9193 (mmp) cc_final: 0.8885 (mmm) REVERT: A 615 MET cc_start: 0.9334 (mmp) cc_final: 0.8819 (mmp) REVERT: A 686 ARG cc_start: 0.8535 (tpp80) cc_final: 0.8171 (tpp-160) REVERT: B 27 ASP cc_start: 0.8435 (p0) cc_final: 0.8175 (p0) REVERT: B 65 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8300 (mm-30) REVERT: B 87 LYS cc_start: 0.9481 (mmmt) cc_final: 0.9241 (tptm) REVERT: B 99 LYS cc_start: 0.9384 (mmtt) cc_final: 0.9092 (mmtt) REVERT: B 104 TYR cc_start: 0.9061 (m-80) cc_final: 0.8743 (m-80) REVERT: B 119 GLU cc_start: 0.9035 (mp0) cc_final: 0.8401 (mp0) REVERT: B 149 TYR cc_start: 0.9423 (t80) cc_final: 0.8962 (t80) REVERT: B 235 ARG cc_start: 0.9139 (ttm-80) cc_final: 0.8804 (mmt90) REVERT: B 236 TYR cc_start: 0.8995 (t80) cc_final: 0.8601 (t80) REVERT: B 246 SER cc_start: 0.7862 (m) cc_final: 0.7597 (p) REVERT: B 250 TYR cc_start: 0.9373 (m-80) cc_final: 0.8583 (m-80) REVERT: B 257 ASP cc_start: 0.8765 (m-30) cc_final: 0.8389 (m-30) REVERT: B 322 MET cc_start: 0.9291 (mmm) cc_final: 0.8800 (mmm) REVERT: B 392 SER cc_start: 0.9241 (m) cc_final: 0.8936 (p) REVERT: B 393 SER cc_start: 0.9335 (m) cc_final: 0.8947 (p) REVERT: B 402 GLU cc_start: 0.8863 (tp30) cc_final: 0.8431 (tp30) REVERT: B 403 ILE cc_start: 0.9104 (mm) cc_final: 0.8462 (tt) REVERT: B 413 SER cc_start: 0.9708 (OUTLIER) cc_final: 0.9283 (p) REVERT: B 452 ARG cc_start: 0.8954 (OUTLIER) cc_final: 0.8262 (ttm-80) REVERT: B 467 ASN cc_start: 0.9327 (OUTLIER) cc_final: 0.9096 (m-40) REVERT: B 515 ASP cc_start: 0.9099 (m-30) cc_final: 0.8696 (m-30) REVERT: B 586 TYR cc_start: 0.9060 (m-80) cc_final: 0.8720 (m-80) REVERT: B 599 GLU cc_start: 0.8662 (pt0) cc_final: 0.8352 (pt0) REVERT: B 601 ILE cc_start: 0.9510 (mm) cc_final: 0.9027 (mm) REVERT: B 602 GLU cc_start: 0.8429 (pt0) cc_final: 0.7697 (pt0) REVERT: B 610 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8693 (ptmt) REVERT: B 612 TYR cc_start: 0.9032 (m-80) cc_final: 0.8598 (m-80) REVERT: B 636 LYS cc_start: 0.9451 (mmmt) cc_final: 0.9172 (mmmm) REVERT: B 684 TYR cc_start: 0.8033 (OUTLIER) cc_final: 0.7444 (m-80) REVERT: B 686 ARG cc_start: 0.8593 (mmt180) cc_final: 0.8124 (mmt180) REVERT: C 74 MET cc_start: 0.9132 (mmm) cc_final: 0.8752 (tpp) REVERT: C 154 PHE cc_start: 0.9195 (t80) cc_final: 0.8714 (t80) REVERT: C 169 TYR cc_start: 0.8553 (m-80) cc_final: 0.8217 (m-80) REVERT: C 204 TYR cc_start: 0.8693 (t80) cc_final: 0.8374 (t80) REVERT: C 212 ILE cc_start: 0.7441 (mt) cc_final: 0.6736 (mt) REVERT: C 318 ASP cc_start: 0.9208 (t0) cc_final: 0.8774 (t0) REVERT: D 16 ASP cc_start: 0.7498 (m-30) cc_final: 0.7190 (t0) REVERT: D 20 MET cc_start: 0.7038 (ttt) cc_final: 0.6577 (ppp) REVERT: D 21 PHE cc_start: 0.8902 (m-80) cc_final: 0.8157 (t80) REVERT: D 137 MET cc_start: 0.1120 (mmt) cc_final: 0.0123 (mtm) REVERT: D 240 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.8018 (mm) outliers start: 59 outliers final: 38 residues processed: 596 average time/residue: 0.2752 time to fit residues: 248.1056 Evaluate side-chains 610 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 561 time to evaluate : 1.708 ------------------------------------------------------------------------------- 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 178 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 411 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 452 ARG Chi-restraints excluded: chain A residue 453 ARG 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 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 346 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 467 ASN 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 652 ILE Chi-restraints excluded: chain B residue 660 ASP 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 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 22 TYR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 204 TYR Chi-restraints excluded: chain D residue 240 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 81 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 2 optimal weight: 7.9990 chunk 97 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 179 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 GLN B 588 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.141663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.101017 restraints weight = 37353.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104656 restraints weight = 18437.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.107056 restraints weight = 11244.660| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.7734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16386 Z= 0.157 Angle : 0.840 14.175 22134 Z= 0.414 Chirality : 0.048 0.297 2360 Planarity : 0.004 0.037 2818 Dihedral : 10.068 159.388 2243 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.80 % Allowed : 34.38 % Favored : 62.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.18), residues: 1932 helix: 0.80 (0.15), residues: 1128 sheet: -0.67 (0.39), residues: 150 loop : -0.07 (0.23), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP D 44 HIS 0.008 0.001 HIS C 201 PHE 0.062 0.002 PHE C 109 TYR 0.055 0.002 TYR D 105 ARG 0.006 0.001 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 871) hydrogen bonds : angle 5.29914 ( 2571) covalent geometry : bond 0.00359 (16386) covalent geometry : angle 0.84044 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6896.91 seconds wall clock time: 120 minutes 35.00 seconds (7235.00 seconds total)