Starting phenix.real_space_refine on Thu Feb 5 07:04:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bza_45061/02_2026/9bza_45061_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bza_45061/02_2026/9bza_45061.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 { model { file = "/net/cci-nas-00/data/ceres_data/9bza_45061/02_2026/9bza_45061_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bza_45061/02_2026/9bza_45061_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bza_45061/02_2026/9bza_45061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bza_45061/02_2026/9bza_45061.map" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.69, per 1000 atoms: 0.23 Number of scatterers: 16038 At special positions: 0 Unit cell: (94.302, 128.778, 130.806, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 755.1 milliseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.985A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.953A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.666A 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: 4.126A 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: 3.694A 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: 4.850A 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: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A 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: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.676A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.872A 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: 3.730A 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: 5.118A 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: 3.514A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.668A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.360A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.425A 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: 6.477A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A 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: 6.479A 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: 7.229A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.048A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.563A 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: 6.549A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.67 Time building geometry restraints manager: 1.86 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: 4960 1.34 - 1.46: 3015 1.46 - 1.58: 8230 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 -0.060 1.25e-02 6.40e+03 2.34e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.579 -0.039 1.20e-02 6.94e+03 1.07e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.032 1.08e-02 8.57e+03 9.01e+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 7.57e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.574 -0.033 1.25e-02 6.40e+03 7.16e+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: 35 6.27 - 8.36: 3 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 110.54 116.64 -6.10 1.36e+00 5.41e-01 2.01e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.10 -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 113.50 117.85 -4.35 1.23e+00 6.61e-01 1.25e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.70 -3.99 1.15e+00 7.56e-01 1.21e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.54 3.65 1.06e+00 8.90e-01 1.19e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 9469 35.81 - 71.61: 338 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 301.68 151.16 150.52 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 31.89 148.08 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 9847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2144 0.093 - 0.186: 184 0.186 - 0.280: 27 0.280 - 0.373: 3 0.373 - 0.466: 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 5.43e+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 2.16 0.35 2.00e-01 2.50e+01 3.01e+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 4.12e-02 2.71e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.017 2.00e-02 2.50e+03 1.11e-02 2.15e+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 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 169 " 0.017 2.00e-02 2.50e+03 9.89e-03 1.95e+00 pdb=" CG TYR C 169 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 169 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 169 " 0.008 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 131 2.51 - 3.11: 11555 3.11 - 3.70: 27053 3.70 - 4.30: 41581 4.30 - 4.90: 65450 Nonbonded interactions: 145770 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 145765 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.100 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: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.580 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6615 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 0.060 16386 Z= 0.316 Angle : 0.740 10.446 22134 Z= 0.463 Chirality : 0.058 0.466 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.952 179.037 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 : 1.40 % Allowed : 15.27 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.18), residues: 1932 helix: 0.58 (0.14), residues: 1151 sheet: 0.47 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 196 TYR 0.020 0.002 TYR C 169 PHE 0.021 0.002 PHE C 227 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.73996 (22134) hydrogen bonds : bond 0.15419 ( 871) hydrogen bonds : angle 6.51766 ( 2571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 1022 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASP cc_start: 0.8196 (m-30) cc_final: 0.7894 (m-30) REVERT: A 127 LEU cc_start: 0.8792 (mt) cc_final: 0.8574 (mt) REVERT: A 172 LEU cc_start: 0.9195 (mp) cc_final: 0.8818 (mp) REVERT: A 191 GLN cc_start: 0.8607 (mm-40) cc_final: 0.7809 (mm-40) REVERT: A 259 ASN cc_start: 0.7879 (m-40) cc_final: 0.7599 (m-40) REVERT: A 322 MET cc_start: 0.7161 (mmp) cc_final: 0.6886 (mmm) REVERT: A 348 MET cc_start: 0.7365 (tmm) cc_final: 0.7125 (tmm) REVERT: A 362 ASP cc_start: 0.5889 (m-30) cc_final: 0.5362 (m-30) REVERT: A 381 LEU cc_start: 0.8959 (tp) cc_final: 0.8667 (tp) REVERT: A 407 ILE cc_start: 0.8805 (mt) cc_final: 0.8377 (mt) REVERT: A 435 SER cc_start: 0.9466 (p) cc_final: 0.9108 (p) REVERT: A 447 ASN cc_start: 0.7903 (m-40) cc_final: 0.7009 (m-40) REVERT: A 456 LYS cc_start: 0.8221 (mtpt) cc_final: 0.8016 (mtmm) REVERT: A 501 GLN cc_start: 0.8088 (tt0) cc_final: 0.7837 (tt0) REVERT: A 531 TYR cc_start: 0.7842 (m-80) cc_final: 0.7525 (m-10) REVERT: A 576 LEU cc_start: 0.8601 (mt) cc_final: 0.8352 (mt) REVERT: A 640 MET cc_start: 0.7640 (tpp) cc_final: 0.7438 (tpp) REVERT: A 644 ILE cc_start: 0.8567 (mt) cc_final: 0.8053 (mt) REVERT: B 12 LEU cc_start: 0.8440 (mt) cc_final: 0.8213 (mp) REVERT: B 109 ASN cc_start: 0.8288 (m-40) cc_final: 0.7488 (m-40) REVERT: B 129 PHE cc_start: 0.8312 (m-10) cc_final: 0.8068 (m-10) REVERT: B 147 GLN cc_start: 0.7673 (mt0) cc_final: 0.7250 (mm-40) REVERT: B 149 TYR cc_start: 0.8499 (t80) cc_final: 0.8223 (t80) REVERT: B 157 LEU cc_start: 0.8570 (tp) cc_final: 0.8364 (tp) REVERT: B 162 LYS cc_start: 0.8390 (tppt) cc_final: 0.8035 (tppt) REVERT: B 172 LEU cc_start: 0.9121 (mp) cc_final: 0.8909 (mp) REVERT: B 190 MET cc_start: 0.7935 (mtm) cc_final: 0.7664 (mtm) REVERT: B 194 LYS cc_start: 0.9063 (tttt) cc_final: 0.8861 (tttt) REVERT: B 202 ASN cc_start: 0.8476 (t0) cc_final: 0.8273 (t0) REVERT: B 203 LEU cc_start: 0.8469 (mt) cc_final: 0.8168 (mt) REVERT: B 204 SER cc_start: 0.8880 (m) cc_final: 0.8058 (t) REVERT: B 256 ARG cc_start: 0.8198 (ttp80) cc_final: 0.7814 (tpt90) REVERT: B 265 LYS cc_start: 0.8574 (mmtt) cc_final: 0.8354 (mmmt) REVERT: B 291 LEU cc_start: 0.9065 (mt) cc_final: 0.8863 (mt) REVERT: B 322 MET cc_start: 0.8200 (mmm) cc_final: 0.7005 (tpp) REVERT: B 366 LYS cc_start: 0.8482 (ptpp) cc_final: 0.8192 (ptpp) REVERT: B 376 VAL cc_start: 0.9555 (t) cc_final: 0.9243 (m) REVERT: B 379 SER cc_start: 0.8386 (t) cc_final: 0.8178 (t) REVERT: B 386 LEU cc_start: 0.9234 (mt) cc_final: 0.8984 (mt) REVERT: B 389 SER cc_start: 0.7863 (p) cc_final: 0.7556 (p) REVERT: B 413 SER cc_start: 0.8473 (m) cc_final: 0.8159 (m) REVERT: B 435 SER cc_start: 0.9382 (p) cc_final: 0.8995 (p) REVERT: B 453 ARG cc_start: 0.8825 (ttt90) cc_final: 0.8541 (ttt-90) REVERT: B 458 MET cc_start: 0.8418 (mmm) cc_final: 0.8047 (mmm) REVERT: B 496 ASN cc_start: 0.8022 (t0) cc_final: 0.7806 (t0) REVERT: B 500 ILE cc_start: 0.9019 (mt) cc_final: 0.8712 (mt) REVERT: B 550 MET cc_start: 0.8055 (mtm) cc_final: 0.7388 (mtp) REVERT: B 558 TRP cc_start: 0.8075 (m100) cc_final: 0.7758 (m100) REVERT: B 575 ARG cc_start: 0.7995 (mtm110) cc_final: 0.7785 (mtm-85) REVERT: B 585 SER cc_start: 0.8843 (p) cc_final: 0.8368 (t) REVERT: B 588 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7082 (mm-40) REVERT: B 590 SER cc_start: 0.9042 (p) cc_final: 0.8718 (t) REVERT: B 597 ILE cc_start: 0.9232 (pt) cc_final: 0.9025 (pt) REVERT: B 658 LEU cc_start: 0.7920 (mt) cc_final: 0.7534 (mt) REVERT: B 667 LEU cc_start: 0.8536 (tp) cc_final: 0.8042 (tp) REVERT: D 158 VAL cc_start: 0.6262 (t) cc_final: 0.4738 (t) REVERT: D 320 PHE cc_start: 0.6635 (m-80) cc_final: 0.6310 (m-10) outliers start: 24 outliers final: 10 residues processed: 1034 average time/residue: 0.1485 time to fit residues: 219.2627 Evaluate side-chains 672 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 662 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 287 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 304 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 43 GLN B 61 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN B 338 ASN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN B 410 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN C 214 ASN D 71 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 210 GLN D 216 GLN D 234 GLN ** D 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.130020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.088635 restraints weight = 36409.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.091929 restraints weight = 17852.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.094194 restraints weight = 10781.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.095664 restraints weight = 7488.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.096572 restraints weight = 5782.897| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3079 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3079 r_free = 0.3079 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3077 r_free = 0.3077 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3077 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 16386 Z= 0.340 Angle : 0.805 10.367 22134 Z= 0.423 Chirality : 0.049 0.314 2360 Planarity : 0.005 0.035 2818 Dihedral : 12.109 170.607 2258 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 18.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 6.29 % Allowed : 19.29 % Favored : 74.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.18), residues: 1932 helix: 1.03 (0.15), residues: 1133 sheet: -0.37 (0.39), residues: 154 loop : 0.59 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 293 TYR 0.030 0.002 TYR D 162 PHE 0.032 0.003 PHE D 168 TRP 0.019 0.003 TRP B 9 HIS 0.009 0.002 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00723 (16386) covalent geometry : angle 0.80455 (22134) hydrogen bonds : bond 0.04864 ( 871) hydrogen bonds : angle 5.27697 ( 2571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 692 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.9416 (t80) cc_final: 0.9209 (t80) REVERT: A 51 LEU cc_start: 0.9509 (tp) cc_final: 0.9295 (tp) REVERT: A 64 TYR cc_start: 0.9308 (m-10) cc_final: 0.8433 (m-10) REVERT: A 65 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8618 (mm-30) REVERT: A 143 LEU cc_start: 0.9289 (tp) cc_final: 0.9089 (tp) REVERT: A 147 GLN cc_start: 0.9037 (mt0) cc_final: 0.8135 (mm-40) REVERT: A 150 GLN cc_start: 0.9100 (tm-30) cc_final: 0.7747 (tm-30) REVERT: A 172 LEU cc_start: 0.9581 (mp) cc_final: 0.8980 (mp) REVERT: A 174 GLU cc_start: 0.8516 (mm-30) cc_final: 0.8257 (mt-10) REVERT: A 228 LYS cc_start: 0.9583 (mmmm) cc_final: 0.9088 (tppt) REVERT: A 231 ASP cc_start: 0.9093 (OUTLIER) cc_final: 0.8816 (t70) REVERT: A 251 LEU cc_start: 0.9574 (tp) cc_final: 0.9309 (tp) REVERT: A 259 ASN cc_start: 0.8883 (m-40) cc_final: 0.8641 (m-40) REVERT: A 286 ASP cc_start: 0.8734 (m-30) cc_final: 0.8281 (m-30) REVERT: A 321 GLU cc_start: 0.9049 (tp30) cc_final: 0.8749 (tp30) REVERT: A 341 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8958 (mmtm) REVERT: A 348 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7871 (tmm) REVERT: A 362 ASP cc_start: 0.8689 (m-30) cc_final: 0.7749 (m-30) REVERT: A 384 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7611 (pm20) REVERT: A 406 ASP cc_start: 0.8338 (m-30) cc_final: 0.7934 (m-30) REVERT: A 407 ILE cc_start: 0.9335 (mt) cc_final: 0.8833 (mt) REVERT: A 493 MET cc_start: 0.9360 (tmm) cc_final: 0.9061 (tmm) REVERT: A 505 GLU cc_start: 0.9130 (mt-10) cc_final: 0.8785 (mp0) REVERT: A 515 ASP cc_start: 0.9018 (m-30) cc_final: 0.8587 (m-30) REVERT: A 583 SER cc_start: 0.9406 (OUTLIER) cc_final: 0.8826 (t) REVERT: A 615 MET cc_start: 0.9103 (mmp) cc_final: 0.8682 (mmp) REVERT: A 640 MET cc_start: 0.9522 (OUTLIER) cc_final: 0.9119 (tpp) REVERT: A 647 HIS cc_start: 0.9309 (m-70) cc_final: 0.8968 (m-70) REVERT: A 668 ASN cc_start: 0.9611 (m-40) cc_final: 0.9319 (m-40) REVERT: B 15 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8682 (mt-10) REVERT: B 99 LYS cc_start: 0.9408 (mmtt) cc_final: 0.8900 (mmmm) REVERT: B 109 ASN cc_start: 0.9262 (m-40) cc_final: 0.9022 (m-40) REVERT: B 128 PHE cc_start: 0.9535 (t80) cc_final: 0.9175 (t80) REVERT: B 147 GLN cc_start: 0.9499 (mt0) cc_final: 0.9126 (mt0) REVERT: B 149 TYR cc_start: 0.9326 (t80) cc_final: 0.8250 (t80) REVERT: B 157 LEU cc_start: 0.9397 (tp) cc_final: 0.9152 (tp) REVERT: B 161 ARG cc_start: 0.8235 (ttm110) cc_final: 0.7073 (ttm110) REVERT: B 202 ASN cc_start: 0.9398 (t0) cc_final: 0.9122 (t0) REVERT: B 214 LYS cc_start: 0.8877 (ttmm) cc_final: 0.8476 (mmtm) REVERT: B 236 TYR cc_start: 0.9344 (t80) cc_final: 0.9053 (t80) REVERT: B 256 ARG cc_start: 0.9207 (OUTLIER) cc_final: 0.8804 (tpt90) REVERT: B 296 LYS cc_start: 0.9080 (mttt) cc_final: 0.8837 (mmmt) REVERT: B 315 ASP cc_start: 0.8579 (p0) cc_final: 0.8340 (p0) REVERT: B 333 LYS cc_start: 0.8778 (tttt) cc_final: 0.8259 (ttmm) REVERT: B 348 MET cc_start: 0.8979 (ptp) cc_final: 0.8496 (ptp) REVERT: B 361 GLN cc_start: 0.9084 (tt0) cc_final: 0.8749 (tp40) REVERT: B 362 ASP cc_start: 0.8976 (m-30) cc_final: 0.8275 (m-30) REVERT: B 376 VAL cc_start: 0.9663 (t) cc_final: 0.9269 (t) REVERT: B 389 SER cc_start: 0.9242 (p) cc_final: 0.8984 (p) REVERT: B 392 SER cc_start: 0.9570 (m) cc_final: 0.9068 (p) REVERT: B 447 ASN cc_start: 0.8564 (m-40) cc_final: 0.8306 (m-40) REVERT: B 459 LYS cc_start: 0.9402 (OUTLIER) cc_final: 0.8828 (mtmm) REVERT: B 483 GLU cc_start: 0.9357 (mp0) cc_final: 0.9017 (mp0) REVERT: B 493 MET cc_start: 0.9682 (tmm) cc_final: 0.9283 (tmm) REVERT: B 505 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8459 (mt-10) REVERT: B 586 TYR cc_start: 0.9195 (m-80) cc_final: 0.8623 (m-10) REVERT: B 604 ARG cc_start: 0.9147 (tpp80) cc_final: 0.8894 (tpp80) REVERT: B 615 MET cc_start: 0.9328 (mmp) cc_final: 0.8910 (mmm) REVERT: B 667 LEU cc_start: 0.9125 (tp) cc_final: 0.8856 (tp) REVERT: B 684 TYR cc_start: 0.8521 (OUTLIER) cc_final: 0.8121 (m-10) REVERT: C 96 MET cc_start: 0.6559 (mmm) cc_final: 0.6099 (mmm) REVERT: C 105 TYR cc_start: 0.7899 (m-80) cc_final: 0.7699 (m-80) REVERT: C 245 ASP cc_start: 0.8564 (t70) cc_final: 0.8194 (m-30) REVERT: C 246 LEU cc_start: 0.8281 (mp) cc_final: 0.7850 (mp) REVERT: D 72 THR cc_start: 0.8553 (p) cc_final: 0.8281 (p) REVERT: D 109 PHE cc_start: 0.8687 (m-10) cc_final: 0.8461 (m-80) REVERT: D 151 ILE cc_start: 0.9233 (mm) cc_final: 0.8878 (mp) REVERT: D 155 LYS cc_start: 0.9096 (mttt) cc_final: 0.8709 (mmtp) REVERT: D 185 MET cc_start: 0.6942 (mmm) cc_final: 0.6688 (mmm) REVERT: D 223 GLU cc_start: 0.9248 (OUTLIER) cc_final: 0.8786 (pt0) REVERT: D 224 LEU cc_start: 0.9226 (mt) cc_final: 0.8842 (mt) REVERT: D 236 TYR cc_start: 0.8838 (t80) cc_final: 0.8605 (t80) REVERT: D 268 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.8021 (mm) outliers start: 108 outliers final: 64 residues processed: 746 average time/residue: 0.1174 time to fit residues: 132.9971 Evaluate side-chains 712 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 637 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 561 LEU Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 193 SER 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 232 ASN Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 557 ASP Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 643 THR Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 652 ILE Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 268 LEU Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 164 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 182 optimal weight: 0.8980 chunk 159 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 150 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 158 optimal weight: 8.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 HIS ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.134366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.092327 restraints weight = 36237.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.095834 restraints weight = 17833.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.098071 restraints weight = 10653.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.099593 restraints weight = 7427.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.100383 restraints weight = 5739.673| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.5610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16386 Z= 0.167 Angle : 0.664 8.830 22134 Z= 0.347 Chirality : 0.044 0.225 2360 Planarity : 0.004 0.035 2818 Dihedral : 11.319 169.682 2251 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.14 % Allowed : 24.53 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.18), residues: 1932 helix: 1.10 (0.15), residues: 1133 sheet: -0.48 (0.37), residues: 158 loop : 0.51 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 669 TYR 0.046 0.002 TYR D 142 PHE 0.041 0.002 PHE D 227 TRP 0.027 0.002 TRP C 124 HIS 0.005 0.001 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00373 (16386) covalent geometry : angle 0.66384 (22134) hydrogen bonds : bond 0.04314 ( 871) hydrogen bonds : angle 5.04280 ( 2571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 676 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8670 (pt0) REVERT: A 51 LEU cc_start: 0.9443 (tp) cc_final: 0.9225 (tp) REVERT: A 107 LYS cc_start: 0.9119 (OUTLIER) cc_final: 0.8826 (mmmm) REVERT: A 150 GLN cc_start: 0.9212 (tm-30) cc_final: 0.7829 (tm-30) REVERT: A 161 ARG cc_start: 0.8493 (ttm110) cc_final: 0.7987 (ttm110) REVERT: A 172 LEU cc_start: 0.9559 (mp) cc_final: 0.9068 (mp) REVERT: A 214 LYS cc_start: 0.8976 (tppt) cc_final: 0.8630 (mmtt) REVERT: A 228 LYS cc_start: 0.9423 (mmmm) cc_final: 0.8794 (tppt) REVERT: A 251 LEU cc_start: 0.9557 (tp) cc_final: 0.9199 (tp) REVERT: A 286 ASP cc_start: 0.8669 (m-30) cc_final: 0.8194 (m-30) REVERT: A 290 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8411 (tm-30) REVERT: A 321 GLU cc_start: 0.9056 (tp30) cc_final: 0.8668 (tp30) REVERT: A 348 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.7935 (tmm) REVERT: A 362 ASP cc_start: 0.8397 (m-30) cc_final: 0.7142 (m-30) REVERT: A 384 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7666 (pm20) REVERT: A 390 GLN cc_start: 0.8955 (mt0) cc_final: 0.8682 (mt0) REVERT: A 400 GLU cc_start: 0.8332 (pp20) cc_final: 0.7801 (pp20) REVERT: A 402 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8326 (mm-30) REVERT: A 406 ASP cc_start: 0.8375 (m-30) cc_final: 0.8013 (m-30) REVERT: A 407 ILE cc_start: 0.9256 (mt) cc_final: 0.8830 (mt) REVERT: A 436 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9280 (mm) REVERT: A 493 MET cc_start: 0.9377 (tmm) cc_final: 0.9171 (tmm) REVERT: A 515 ASP cc_start: 0.9019 (m-30) cc_final: 0.8528 (m-30) REVERT: A 570 MET cc_start: 0.9358 (mtp) cc_final: 0.9033 (mtp) REVERT: A 583 SER cc_start: 0.9392 (m) cc_final: 0.9069 (t) REVERT: A 590 SER cc_start: 0.9428 (t) cc_final: 0.9018 (m) REVERT: A 615 MET cc_start: 0.9193 (mmp) cc_final: 0.8585 (mmp) REVERT: A 634 MET cc_start: 0.9223 (mmm) cc_final: 0.8997 (mmt) REVERT: A 640 MET cc_start: 0.9593 (OUTLIER) cc_final: 0.9006 (tpp) REVERT: A 647 HIS cc_start: 0.9179 (m-70) cc_final: 0.8834 (m170) REVERT: A 654 PHE cc_start: 0.8808 (t80) cc_final: 0.8347 (t80) REVERT: A 668 ASN cc_start: 0.9646 (m-40) cc_final: 0.9346 (m-40) REVERT: B 31 GLU cc_start: 0.8784 (mp0) cc_final: 0.8465 (mp0) REVERT: B 95 MET cc_start: 0.9341 (tpp) cc_final: 0.8840 (tpp) REVERT: B 119 GLU cc_start: 0.9071 (mp0) cc_final: 0.8502 (mp0) REVERT: B 128 PHE cc_start: 0.9500 (t80) cc_final: 0.9088 (t80) REVERT: B 149 TYR cc_start: 0.9373 (t80) cc_final: 0.8491 (t80) REVERT: B 157 LEU cc_start: 0.9313 (tp) cc_final: 0.9073 (tp) REVERT: B 161 ARG cc_start: 0.8138 (ttm110) cc_final: 0.7048 (ttm110) REVERT: B 164 ARG cc_start: 0.8807 (ptt-90) cc_final: 0.8467 (ttp80) REVERT: B 202 ASN cc_start: 0.9478 (t0) cc_final: 0.9141 (t0) REVERT: B 214 LYS cc_start: 0.8875 (ttmm) cc_final: 0.8402 (mmtp) REVERT: B 236 TYR cc_start: 0.9272 (t80) cc_final: 0.8899 (t80) REVERT: B 256 ARG cc_start: 0.9088 (OUTLIER) cc_final: 0.8627 (tpt90) REVERT: B 296 LYS cc_start: 0.9141 (mttt) cc_final: 0.8864 (mmmt) REVERT: B 333 LYS cc_start: 0.8759 (tttt) cc_final: 0.8325 (ttmm) REVERT: B 362 ASP cc_start: 0.8866 (m-30) cc_final: 0.8293 (m-30) REVERT: B 389 SER cc_start: 0.9151 (p) cc_final: 0.8898 (p) REVERT: B 392 SER cc_start: 0.9530 (m) cc_final: 0.9038 (p) REVERT: B 394 TYR cc_start: 0.9386 (m-80) cc_final: 0.9166 (m-80) REVERT: B 415 ASN cc_start: 0.9539 (t0) cc_final: 0.9260 (t0) REVERT: B 447 ASN cc_start: 0.8288 (m-40) cc_final: 0.8046 (m-40) REVERT: B 459 LYS cc_start: 0.9333 (OUTLIER) cc_final: 0.8772 (mtmm) REVERT: B 467 ASN cc_start: 0.9369 (t0) cc_final: 0.8578 (t0) REVERT: B 474 GLN cc_start: 0.9298 (mt0) cc_final: 0.9086 (mt0) REVERT: B 493 MET cc_start: 0.9627 (tmm) cc_final: 0.9104 (tmm) REVERT: B 586 TYR cc_start: 0.9124 (m-80) cc_final: 0.8588 (m-10) REVERT: B 604 ARG cc_start: 0.9138 (tpp80) cc_final: 0.8693 (mmm-85) REVERT: B 615 MET cc_start: 0.9192 (mmp) cc_final: 0.8767 (mmm) REVERT: B 659 LYS cc_start: 0.7988 (tptt) cc_final: 0.7624 (tptt) REVERT: B 667 LEU cc_start: 0.9224 (tp) cc_final: 0.8996 (tp) REVERT: B 669 ARG cc_start: 0.9273 (mmm-85) cc_final: 0.9069 (mtp85) REVERT: C 245 ASP cc_start: 0.8496 (t70) cc_final: 0.8143 (m-30) REVERT: D 96 MET cc_start: 0.7585 (mmt) cc_final: 0.7095 (mmt) REVERT: D 110 MET cc_start: 0.8167 (mtm) cc_final: 0.7955 (ppp) REVERT: D 149 ASP cc_start: 0.8268 (t70) cc_final: 0.7902 (t70) REVERT: D 151 ILE cc_start: 0.9181 (mm) cc_final: 0.8858 (tt) REVERT: D 233 ASN cc_start: 0.9571 (m-40) cc_final: 0.9364 (m-40) outliers start: 71 outliers final: 42 residues processed: 716 average time/residue: 0.1130 time to fit residues: 123.0897 Evaluate side-chains 683 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 634 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 ASN 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 409 CYS Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 352 GLU 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 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 262 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 4.9990 chunk 157 optimal weight: 20.0000 chunk 168 optimal weight: 4.9990 chunk 89 optimal weight: 7.9990 chunk 127 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 185 optimal weight: 1.9990 chunk 191 optimal weight: 7.9990 chunk 159 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 chunk 93 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN D 85 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN D 136 GLN D 146 GLN D 234 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.129897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.088860 restraints weight = 37066.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.092064 restraints weight = 18222.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.094258 restraints weight = 11120.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.095687 restraints weight = 7742.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.096581 restraints weight = 6009.424| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.6228 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= 0.275 Angle : 0.723 8.585 22134 Z= 0.378 Chirality : 0.047 0.242 2360 Planarity : 0.004 0.043 2818 Dihedral : 11.254 169.818 2249 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 5.77 % Allowed : 24.71 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.18), residues: 1932 helix: 0.96 (0.15), residues: 1143 sheet: -0.48 (0.38), residues: 162 loop : 0.38 (0.24), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 446 TYR 0.030 0.002 TYR D 142 PHE 0.030 0.002 PHE D 109 TRP 0.020 0.002 TRP C 124 HIS 0.006 0.002 HIS B 304 Details of bonding type rmsd covalent geometry : bond 0.00597 (16386) covalent geometry : angle 0.72311 (22134) hydrogen bonds : bond 0.04330 ( 871) hydrogen bonds : angle 5.17648 ( 2571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 650 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.9349 (m-10) cc_final: 0.9091 (m-10) REVERT: A 65 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8193 (mm-30) REVERT: A 103 ASP cc_start: 0.8822 (m-30) cc_final: 0.8526 (m-30) REVERT: A 107 LYS cc_start: 0.9195 (OUTLIER) cc_final: 0.8974 (mmmm) REVERT: A 119 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8277 (mt-10) REVERT: A 147 GLN cc_start: 0.9100 (mt0) cc_final: 0.8032 (mm-40) REVERT: A 161 ARG cc_start: 0.8637 (ttm110) cc_final: 0.8242 (ttm110) REVERT: A 172 LEU cc_start: 0.9575 (mp) cc_final: 0.9033 (mp) REVERT: A 174 GLU cc_start: 0.8471 (mm-30) cc_final: 0.8254 (mt-10) REVERT: A 191 GLN cc_start: 0.8742 (mm110) cc_final: 0.8476 (mm-40) REVERT: A 214 LYS cc_start: 0.9038 (tppt) cc_final: 0.8735 (mmtt) REVERT: A 251 LEU cc_start: 0.9588 (tp) cc_final: 0.9344 (tp) REVERT: A 286 ASP cc_start: 0.8713 (m-30) cc_final: 0.8162 (m-30) REVERT: A 290 GLU cc_start: 0.8715 (tm-30) cc_final: 0.8471 (tm-30) REVERT: A 321 GLU cc_start: 0.9103 (tp30) cc_final: 0.8801 (tp30) REVERT: A 348 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8173 (tmm) REVERT: A 361 GLN cc_start: 0.9229 (tp40) cc_final: 0.8838 (tp-100) REVERT: A 362 ASP cc_start: 0.8421 (m-30) cc_final: 0.7160 (m-30) REVERT: A 379 SER cc_start: 0.9443 (t) cc_final: 0.9220 (t) REVERT: A 384 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.7708 (pm20) REVERT: A 390 GLN cc_start: 0.8962 (mt0) cc_final: 0.8599 (mt0) REVERT: A 400 GLU cc_start: 0.8319 (pp20) cc_final: 0.7771 (pp20) REVERT: A 402 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8369 (mm-30) REVERT: A 406 ASP cc_start: 0.8348 (m-30) cc_final: 0.7930 (m-30) REVERT: A 407 ILE cc_start: 0.9292 (mt) cc_final: 0.8831 (mt) REVERT: A 479 TYR cc_start: 0.9155 (t80) cc_final: 0.8844 (t80) REVERT: A 493 MET cc_start: 0.9326 (tmm) cc_final: 0.9020 (tmm) REVERT: A 515 ASP cc_start: 0.9000 (m-30) cc_final: 0.8639 (m-30) REVERT: A 570 MET cc_start: 0.9306 (mtp) cc_final: 0.8838 (mtp) REVERT: A 583 SER cc_start: 0.9471 (OUTLIER) cc_final: 0.9206 (t) REVERT: A 590 SER cc_start: 0.9263 (t) cc_final: 0.9006 (m) REVERT: A 615 MET cc_start: 0.9243 (mmp) cc_final: 0.8573 (mmp) REVERT: A 640 MET cc_start: 0.9679 (OUTLIER) cc_final: 0.9064 (tpp) REVERT: A 654 PHE cc_start: 0.8877 (t80) cc_final: 0.8421 (t80) REVERT: A 668 ASN cc_start: 0.9662 (m-40) cc_final: 0.9415 (m-40) REVERT: B 31 GLU cc_start: 0.8833 (mp0) cc_final: 0.8531 (mt-10) REVERT: B 54 LYS cc_start: 0.9702 (ttmt) cc_final: 0.9376 (ttmt) REVERT: B 65 GLU cc_start: 0.8612 (mm-30) cc_final: 0.7862 (mp0) REVERT: B 95 MET cc_start: 0.9351 (tpp) cc_final: 0.8901 (tpp) REVERT: B 106 LEU cc_start: 0.9277 (tt) cc_final: 0.8794 (tt) REVERT: B 112 LYS cc_start: 0.9621 (mmmt) cc_final: 0.9318 (mmmt) REVERT: B 119 GLU cc_start: 0.9094 (mp0) cc_final: 0.8486 (mp0) REVERT: B 128 PHE cc_start: 0.9554 (t80) cc_final: 0.9228 (t80) REVERT: B 149 TYR cc_start: 0.9471 (t80) cc_final: 0.8259 (t80) REVERT: B 157 LEU cc_start: 0.9347 (tp) cc_final: 0.9084 (tp) REVERT: B 161 ARG cc_start: 0.8263 (ttm110) cc_final: 0.7019 (ttm110) REVERT: B 164 ARG cc_start: 0.8727 (ptt-90) cc_final: 0.8268 (ttp80) REVERT: B 202 ASN cc_start: 0.9430 (t0) cc_final: 0.9150 (t0) REVERT: B 214 LYS cc_start: 0.8897 (ttmm) cc_final: 0.8385 (mmtp) REVERT: B 256 ARG cc_start: 0.9150 (OUTLIER) cc_final: 0.8601 (tpt90) REVERT: B 267 ILE cc_start: 0.9388 (OUTLIER) cc_final: 0.9173 (pp) REVERT: B 296 LYS cc_start: 0.9260 (mttt) cc_final: 0.8977 (mmmt) REVERT: B 333 LYS cc_start: 0.8804 (tttt) cc_final: 0.8354 (ttmm) REVERT: B 389 SER cc_start: 0.9117 (p) cc_final: 0.8911 (p) REVERT: B 392 SER cc_start: 0.9508 (m) cc_final: 0.9095 (p) REVERT: B 394 TYR cc_start: 0.9442 (m-80) cc_final: 0.9102 (m-80) REVERT: B 415 ASN cc_start: 0.9414 (t0) cc_final: 0.9193 (t0) REVERT: B 447 ASN cc_start: 0.8465 (m-40) cc_final: 0.8240 (m-40) REVERT: B 459 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.8797 (mtmm) REVERT: B 467 ASN cc_start: 0.9307 (t0) cc_final: 0.8405 (t0) REVERT: B 474 GLN cc_start: 0.9271 (mt0) cc_final: 0.9058 (mt0) REVERT: B 483 GLU cc_start: 0.9357 (mp0) cc_final: 0.9151 (mp0) REVERT: B 493 MET cc_start: 0.9637 (tmm) cc_final: 0.9077 (tmm) REVERT: B 505 GLU cc_start: 0.8907 (mt-10) cc_final: 0.8370 (mt-10) REVERT: B 548 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8472 (mm-30) REVERT: B 604 ARG cc_start: 0.9156 (tpp80) cc_final: 0.8712 (mmm-85) REVERT: B 615 MET cc_start: 0.9178 (mmp) cc_final: 0.8851 (mmp) REVERT: B 632 MET cc_start: 0.8767 (mtm) cc_final: 0.8151 (ttm) REVERT: B 640 MET cc_start: 0.9517 (tpp) cc_final: 0.9170 (tpp) REVERT: B 645 GLN cc_start: 0.9604 (tp40) cc_final: 0.9247 (tp-100) REVERT: B 659 LYS cc_start: 0.8070 (tptt) cc_final: 0.7750 (tptt) REVERT: C 74 MET cc_start: 0.4937 (mpp) cc_final: 0.4664 (mpp) REVERT: D 96 MET cc_start: 0.7732 (mmt) cc_final: 0.7318 (mmt) REVERT: D 98 ASN cc_start: 0.8892 (m-40) cc_final: 0.8631 (m-40) REVERT: D 110 MET cc_start: 0.8370 (mtm) cc_final: 0.8033 (ppp) REVERT: D 148 ASP cc_start: 0.7663 (t0) cc_final: 0.7387 (t0) REVERT: D 149 ASP cc_start: 0.8399 (t70) cc_final: 0.8149 (m-30) REVERT: D 151 ILE cc_start: 0.9232 (mm) cc_final: 0.9021 (tt) outliers start: 99 outliers final: 66 residues processed: 690 average time/residue: 0.1068 time to fit residues: 112.8293 Evaluate side-chains 687 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 613 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 408 SER 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 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 120 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 129 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 168 optimal weight: 8.9990 chunk 157 optimal weight: 9.9990 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 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN A 646 GLN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.134730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.094249 restraints weight = 36191.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.097743 restraints weight = 17290.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.100020 restraints weight = 10327.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.101519 restraints weight = 7187.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.102379 restraints weight = 5540.460| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.6559 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= 0.145 Angle : 0.684 13.360 22134 Z= 0.355 Chirality : 0.046 0.242 2360 Planarity : 0.004 0.041 2818 Dihedral : 10.776 160.157 2246 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.43 % Allowed : 28.32 % Favored : 67.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.19), residues: 1932 helix: 0.94 (0.15), residues: 1140 sheet: -0.42 (0.39), residues: 158 loop : 0.28 (0.24), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 485 TYR 0.045 0.002 TYR D 142 PHE 0.055 0.002 PHE D 109 TRP 0.030 0.002 TRP C 124 HIS 0.005 0.001 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00327 (16386) covalent geometry : angle 0.68433 (22134) hydrogen bonds : bond 0.04232 ( 871) hydrogen bonds : angle 5.11628 ( 2571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 662 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.9312 (m-10) cc_final: 0.8704 (m-10) REVERT: A 107 LYS cc_start: 0.9186 (OUTLIER) cc_final: 0.8932 (mmmm) REVERT: A 144 MET cc_start: 0.8952 (mtm) cc_final: 0.8546 (mtt) REVERT: A 150 GLN cc_start: 0.9059 (tm-30) cc_final: 0.8604 (tm-30) REVERT: A 191 GLN cc_start: 0.8566 (mm110) cc_final: 0.8361 (mm-40) REVERT: A 214 LYS cc_start: 0.8856 (tppt) cc_final: 0.8615 (mmtt) REVERT: A 252 ASN cc_start: 0.9091 (t0) cc_final: 0.8679 (t0) REVERT: A 290 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8446 (tm-30) REVERT: A 321 GLU cc_start: 0.9076 (tp30) cc_final: 0.8792 (tp30) REVERT: A 348 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.8135 (tmm) REVERT: A 384 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.7607 (pm20) REVERT: A 390 GLN cc_start: 0.9032 (mt0) cc_final: 0.8786 (mt0) REVERT: A 400 GLU cc_start: 0.8298 (pp20) cc_final: 0.7742 (pp20) REVERT: A 402 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8342 (mm-30) REVERT: A 406 ASP cc_start: 0.8215 (m-30) cc_final: 0.7914 (m-30) REVERT: A 458 MET cc_start: 0.8757 (mmp) cc_final: 0.8084 (mmp) REVERT: A 515 ASP cc_start: 0.9014 (m-30) cc_final: 0.8567 (m-30) REVERT: A 526 GLU cc_start: 0.8449 (mp0) cc_final: 0.8238 (mp0) REVERT: A 570 MET cc_start: 0.9387 (mtp) cc_final: 0.9121 (mtp) REVERT: A 576 LEU cc_start: 0.9116 (mt) cc_final: 0.8905 (mt) REVERT: A 583 SER cc_start: 0.9448 (m) cc_final: 0.8848 (t) REVERT: A 588 GLN cc_start: 0.9152 (mm-40) cc_final: 0.8592 (mm-40) REVERT: A 590 SER cc_start: 0.9183 (t) cc_final: 0.8658 (p) REVERT: A 595 MET cc_start: 0.8946 (mmp) cc_final: 0.8623 (mmm) REVERT: A 615 MET cc_start: 0.9301 (mmp) cc_final: 0.8536 (mmp) REVERT: A 640 MET cc_start: 0.9654 (OUTLIER) cc_final: 0.9022 (tpp) REVERT: A 647 HIS cc_start: 0.9000 (m90) cc_final: 0.8768 (m170) REVERT: A 668 ASN cc_start: 0.9685 (m-40) cc_final: 0.9419 (m-40) REVERT: B 31 GLU cc_start: 0.8820 (mp0) cc_final: 0.8512 (mt-10) REVERT: B 65 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8342 (mm-30) REVERT: B 95 MET cc_start: 0.9335 (tpp) cc_final: 0.8797 (tpp) REVERT: B 112 LYS cc_start: 0.9556 (mmmt) cc_final: 0.9222 (mmmt) REVERT: B 119 GLU cc_start: 0.9046 (mp0) cc_final: 0.8444 (mp0) REVERT: B 128 PHE cc_start: 0.9522 (t80) cc_final: 0.9200 (t80) REVERT: B 149 TYR cc_start: 0.9426 (t80) cc_final: 0.8389 (t80) REVERT: B 157 LEU cc_start: 0.9306 (tp) cc_final: 0.9021 (tp) REVERT: B 161 ARG cc_start: 0.8064 (ttm110) cc_final: 0.7115 (ttm110) REVERT: B 202 ASN cc_start: 0.9383 (t0) cc_final: 0.8999 (t0) REVERT: B 214 LYS cc_start: 0.8883 (ttmm) cc_final: 0.8296 (mmtp) REVERT: B 221 LYS cc_start: 0.9317 (mmtp) cc_final: 0.9068 (mttp) REVERT: B 263 ASP cc_start: 0.9193 (m-30) cc_final: 0.8827 (m-30) REVERT: B 296 LYS cc_start: 0.9324 (mttt) cc_final: 0.8994 (mmmt) REVERT: B 322 MET cc_start: 0.9623 (mmm) cc_final: 0.9383 (tpp) REVERT: B 333 LYS cc_start: 0.8722 (tttt) cc_final: 0.8261 (ttmm) REVERT: B 389 SER cc_start: 0.9087 (p) cc_final: 0.8593 (p) REVERT: B 392 SER cc_start: 0.9461 (m) cc_final: 0.8961 (p) REVERT: B 394 TYR cc_start: 0.9412 (m-80) cc_final: 0.9120 (m-80) REVERT: B 402 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7672 (tm-30) REVERT: B 415 ASN cc_start: 0.9309 (t0) cc_final: 0.9058 (t0) REVERT: B 459 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8723 (mtmm) REVERT: B 466 MET cc_start: 0.9111 (ptp) cc_final: 0.8892 (ptp) REVERT: B 467 ASN cc_start: 0.9114 (t0) cc_final: 0.8255 (t0) REVERT: B 474 GLN cc_start: 0.9224 (mt0) cc_final: 0.8994 (mt0) REVERT: B 483 GLU cc_start: 0.9340 (mp0) cc_final: 0.9138 (mp0) REVERT: B 493 MET cc_start: 0.9612 (tmm) cc_final: 0.9053 (tmm) REVERT: B 548 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8305 (mm-30) REVERT: B 550 MET cc_start: 0.8265 (mtm) cc_final: 0.8030 (mtt) REVERT: B 586 TYR cc_start: 0.9082 (m-80) cc_final: 0.8759 (m-10) REVERT: B 604 ARG cc_start: 0.9082 (tpp80) cc_final: 0.8737 (mmm-85) REVERT: B 615 MET cc_start: 0.9331 (mmp) cc_final: 0.9032 (mmm) REVERT: B 632 MET cc_start: 0.8660 (mtm) cc_final: 0.8414 (ttm) REVERT: B 640 MET cc_start: 0.9549 (tpp) cc_final: 0.9193 (tpp) REVERT: B 645 GLN cc_start: 0.9569 (tp40) cc_final: 0.9111 (tp-100) REVERT: B 659 LYS cc_start: 0.7996 (tptt) cc_final: 0.7624 (tptt) REVERT: C 96 MET cc_start: 0.7034 (mmm) cc_final: 0.6314 (mmm) REVERT: C 277 PHE cc_start: 0.7891 (m-80) cc_final: 0.7511 (m-80) REVERT: D 55 TYR cc_start: 0.7439 (t80) cc_final: 0.7217 (t80) REVERT: D 96 MET cc_start: 0.7497 (mmt) cc_final: 0.7234 (mmt) REVERT: D 100 VAL cc_start: 0.8049 (OUTLIER) cc_final: 0.7715 (p) REVERT: D 148 ASP cc_start: 0.7606 (t0) cc_final: 0.7281 (t0) outliers start: 76 outliers final: 50 residues processed: 689 average time/residue: 0.1232 time to fit residues: 128.6825 Evaluate side-chains 676 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 620 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 ASN 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 405 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 408 SER 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 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 262 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 172 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 136 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 418 ASN B 447 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN D 270 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.135033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.094278 restraints weight = 36621.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.097721 restraints weight = 17700.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.099967 restraints weight = 10572.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.101423 restraints weight = 7353.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.102373 restraints weight = 5685.538| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.6862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16386 Z= 0.181 Angle : 0.718 10.868 22134 Z= 0.372 Chirality : 0.047 0.225 2360 Planarity : 0.004 0.039 2818 Dihedral : 10.587 160.152 2246 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 5.19 % Allowed : 28.90 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.19), residues: 1932 helix: 0.93 (0.15), residues: 1127 sheet: -0.40 (0.40), residues: 162 loop : 0.18 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 261 TYR 0.039 0.002 TYR D 142 PHE 0.039 0.002 PHE D 109 TRP 0.029 0.002 TRP C 124 HIS 0.008 0.001 HIS A 469 Details of bonding type rmsd covalent geometry : bond 0.00409 (16386) covalent geometry : angle 0.71815 (22134) hydrogen bonds : bond 0.04197 ( 871) hydrogen bonds : angle 5.19188 ( 2571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 626 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8902 (mmmm) REVERT: A 121 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.8899 (tpt90) REVERT: A 150 GLN cc_start: 0.9053 (tm-30) cc_final: 0.8555 (tm-30) REVERT: A 172 LEU cc_start: 0.9417 (mp) cc_final: 0.8953 (mp) REVERT: A 174 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7998 (mt-10) REVERT: A 184 ARG cc_start: 0.9284 (mmm-85) cc_final: 0.8869 (tpt90) REVERT: A 214 LYS cc_start: 0.8888 (tppt) cc_final: 0.8662 (mmtt) REVERT: A 231 ASP cc_start: 0.8947 (t70) cc_final: 0.8643 (t0) REVERT: A 232 ASN cc_start: 0.9387 (m-40) cc_final: 0.9104 (m-40) REVERT: A 252 ASN cc_start: 0.9090 (t0) cc_final: 0.8763 (t0) REVERT: A 286 ASP cc_start: 0.8727 (m-30) cc_final: 0.8354 (m-30) REVERT: A 290 GLU cc_start: 0.8696 (tm-30) cc_final: 0.8458 (tm-30) REVERT: A 321 GLU cc_start: 0.9115 (tp30) cc_final: 0.8843 (tp30) REVERT: A 341 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8752 (mmtm) REVERT: A 348 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8242 (tmm) REVERT: A 355 TYR cc_start: 0.8508 (m-10) cc_final: 0.8307 (m-10) REVERT: A 361 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.8760 (tp40) REVERT: A 362 ASP cc_start: 0.8554 (m-30) cc_final: 0.7887 (m-30) REVERT: A 379 SER cc_start: 0.9430 (t) cc_final: 0.9204 (t) REVERT: A 384 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7748 (pm20) REVERT: A 389 SER cc_start: 0.9625 (OUTLIER) cc_final: 0.8878 (p) REVERT: A 390 GLN cc_start: 0.8983 (mt0) cc_final: 0.8608 (mt0) REVERT: A 400 GLU cc_start: 0.8361 (pp20) cc_final: 0.7831 (pp20) REVERT: A 402 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8390 (mm-30) REVERT: A 406 ASP cc_start: 0.8228 (m-30) cc_final: 0.7867 (m-30) REVERT: A 479 TYR cc_start: 0.9118 (t80) cc_final: 0.8850 (t80) REVERT: A 515 ASP cc_start: 0.8981 (m-30) cc_final: 0.8598 (m-30) REVERT: A 583 SER cc_start: 0.9485 (OUTLIER) cc_final: 0.8959 (t) REVERT: A 588 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8717 (mm-40) REVERT: A 615 MET cc_start: 0.9311 (mmp) cc_final: 0.8768 (mmp) REVERT: A 640 MET cc_start: 0.9643 (OUTLIER) cc_final: 0.9030 (tpp) REVERT: A 646 GLN cc_start: 0.9335 (pt0) cc_final: 0.9091 (pt0) REVERT: A 668 ASN cc_start: 0.9679 (m-40) cc_final: 0.9421 (m-40) REVERT: B 31 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8508 (mt-10) REVERT: B 65 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8287 (mm-30) REVERT: B 95 MET cc_start: 0.9300 (tpp) cc_final: 0.8762 (tpp) REVERT: B 98 PHE cc_start: 0.9717 (t80) cc_final: 0.9512 (t80) REVERT: B 106 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8851 (tt) REVERT: B 112 LYS cc_start: 0.9556 (mmmt) cc_final: 0.9200 (mmmt) REVERT: B 119 GLU cc_start: 0.9049 (mp0) cc_final: 0.8478 (mp0) REVERT: B 128 PHE cc_start: 0.9539 (t80) cc_final: 0.9211 (t80) REVERT: B 149 TYR cc_start: 0.9387 (t80) cc_final: 0.8428 (t80) REVERT: B 157 LEU cc_start: 0.9319 (tp) cc_final: 0.9048 (tp) REVERT: B 161 ARG cc_start: 0.8086 (ttm110) cc_final: 0.7127 (ttm110) REVERT: B 214 LYS cc_start: 0.8815 (ttmm) cc_final: 0.8209 (mmtp) REVERT: B 256 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.8602 (tpt90) REVERT: B 263 ASP cc_start: 0.9182 (m-30) cc_final: 0.8815 (m-30) REVERT: B 267 ILE cc_start: 0.9283 (OUTLIER) cc_final: 0.9044 (pp) REVERT: B 296 LYS cc_start: 0.9323 (mttt) cc_final: 0.9037 (mmmt) REVERT: B 333 LYS cc_start: 0.8831 (tttt) cc_final: 0.8362 (ttmm) REVERT: B 386 LEU cc_start: 0.9257 (mt) cc_final: 0.8966 (mt) REVERT: B 389 SER cc_start: 0.8959 (p) cc_final: 0.8693 (p) REVERT: B 392 SER cc_start: 0.9364 (m) cc_final: 0.8893 (p) REVERT: B 394 TYR cc_start: 0.9396 (m-80) cc_final: 0.9076 (m-80) REVERT: B 415 ASN cc_start: 0.9312 (t0) cc_final: 0.8992 (t0) REVERT: B 459 LYS cc_start: 0.9315 (OUTLIER) cc_final: 0.8735 (mtmm) REVERT: B 466 MET cc_start: 0.9099 (ptp) cc_final: 0.8857 (ptp) REVERT: B 467 ASN cc_start: 0.9045 (t0) cc_final: 0.8296 (t0) REVERT: B 474 GLN cc_start: 0.9226 (mt0) cc_final: 0.8997 (mt0) REVERT: B 493 MET cc_start: 0.9627 (tmm) cc_final: 0.9043 (tmm) REVERT: B 494 MET cc_start: 0.9300 (ttm) cc_final: 0.8928 (mmt) REVERT: B 550 MET cc_start: 0.8298 (mtm) cc_final: 0.8043 (mtt) REVERT: B 586 TYR cc_start: 0.9069 (m-80) cc_final: 0.8800 (m-10) REVERT: B 604 ARG cc_start: 0.9065 (tpp80) cc_final: 0.8773 (mmm-85) REVERT: B 615 MET cc_start: 0.9419 (mmp) cc_final: 0.9112 (mmm) REVERT: B 640 MET cc_start: 0.9514 (tpp) cc_final: 0.8863 (tpp) REVERT: B 645 GLN cc_start: 0.9543 (tp40) cc_final: 0.9082 (tp-100) REVERT: B 659 LYS cc_start: 0.8002 (tptt) cc_final: 0.7666 (tptt) REVERT: B 665 ARG cc_start: 0.9267 (OUTLIER) cc_final: 0.9048 (tmm-80) REVERT: C 96 MET cc_start: 0.7052 (mmm) cc_final: 0.6493 (mmm) REVERT: C 174 TYR cc_start: 0.4523 (OUTLIER) cc_final: 0.4093 (t80) REVERT: C 249 GLN cc_start: 0.5940 (pm20) cc_final: 0.4817 (pp30) REVERT: D 46 TYR cc_start: 0.9495 (m-80) cc_final: 0.8970 (m-10) REVERT: D 100 VAL cc_start: 0.8039 (OUTLIER) cc_final: 0.7551 (p) REVERT: D 155 LYS cc_start: 0.9063 (mttt) cc_final: 0.8610 (mmmt) outliers start: 89 outliers final: 61 residues processed: 664 average time/residue: 0.1238 time to fit residues: 124.1689 Evaluate side-chains 696 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 618 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 408 SER 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 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 665 ARG Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 6.9990 chunk 51 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 105 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 186 optimal weight: 9.9990 chunk 140 optimal weight: 9.9990 chunk 115 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 156 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.134550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.094055 restraints weight = 36347.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.097455 restraints weight = 17805.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.099675 restraints weight = 10696.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.101114 restraints weight = 7487.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.102015 restraints weight = 5800.552| |-----------------------------------------------------------------------------| r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.7079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16386 Z= 0.189 Angle : 0.748 12.971 22134 Z= 0.385 Chirality : 0.048 0.265 2360 Planarity : 0.004 0.062 2818 Dihedral : 10.354 157.691 2246 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 5.42 % Allowed : 29.55 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.19), residues: 1932 helix: 0.82 (0.15), residues: 1139 sheet: -0.37 (0.41), residues: 164 loop : 0.15 (0.24), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 235 TYR 0.044 0.002 TYR D 142 PHE 0.042 0.002 PHE D 168 TRP 0.021 0.001 TRP C 124 HIS 0.006 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00430 (16386) covalent geometry : angle 0.74809 (22134) hydrogen bonds : bond 0.04151 ( 871) hydrogen bonds : angle 5.22379 ( 2571) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 628 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.9220 (OUTLIER) cc_final: 0.8930 (mmmm) REVERT: A 119 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8079 (mt-10) REVERT: A 121 ARG cc_start: 0.9235 (OUTLIER) cc_final: 0.8768 (tpt170) REVERT: A 144 MET cc_start: 0.8958 (mtm) cc_final: 0.8448 (mtt) REVERT: A 161 ARG cc_start: 0.8432 (ttm110) cc_final: 0.7740 (ttm110) REVERT: A 174 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7942 (mm-30) REVERT: A 184 ARG cc_start: 0.9262 (mmm-85) cc_final: 0.8910 (tpt90) REVERT: A 214 LYS cc_start: 0.8919 (tppt) cc_final: 0.8669 (mmtt) REVERT: A 252 ASN cc_start: 0.9098 (t0) cc_final: 0.8808 (t0) REVERT: A 286 ASP cc_start: 0.8692 (m-30) cc_final: 0.8352 (m-30) REVERT: A 290 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8423 (tm-30) REVERT: A 321 GLU cc_start: 0.9116 (tp30) cc_final: 0.8847 (tp30) REVERT: A 341 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8739 (mmtm) REVERT: A 348 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8223 (tmm) REVERT: A 355 TYR cc_start: 0.8471 (m-10) cc_final: 0.8252 (m-10) REVERT: A 361 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8824 (tp40) REVERT: A 362 ASP cc_start: 0.8525 (m-30) cc_final: 0.7756 (m-30) REVERT: A 379 SER cc_start: 0.9402 (t) cc_final: 0.9148 (t) REVERT: A 384 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.7804 (pm20) REVERT: A 389 SER cc_start: 0.9604 (OUTLIER) cc_final: 0.9138 (p) REVERT: A 390 GLN cc_start: 0.8985 (mt0) cc_final: 0.8711 (mt0) REVERT: A 400 GLU cc_start: 0.8376 (pp20) cc_final: 0.7928 (pp20) REVERT: A 402 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8438 (mm-30) REVERT: A 406 ASP cc_start: 0.8228 (m-30) cc_final: 0.7877 (m-30) REVERT: A 479 TYR cc_start: 0.9152 (t80) cc_final: 0.8878 (t80) REVERT: A 515 ASP cc_start: 0.8979 (m-30) cc_final: 0.8602 (m-30) REVERT: A 570 MET cc_start: 0.9303 (mtp) cc_final: 0.8932 (mtp) REVERT: A 590 SER cc_start: 0.9194 (t) cc_final: 0.8759 (p) REVERT: A 615 MET cc_start: 0.9299 (mmp) cc_final: 0.8757 (mmp) REVERT: A 640 MET cc_start: 0.9630 (OUTLIER) cc_final: 0.8909 (tpp) REVERT: A 646 GLN cc_start: 0.9357 (pt0) cc_final: 0.9127 (pt0) REVERT: A 668 ASN cc_start: 0.9687 (m-40) cc_final: 0.9405 (m-40) REVERT: B 31 GLU cc_start: 0.8870 (OUTLIER) cc_final: 0.8533 (mt-10) REVERT: B 95 MET cc_start: 0.9316 (tpp) cc_final: 0.8782 (tpp) REVERT: B 98 PHE cc_start: 0.9715 (t80) cc_final: 0.9397 (t80) REVERT: B 106 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8947 (tt) REVERT: B 112 LYS cc_start: 0.9578 (mmmt) cc_final: 0.9267 (mmmt) REVERT: B 116 GLU cc_start: 0.8493 (mt-10) cc_final: 0.7843 (mt-10) REVERT: B 119 GLU cc_start: 0.9055 (mp0) cc_final: 0.8405 (mp0) REVERT: B 128 PHE cc_start: 0.9553 (t80) cc_final: 0.9250 (t80) REVERT: B 149 TYR cc_start: 0.9379 (t80) cc_final: 0.8305 (t80) REVERT: B 161 ARG cc_start: 0.8106 (ttm110) cc_final: 0.7613 (mmm-85) REVERT: B 214 LYS cc_start: 0.8812 (ttmm) cc_final: 0.8459 (tppt) REVERT: B 256 ARG cc_start: 0.9212 (OUTLIER) cc_final: 0.8589 (tpt90) REVERT: B 263 ASP cc_start: 0.9173 (m-30) cc_final: 0.8790 (m-30) REVERT: B 267 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.9031 (pp) REVERT: B 296 LYS cc_start: 0.9335 (mttt) cc_final: 0.9068 (mmmt) REVERT: B 333 LYS cc_start: 0.8844 (tttt) cc_final: 0.8387 (ttmm) REVERT: B 362 ASP cc_start: 0.8734 (OUTLIER) cc_final: 0.8480 (m-30) REVERT: B 386 LEU cc_start: 0.9198 (mt) cc_final: 0.8924 (mt) REVERT: B 389 SER cc_start: 0.8855 (p) cc_final: 0.8587 (p) REVERT: B 392 SER cc_start: 0.9388 (m) cc_final: 0.8941 (p) REVERT: B 394 TYR cc_start: 0.9407 (m-80) cc_final: 0.9098 (m-80) REVERT: B 396 ASP cc_start: 0.8213 (p0) cc_final: 0.8004 (p0) REVERT: B 415 ASN cc_start: 0.9254 (t0) cc_final: 0.8869 (t0) REVERT: B 447 ASN cc_start: 0.9051 (m-40) cc_final: 0.8628 (t0) REVERT: B 459 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8657 (mtmm) REVERT: B 466 MET cc_start: 0.9131 (ptp) cc_final: 0.8830 (ptp) REVERT: B 467 ASN cc_start: 0.9116 (t0) cc_final: 0.8299 (t0) REVERT: B 471 TYR cc_start: 0.9326 (t80) cc_final: 0.8638 (t80) REVERT: B 474 GLN cc_start: 0.9230 (mt0) cc_final: 0.8987 (mt0) REVERT: B 493 MET cc_start: 0.9620 (tmm) cc_final: 0.9044 (tmm) REVERT: B 550 MET cc_start: 0.8316 (mtm) cc_final: 0.8086 (mtm) REVERT: B 586 TYR cc_start: 0.9086 (m-80) cc_final: 0.8775 (m-10) REVERT: B 604 ARG cc_start: 0.9036 (tpp80) cc_final: 0.8759 (mmm-85) REVERT: B 610 LYS cc_start: 0.9132 (ptpt) cc_final: 0.8685 (ptmm) REVERT: B 640 MET cc_start: 0.9488 (tpp) cc_final: 0.9190 (tpp) REVERT: B 645 GLN cc_start: 0.9547 (tp40) cc_final: 0.9106 (tp-100) REVERT: B 659 LYS cc_start: 0.7832 (tptt) cc_final: 0.7459 (tptt) REVERT: C 174 TYR cc_start: 0.4660 (OUTLIER) cc_final: 0.4244 (t80) REVERT: C 249 GLN cc_start: 0.5988 (pm20) cc_final: 0.5697 (pm20) REVERT: C 261 ARG cc_start: 0.8050 (mpp80) cc_final: 0.7725 (mpp80) REVERT: D 46 TYR cc_start: 0.9487 (m-80) cc_final: 0.8965 (m-10) REVERT: D 80 HIS cc_start: 0.8186 (m90) cc_final: 0.7333 (t-90) REVERT: D 93 MET cc_start: 0.7514 (ppp) cc_final: 0.6811 (pmm) REVERT: D 96 MET cc_start: 0.7416 (mmt) cc_final: 0.7169 (mmt) REVERT: D 98 ASN cc_start: 0.8397 (m-40) cc_final: 0.8049 (m-40) REVERT: D 155 LYS cc_start: 0.9231 (mttt) cc_final: 0.8826 (mmtt) REVERT: D 196 ARG cc_start: 0.8819 (ptp-170) cc_final: 0.8436 (ptp-170) outliers start: 93 outliers final: 64 residues processed: 664 average time/residue: 0.1090 time to fit residues: 110.3222 Evaluate side-chains 685 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 606 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 408 SER 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 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 0.0770 chunk 19 optimal weight: 2.9990 chunk 134 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 158 optimal weight: 7.9990 chunk 97 optimal weight: 3.9990 chunk 151 optimal weight: 20.0000 chunk 81 optimal weight: 0.8980 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.136461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.095907 restraints weight = 36555.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.099410 restraints weight = 17620.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.101607 restraints weight = 10648.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103058 restraints weight = 7457.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.103924 restraints weight = 5805.974| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.7304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16386 Z= 0.183 Angle : 0.760 12.104 22134 Z= 0.390 Chirality : 0.049 0.282 2360 Planarity : 0.004 0.048 2818 Dihedral : 10.104 153.646 2246 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.24 % Allowed : 29.95 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.19), residues: 1932 helix: 0.69 (0.15), residues: 1142 sheet: -0.36 (0.41), residues: 164 loop : 0.16 (0.24), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 235 TYR 0.042 0.002 TYR D 142 PHE 0.064 0.002 PHE D 109 TRP 0.022 0.002 TRP C 124 HIS 0.005 0.001 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00422 (16386) covalent geometry : angle 0.76037 (22134) hydrogen bonds : bond 0.04255 ( 871) hydrogen bonds : angle 5.27681 ( 2571) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 625 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8932 (mmmm) REVERT: A 119 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8046 (mt-10) REVERT: A 121 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8871 (tpt170) REVERT: A 144 MET cc_start: 0.8928 (mtm) cc_final: 0.8462 (mtt) REVERT: A 172 LEU cc_start: 0.9441 (mp) cc_final: 0.9051 (mp) REVERT: A 174 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7997 (mm-30) REVERT: A 184 ARG cc_start: 0.9246 (mmm-85) cc_final: 0.8898 (tpt90) REVERT: A 214 LYS cc_start: 0.8951 (tppt) cc_final: 0.8678 (mmtt) REVERT: A 231 ASP cc_start: 0.9024 (t0) cc_final: 0.8728 (t0) REVERT: A 252 ASN cc_start: 0.9066 (t0) cc_final: 0.8803 (t0) REVERT: A 286 ASP cc_start: 0.8679 (m-30) cc_final: 0.8344 (m-30) REVERT: A 290 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8416 (tm-30) REVERT: A 321 GLU cc_start: 0.9092 (tp30) cc_final: 0.8664 (tp30) REVERT: A 341 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8723 (mmtm) REVERT: A 348 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8227 (tmm) REVERT: A 355 TYR cc_start: 0.8433 (m-10) cc_final: 0.8201 (m-10) REVERT: A 361 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8791 (tp40) REVERT: A 362 ASP cc_start: 0.8539 (m-30) cc_final: 0.7704 (m-30) REVERT: A 379 SER cc_start: 0.9370 (t) cc_final: 0.9141 (t) REVERT: A 384 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.7817 (pm20) REVERT: A 389 SER cc_start: 0.9601 (OUTLIER) cc_final: 0.9220 (p) REVERT: A 390 GLN cc_start: 0.9000 (mt0) cc_final: 0.8725 (mt0) REVERT: A 399 GLU cc_start: 0.8657 (tp30) cc_final: 0.8237 (tp30) REVERT: A 400 GLU cc_start: 0.8423 (pp20) cc_final: 0.7861 (pp20) REVERT: A 402 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8375 (mm-30) REVERT: A 406 ASP cc_start: 0.8271 (m-30) cc_final: 0.7964 (m-30) REVERT: A 458 MET cc_start: 0.8701 (mmp) cc_final: 0.8003 (mmt) REVERT: A 459 LYS cc_start: 0.8988 (mttp) cc_final: 0.8576 (mtmm) REVERT: A 479 TYR cc_start: 0.9149 (t80) cc_final: 0.8892 (t80) REVERT: A 515 ASP cc_start: 0.8981 (m-30) cc_final: 0.8637 (m-30) REVERT: A 570 MET cc_start: 0.9302 (mtp) cc_final: 0.8943 (mtp) REVERT: A 595 MET cc_start: 0.8677 (mmm) cc_final: 0.8336 (mmm) REVERT: A 615 MET cc_start: 0.9302 (mmp) cc_final: 0.8771 (mmp) REVERT: A 636 LYS cc_start: 0.9625 (mmtp) cc_final: 0.9302 (mmmt) REVERT: A 640 MET cc_start: 0.9629 (OUTLIER) cc_final: 0.8891 (tpp) REVERT: A 668 ASN cc_start: 0.9675 (m-40) cc_final: 0.9381 (m-40) REVERT: B 31 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.8609 (mt-10) REVERT: B 95 MET cc_start: 0.9329 (tpp) cc_final: 0.8793 (tpp) REVERT: B 98 PHE cc_start: 0.9714 (t80) cc_final: 0.9335 (t80) REVERT: B 106 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8953 (tt) REVERT: B 112 LYS cc_start: 0.9550 (mmmt) cc_final: 0.9229 (mmmt) REVERT: B 119 GLU cc_start: 0.9016 (mp0) cc_final: 0.8401 (mp0) REVERT: B 128 PHE cc_start: 0.9563 (t80) cc_final: 0.9253 (t80) REVERT: B 149 TYR cc_start: 0.9388 (t80) cc_final: 0.8314 (t80) REVERT: B 164 ARG cc_start: 0.9134 (ttp80) cc_final: 0.8676 (tmm-80) REVERT: B 166 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8294 (mm-30) REVERT: B 214 LYS cc_start: 0.8804 (ttmm) cc_final: 0.8434 (tppt) REVERT: B 221 LYS cc_start: 0.9297 (mmtp) cc_final: 0.8954 (mmmm) REVERT: B 256 ARG cc_start: 0.9215 (OUTLIER) cc_final: 0.8602 (tpt90) REVERT: B 263 ASP cc_start: 0.9141 (m-30) cc_final: 0.8752 (m-30) REVERT: B 267 ILE cc_start: 0.9273 (OUTLIER) cc_final: 0.9025 (pp) REVERT: B 296 LYS cc_start: 0.9346 (mttt) cc_final: 0.9066 (mmmt) REVERT: B 333 LYS cc_start: 0.8847 (tttt) cc_final: 0.8406 (ttmm) REVERT: B 357 TYR cc_start: 0.8757 (m-10) cc_final: 0.8016 (m-10) REVERT: B 359 MET cc_start: 0.9023 (ttt) cc_final: 0.8684 (tmm) REVERT: B 362 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8487 (m-30) REVERT: B 389 SER cc_start: 0.8841 (p) cc_final: 0.8552 (p) REVERT: B 392 SER cc_start: 0.9384 (m) cc_final: 0.8973 (p) REVERT: B 394 TYR cc_start: 0.9390 (m-80) cc_final: 0.9124 (m-80) REVERT: B 415 ASN cc_start: 0.9245 (t0) cc_final: 0.8887 (t0) REVERT: B 447 ASN cc_start: 0.9059 (m-40) cc_final: 0.8595 (t0) REVERT: B 459 LYS cc_start: 0.9212 (OUTLIER) cc_final: 0.8630 (mtmm) REVERT: B 467 ASN cc_start: 0.9088 (t0) cc_final: 0.8318 (t0) REVERT: B 471 TYR cc_start: 0.9305 (t80) cc_final: 0.8642 (t80) REVERT: B 474 GLN cc_start: 0.9223 (mt0) cc_final: 0.8994 (mt0) REVERT: B 493 MET cc_start: 0.9631 (tmm) cc_final: 0.9065 (tmm) REVERT: B 494 MET cc_start: 0.9283 (ttm) cc_final: 0.9000 (mmt) REVERT: B 585 SER cc_start: 0.9401 (p) cc_final: 0.8871 (t) REVERT: B 586 TYR cc_start: 0.9090 (m-80) cc_final: 0.8687 (m-10) REVERT: B 602 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.6918 (pt0) REVERT: B 610 LYS cc_start: 0.9109 (ptpt) cc_final: 0.8667 (ptmm) REVERT: B 640 MET cc_start: 0.9480 (tpp) cc_final: 0.9165 (tpp) REVERT: B 659 LYS cc_start: 0.7755 (tptt) cc_final: 0.7496 (tptt) REVERT: C 44 TRP cc_start: 0.7384 (t-100) cc_final: 0.6263 (t-100) REVERT: C 174 TYR cc_start: 0.4753 (OUTLIER) cc_final: 0.4318 (t80) REVERT: C 249 GLN cc_start: 0.6024 (pm20) cc_final: 0.5736 (pm20) REVERT: D 46 TYR cc_start: 0.9454 (m-80) cc_final: 0.8794 (m-10) REVERT: D 80 HIS cc_start: 0.8260 (m90) cc_final: 0.7429 (t-90) REVERT: D 93 MET cc_start: 0.7540 (ppp) cc_final: 0.7232 (ppp) REVERT: D 96 MET cc_start: 0.7278 (mmt) cc_final: 0.7038 (mmt) REVERT: D 98 ASN cc_start: 0.8262 (m-40) cc_final: 0.8016 (m110) REVERT: D 157 MET cc_start: 0.9614 (ptp) cc_final: 0.9137 (ttp) REVERT: D 242 TYR cc_start: 0.8716 (OUTLIER) cc_final: 0.8365 (m-80) REVERT: D 257 LYS cc_start: 0.9062 (mmtp) cc_final: 0.8686 (mmmt) outliers start: 90 outliers final: 63 residues processed: 660 average time/residue: 0.1155 time to fit residues: 115.9588 Evaluate side-chains 691 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 611 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 408 SER 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 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 3.9990 chunk 133 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.137339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.097115 restraints weight = 36282.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.100599 restraints weight = 17476.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.102841 restraints weight = 10426.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.104377 restraints weight = 7277.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.105349 restraints weight = 5600.756| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3232 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3232 r_free = 0.3232 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3232 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.7518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16386 Z= 0.161 Angle : 0.784 12.316 22134 Z= 0.401 Chirality : 0.049 0.300 2360 Planarity : 0.004 0.057 2818 Dihedral : 9.917 146.243 2246 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.66 % Allowed : 31.41 % Favored : 63.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.19), residues: 1932 helix: 0.64 (0.15), residues: 1155 sheet: -0.35 (0.41), residues: 158 loop : 0.13 (0.24), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 261 TYR 0.050 0.002 TYR D 142 PHE 0.044 0.002 PHE D 109 TRP 0.035 0.002 TRP C 124 HIS 0.005 0.001 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00371 (16386) covalent geometry : angle 0.78433 (22134) hydrogen bonds : bond 0.04224 ( 871) hydrogen bonds : angle 5.27888 ( 2571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 707 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 627 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 LYS cc_start: 0.9271 (OUTLIER) cc_final: 0.8944 (mmmm) REVERT: A 119 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8043 (mt-10) REVERT: A 121 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8632 (tpt170) REVERT: A 147 GLN cc_start: 0.9197 (mt0) cc_final: 0.8905 (mm-40) REVERT: A 161 ARG cc_start: 0.8276 (ttm110) cc_final: 0.7487 (ttm110) REVERT: A 172 LEU cc_start: 0.9403 (mp) cc_final: 0.9037 (mp) REVERT: A 184 ARG cc_start: 0.9194 (mmm-85) cc_final: 0.8817 (tpt90) REVERT: A 214 LYS cc_start: 0.8951 (tppt) cc_final: 0.8651 (mmtt) REVERT: A 221 LYS cc_start: 0.9424 (mmtp) cc_final: 0.8700 (mptt) REVERT: A 252 ASN cc_start: 0.9018 (t0) cc_final: 0.8683 (t0) REVERT: A 286 ASP cc_start: 0.8663 (m-30) cc_final: 0.8371 (m-30) REVERT: A 290 GLU cc_start: 0.8725 (tm-30) cc_final: 0.8407 (tm-30) REVERT: A 321 GLU cc_start: 0.9104 (tp30) cc_final: 0.8688 (tp30) REVERT: A 341 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8701 (mmtm) REVERT: A 361 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8747 (tp40) REVERT: A 362 ASP cc_start: 0.8543 (m-30) cc_final: 0.7743 (m-30) REVERT: A 384 GLU cc_start: 0.8643 (OUTLIER) cc_final: 0.7760 (pm20) REVERT: A 389 SER cc_start: 0.9579 (OUTLIER) cc_final: 0.8850 (p) REVERT: A 390 GLN cc_start: 0.9012 (mt0) cc_final: 0.8658 (mt0) REVERT: A 406 ASP cc_start: 0.8238 (m-30) cc_final: 0.7915 (m-30) REVERT: A 420 MET cc_start: 0.9281 (mmm) cc_final: 0.8800 (mmm) REVERT: A 479 TYR cc_start: 0.9096 (t80) cc_final: 0.8850 (t80) REVERT: A 515 ASP cc_start: 0.8987 (m-30) cc_final: 0.8658 (m-30) REVERT: A 570 MET cc_start: 0.9338 (mtp) cc_final: 0.8948 (mtp) REVERT: A 576 LEU cc_start: 0.9132 (mt) cc_final: 0.8759 (mt) REVERT: A 615 MET cc_start: 0.9322 (mmp) cc_final: 0.8758 (mmp) REVERT: A 636 LYS cc_start: 0.9582 (mmtp) cc_final: 0.9247 (mmmt) REVERT: A 640 MET cc_start: 0.9638 (OUTLIER) cc_final: 0.8811 (tpp) REVERT: A 668 ASN cc_start: 0.9674 (m-40) cc_final: 0.9381 (m-40) REVERT: B 31 GLU cc_start: 0.8850 (OUTLIER) cc_final: 0.8568 (mt-10) REVERT: B 65 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8377 (mp0) REVERT: B 95 MET cc_start: 0.9286 (tpp) cc_final: 0.8101 (tpp) REVERT: B 98 PHE cc_start: 0.9710 (t80) cc_final: 0.9348 (t80) REVERT: B 99 LYS cc_start: 0.9307 (mmtt) cc_final: 0.8487 (tppp) REVERT: B 112 LYS cc_start: 0.9506 (mmmt) cc_final: 0.9185 (mmmt) REVERT: B 119 GLU cc_start: 0.8925 (mp0) cc_final: 0.8463 (mp0) REVERT: B 128 PHE cc_start: 0.9530 (t80) cc_final: 0.9237 (t80) REVERT: B 147 GLN cc_start: 0.9530 (mt0) cc_final: 0.9200 (mm-40) REVERT: B 149 TYR cc_start: 0.9362 (t80) cc_final: 0.8360 (t80) REVERT: B 164 ARG cc_start: 0.9145 (ttp80) cc_final: 0.8863 (ttp80) REVERT: B 181 ASP cc_start: 0.8791 (m-30) cc_final: 0.8526 (m-30) REVERT: B 221 LYS cc_start: 0.9309 (mmtp) cc_final: 0.8955 (mmmm) REVERT: B 256 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.8739 (tpt90) REVERT: B 257 ASP cc_start: 0.9017 (m-30) cc_final: 0.8728 (m-30) REVERT: B 263 ASP cc_start: 0.9122 (m-30) cc_final: 0.8730 (m-30) REVERT: B 267 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.9011 (pp) REVERT: B 296 LYS cc_start: 0.9346 (mttt) cc_final: 0.9054 (mmmt) REVERT: B 322 MET cc_start: 0.9570 (tpp) cc_final: 0.9198 (tpp) REVERT: B 333 LYS cc_start: 0.8853 (tttt) cc_final: 0.8394 (ttmm) REVERT: B 357 TYR cc_start: 0.8683 (m-10) cc_final: 0.8155 (m-10) REVERT: B 359 MET cc_start: 0.9029 (ttt) cc_final: 0.8775 (tmm) REVERT: B 362 ASP cc_start: 0.8759 (OUTLIER) cc_final: 0.8489 (m-30) REVERT: B 366 LYS cc_start: 0.9528 (ptpt) cc_final: 0.9317 (ptmm) REVERT: B 389 SER cc_start: 0.8856 (p) cc_final: 0.8567 (p) REVERT: B 392 SER cc_start: 0.9380 (m) cc_final: 0.8946 (p) REVERT: B 394 TYR cc_start: 0.9337 (m-80) cc_final: 0.9103 (m-80) REVERT: B 415 ASN cc_start: 0.9207 (t0) cc_final: 0.8882 (t0) REVERT: B 447 ASN cc_start: 0.9009 (m-40) cc_final: 0.8383 (t0) REVERT: B 459 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8522 (mtmm) REVERT: B 466 MET cc_start: 0.9109 (ptp) cc_final: 0.8767 (ptp) REVERT: B 467 ASN cc_start: 0.9011 (t0) cc_final: 0.8317 (t0) REVERT: B 471 TYR cc_start: 0.9262 (t80) cc_final: 0.8662 (t80) REVERT: B 474 GLN cc_start: 0.9199 (mt0) cc_final: 0.8970 (mt0) REVERT: B 483 GLU cc_start: 0.9313 (mp0) cc_final: 0.8568 (mm-30) REVERT: B 493 MET cc_start: 0.9630 (tmm) cc_final: 0.9064 (tmm) REVERT: B 494 MET cc_start: 0.9205 (ttm) cc_final: 0.8926 (mmt) REVERT: B 548 GLU cc_start: 0.8941 (mm-30) cc_final: 0.8356 (mm-30) REVERT: B 586 TYR cc_start: 0.9053 (m-80) cc_final: 0.8585 (m-10) REVERT: B 610 LYS cc_start: 0.9085 (ptpt) cc_final: 0.8649 (ptmm) REVERT: B 618 LEU cc_start: 0.9522 (tp) cc_final: 0.9151 (mp) REVERT: B 632 MET cc_start: 0.8382 (mtm) cc_final: 0.7975 (mpp) REVERT: B 640 MET cc_start: 0.9481 (tpp) cc_final: 0.9227 (tpp) REVERT: B 659 LYS cc_start: 0.7515 (tptt) cc_final: 0.7192 (tptt) REVERT: C 44 TRP cc_start: 0.7262 (t-100) cc_final: 0.6440 (t-100) REVERT: C 174 TYR cc_start: 0.4755 (OUTLIER) cc_final: 0.4450 (t80) REVERT: C 249 GLN cc_start: 0.6004 (pm20) cc_final: 0.4683 (pp30) REVERT: D 46 TYR cc_start: 0.9425 (m-80) cc_final: 0.8887 (m-10) REVERT: D 80 HIS cc_start: 0.8288 (m90) cc_final: 0.7397 (t-90) REVERT: D 93 MET cc_start: 0.7405 (ppp) cc_final: 0.7144 (ppp) REVERT: D 96 MET cc_start: 0.7324 (mmt) cc_final: 0.7117 (mmt) REVERT: D 157 MET cc_start: 0.9641 (ptp) cc_final: 0.9193 (ttp) REVERT: D 242 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.8394 (m-80) REVERT: D 257 LYS cc_start: 0.9106 (mmtp) cc_final: 0.8811 (mmmt) outliers start: 80 outliers final: 58 residues processed: 654 average time/residue: 0.1114 time to fit residues: 110.1206 Evaluate side-chains 676 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 603 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 362 ASP 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 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 512 GLU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 5.9990 chunk 62 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 189 optimal weight: 0.9980 chunk 181 optimal weight: 9.9990 chunk 165 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 0.1980 chunk 132 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.138292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.097925 restraints weight = 36355.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.101399 restraints weight = 17818.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.103641 restraints weight = 10875.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.105113 restraints weight = 7655.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.105971 restraints weight = 5936.152| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.7715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16386 Z= 0.172 Angle : 0.818 11.628 22134 Z= 0.417 Chirality : 0.050 0.288 2360 Planarity : 0.004 0.060 2818 Dihedral : 9.734 138.030 2245 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.55 % Allowed : 32.58 % Favored : 62.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.19), residues: 1932 helix: 0.68 (0.15), residues: 1141 sheet: -0.37 (0.41), residues: 158 loop : -0.01 (0.24), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 235 TYR 0.049 0.002 TYR D 142 PHE 0.039 0.002 PHE D 109 TRP 0.032 0.002 TRP C 124 HIS 0.012 0.001 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00398 (16386) covalent geometry : angle 0.81784 (22134) hydrogen bonds : bond 0.04242 ( 871) hydrogen bonds : angle 5.31213 ( 2571) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 613 time to evaluate : 0.590 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 95 MET cc_start: 0.9478 (tpp) cc_final: 0.9246 (tpp) REVERT: A 107 LYS cc_start: 0.9237 (OUTLIER) cc_final: 0.9028 (mmmm) REVERT: A 119 GLU cc_start: 0.8471 (mt-10) cc_final: 0.8061 (mt-10) REVERT: A 161 ARG cc_start: 0.8277 (ttm110) cc_final: 0.8031 (ttm-80) REVERT: A 174 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8061 (mt-10) REVERT: A 184 ARG cc_start: 0.9208 (mmm-85) cc_final: 0.8837 (tpt90) REVERT: A 221 LYS cc_start: 0.9466 (mmtp) cc_final: 0.8785 (mptt) REVERT: A 232 ASN cc_start: 0.9195 (m-40) cc_final: 0.8634 (m110) REVERT: A 252 ASN cc_start: 0.9004 (t0) cc_final: 0.8798 (t0) REVERT: A 286 ASP cc_start: 0.8637 (m-30) cc_final: 0.8334 (m-30) REVERT: A 290 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8427 (tm-30) REVERT: A 321 GLU cc_start: 0.9095 (tp30) cc_final: 0.8794 (tp30) REVERT: A 341 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8718 (mmtm) REVERT: A 361 GLN cc_start: 0.9087 (OUTLIER) cc_final: 0.8741 (tp40) REVERT: A 362 ASP cc_start: 0.8473 (m-30) cc_final: 0.7596 (m-30) REVERT: A 384 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7758 (pm20) REVERT: A 389 SER cc_start: 0.9439 (OUTLIER) cc_final: 0.8896 (p) REVERT: A 390 GLN cc_start: 0.9019 (mt0) cc_final: 0.8629 (mt0) REVERT: A 420 MET cc_start: 0.9234 (mmm) cc_final: 0.8910 (mmm) REVERT: A 441 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8494 (mm-30) REVERT: A 459 LYS cc_start: 0.8934 (mttp) cc_final: 0.8603 (ttmm) REVERT: A 479 TYR cc_start: 0.9127 (t80) cc_final: 0.8854 (t80) REVERT: A 515 ASP cc_start: 0.8967 (m-30) cc_final: 0.8659 (m-30) REVERT: A 570 MET cc_start: 0.9314 (mtp) cc_final: 0.8883 (mtp) REVERT: A 576 LEU cc_start: 0.9175 (mt) cc_final: 0.8793 (mt) REVERT: A 615 MET cc_start: 0.9323 (mmp) cc_final: 0.8782 (mmp) REVERT: A 636 LYS cc_start: 0.9585 (mmtp) cc_final: 0.9252 (mmmt) REVERT: A 640 MET cc_start: 0.9606 (OUTLIER) cc_final: 0.8834 (tpp) REVERT: A 668 ASN cc_start: 0.9677 (m-40) cc_final: 0.9387 (m-40) REVERT: B 31 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8502 (mt-10) REVERT: B 65 GLU cc_start: 0.8814 (OUTLIER) cc_final: 0.7963 (mp0) REVERT: B 95 MET cc_start: 0.9285 (tpp) cc_final: 0.8095 (tpp) REVERT: B 98 PHE cc_start: 0.9718 (t80) cc_final: 0.9353 (t80) REVERT: B 99 LYS cc_start: 0.9312 (mmtt) cc_final: 0.8479 (tppp) REVERT: B 112 LYS cc_start: 0.9491 (mmmt) cc_final: 0.9168 (mmmt) REVERT: B 119 GLU cc_start: 0.8884 (mp0) cc_final: 0.8279 (mp0) REVERT: B 128 PHE cc_start: 0.9532 (t80) cc_final: 0.9247 (t80) REVERT: B 147 GLN cc_start: 0.9513 (mt0) cc_final: 0.9196 (mm-40) REVERT: B 149 TYR cc_start: 0.9369 (t80) cc_final: 0.8316 (t80) REVERT: B 164 ARG cc_start: 0.9120 (ttp80) cc_final: 0.8895 (ttp80) REVERT: B 214 LYS cc_start: 0.9039 (mtpp) cc_final: 0.8718 (mmtt) REVERT: B 221 LYS cc_start: 0.9271 (mmtp) cc_final: 0.8901 (mmmm) REVERT: B 256 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.8711 (tpt90) REVERT: B 257 ASP cc_start: 0.9032 (m-30) cc_final: 0.8719 (m-30) REVERT: B 263 ASP cc_start: 0.9117 (m-30) cc_final: 0.8721 (m-30) REVERT: B 267 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.9016 (pp) REVERT: B 290 GLU cc_start: 0.8879 (tm-30) cc_final: 0.8493 (pp20) REVERT: B 296 LYS cc_start: 0.9353 (mttt) cc_final: 0.9053 (mmmt) REVERT: B 322 MET cc_start: 0.9545 (tpp) cc_final: 0.9239 (tpp) REVERT: B 333 LYS cc_start: 0.8902 (tttt) cc_final: 0.8492 (ttmm) REVERT: B 357 TYR cc_start: 0.8797 (m-10) cc_final: 0.8245 (m-10) REVERT: B 359 MET cc_start: 0.9080 (ttt) cc_final: 0.8814 (tmm) REVERT: B 362 ASP cc_start: 0.8721 (OUTLIER) cc_final: 0.8481 (m-30) REVERT: B 366 LYS cc_start: 0.9536 (ptpt) cc_final: 0.9335 (ptmm) REVERT: B 389 SER cc_start: 0.8758 (p) cc_final: 0.8470 (p) REVERT: B 392 SER cc_start: 0.9420 (m) cc_final: 0.8991 (p) REVERT: B 394 TYR cc_start: 0.9437 (m-80) cc_final: 0.9163 (m-80) REVERT: B 415 ASN cc_start: 0.9218 (t0) cc_final: 0.8865 (t0) REVERT: B 443 THR cc_start: 0.9286 (OUTLIER) cc_final: 0.9082 (m) REVERT: B 459 LYS cc_start: 0.9106 (OUTLIER) cc_final: 0.8579 (mtmm) REVERT: B 467 ASN cc_start: 0.9018 (t0) cc_final: 0.8394 (t0) REVERT: B 471 TYR cc_start: 0.9251 (t80) cc_final: 0.8616 (t80) REVERT: B 474 GLN cc_start: 0.9208 (mt0) cc_final: 0.8983 (mt0) REVERT: B 493 MET cc_start: 0.9616 (tmm) cc_final: 0.9054 (tmm) REVERT: B 494 MET cc_start: 0.9245 (ttm) cc_final: 0.8977 (mmt) REVERT: B 548 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8331 (mm-30) REVERT: B 585 SER cc_start: 0.9346 (p) cc_final: 0.8809 (t) REVERT: B 586 TYR cc_start: 0.9072 (m-80) cc_final: 0.8503 (m-10) REVERT: B 610 LYS cc_start: 0.9104 (ptpt) cc_final: 0.8685 (ptmm) REVERT: B 618 LEU cc_start: 0.9544 (tp) cc_final: 0.9194 (mp) REVERT: B 631 ASP cc_start: 0.9281 (m-30) cc_final: 0.9065 (p0) REVERT: B 640 MET cc_start: 0.9436 (tpp) cc_final: 0.9194 (tpp) REVERT: C 44 TRP cc_start: 0.7314 (t-100) cc_final: 0.6655 (t-100) REVERT: C 174 TYR cc_start: 0.4836 (OUTLIER) cc_final: 0.4344 (t80) REVERT: C 249 GLN cc_start: 0.6019 (pm20) cc_final: 0.4762 (pp30) REVERT: D 46 TYR cc_start: 0.9402 (m-80) cc_final: 0.8895 (m-10) REVERT: D 80 HIS cc_start: 0.8349 (m90) cc_final: 0.7551 (t-90) REVERT: D 100 VAL cc_start: 0.7938 (OUTLIER) cc_final: 0.7529 (p) REVERT: D 157 MET cc_start: 0.9650 (ptp) cc_final: 0.9235 (ttp) REVERT: D 242 TYR cc_start: 0.8748 (OUTLIER) cc_final: 0.8399 (m-80) REVERT: D 257 LYS cc_start: 0.9198 (mmtp) cc_final: 0.8920 (mmmt) REVERT: D 281 ASP cc_start: 0.7335 (p0) cc_final: 0.6627 (t70) outliers start: 78 outliers final: 55 residues processed: 642 average time/residue: 0.1104 time to fit residues: 107.8066 Evaluate side-chains 671 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 600 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 65 GLU Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 362 ASP 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 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 77 VAL Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 148 optimal weight: 30.0000 chunk 125 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.140548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.099881 restraints weight = 36359.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.103436 restraints weight = 17646.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.105719 restraints weight = 10488.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107245 restraints weight = 7279.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.108144 restraints weight = 5610.447| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3265 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3265 r_free = 0.3265 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3265 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.7918 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= 0.160 Angle : 0.835 12.679 22134 Z= 0.425 Chirality : 0.050 0.306 2360 Planarity : 0.004 0.062 2818 Dihedral : 9.474 136.806 2245 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.02 % Allowed : 34.38 % Favored : 61.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.18), residues: 1932 helix: 0.62 (0.15), residues: 1151 sheet: -0.00 (0.44), residues: 142 loop : -0.18 (0.23), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 665 TYR 0.053 0.002 TYR D 142 PHE 0.046 0.002 PHE A 491 TRP 0.029 0.001 TRP C 124 HIS 0.011 0.001 HIS D 101 Details of bonding type rmsd covalent geometry : bond 0.00367 (16386) covalent geometry : angle 0.83535 (22134) hydrogen bonds : bond 0.04250 ( 871) hydrogen bonds : angle 5.32295 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3336.26 seconds wall clock time: 58 minutes 32.36 seconds (3512.36 seconds total)