Starting phenix.real_space_refine on Fri Jul 3 19:49:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bza_45061/07_2026/9bza_45061_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bza_45061/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bza_45061/07_2026/9bza_45061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bza_45061/07_2026/9bza_45061.map" model { file = "/net/cci-nas-00/data/ceres_data/9bza_45061/07_2026/9bza_45061_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bza_45061/07_2026/9bza_45061_neut.cif" } 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-dev-6108/lib/python3.11/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, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 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: 3.33, per 1000 atoms: 0.21 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: 1.32 Conformation dependent library (CDL) restraints added in 588.4 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: 0.39 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: 2.56 Time building geometry restraints manager: 1.69 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=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" O3B TTP A 803 " pdb=" PG TTP A 803 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.81e+01 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=" O3A TTP A 803 " pdb=" PB TTP A 803 " ideal model delta sigma weight residual 1.675 1.606 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21522 2.09 - 4.18: 531 4.18 - 6.27: 62 6.27 - 8.36: 10 8.36 - 10.45: 9 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 - 25.06: 9088 25.06 - 50.12: 656 50.12 - 75.17: 126 75.17 - 100.23: 26 100.23 - 125.29: 2 Dihedral angle restraints: 9898 sinusoidal: 4140 harmonic: 5758 Sorted by residual: dihedral pdb=" O4' GDP A 802 " pdb=" C1' GDP A 802 " pdb=" N9 GDP A 802 " pdb=" C8 GDP A 802 " ideal model delta sinusoidal sigma weight residual 27.02 -98.27 125.29 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" O4' GDP B 804 " pdb=" C1' GDP B 804 " pdb=" N9 GDP B 804 " pdb=" C8 GDP B 804 " ideal model delta sinusoidal sigma weight residual 27.02 -95.56 122.58 1 2.00e+01 2.50e-03 3.69e+01 dihedral pdb=" C VAL C 125 " pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual -122.00 -134.29 12.29 0 2.50e+00 1.60e-01 2.42e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2139 0.093 - 0.186: 189 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 3.060 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 3.060 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 3.060 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.400 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 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 0.139 16386 Z= 0.335 Angle : 0.788 10.446 22134 Z= 0.471 Chirality : 0.058 0.466 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.680 125.289 6202 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/Z covalent geometry : bond 0.00597 / 0.33 (16386) covalent geometry : angle 0.78758 / 0.47 (22134) hydrogen bonds : bond 0.15419 / 9.51 ( 871) hydrogen bonds : angle 6.51766 / 4.65 ( 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 : 0.573 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: 0.6885 (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: 0.5363 (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: 0.7526 (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: 0.7004 (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: 0.8711 (mt) REVERT: B 550 MET cc_start: 0.8055 (mtm) cc_final: 0.7387 (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: 0.8367 (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: 0.8717 (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: 0.4739 (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: 0.1327 time to fit residues: 196.9355 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 : 0.580 ------------------------------------------------------------------------------- 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: 4.9990 chunk 149 optimal weight: 8.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 19 GLN B 43 GLN B 61 ASN B 158 ASN ** 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 C 28 GLN C 101 HIS C 214 ASN D 71 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 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 = 0.3647 r_free = 0.3647 target = 0.130079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.088729 restraints weight = 36618.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.092010 restraints weight = 17820.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.094299 restraints weight = 10687.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.095771 restraints weight = 7381.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.096721 restraints weight = 5683.004| |-----------------------------------------------------------------------------| r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 11 (24 function evaluations) r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 16386 Z= 0.323 Angle : 0.780 11.255 22134 Z= 0.412 Chirality : 0.048 0.300 2360 Planarity : 0.005 0.033 2818 Dihedral : 10.222 131.538 2306 Min Nonbonded Distance : 1.705 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 5.89 % Allowed : 19.93 % Favored : 74.18 % 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: 1.18 (0.18), residues: 1932 helix: 1.16 (0.15), residues: 1134 sheet: -0.33 (0.39), residues: 154 loop : 0.64 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 669 TYR 0.026 0.002 TYR D 162 PHE 0.033 0.003 PHE D 168 TRP 0.017 0.002 TRP B 9 HIS 0.008 0.002 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.32 (16386) covalent geometry : angle 0.77974 / 0.41 (22134) hydrogen bonds : bond 0.04941 / 3.10 ( 871) hydrogen bonds : angle 5.25521 / 3.75 ( 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 785 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 684 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.9406 (t80) cc_final: 0.9116 (t80) REVERT: A 51 LEU cc_start: 0.9481 (tp) cc_final: 0.9253 (tp) REVERT: A 64 TYR cc_start: 0.9279 (m-10) cc_final: 0.8471 (m-80) REVERT: A 65 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8549 (mm-30) REVERT: A 127 LEU cc_start: 0.9641 (mt) cc_final: 0.9408 (mt) REVERT: A 143 LEU cc_start: 0.9284 (tp) cc_final: 0.9070 (tp) REVERT: A 147 GLN cc_start: 0.9056 (mt0) cc_final: 0.8167 (mm-40) REVERT: A 172 LEU cc_start: 0.9584 (mp) cc_final: 0.8984 (mp) REVERT: A 202 ASN cc_start: 0.9582 (t0) cc_final: 0.9365 (t0) REVERT: A 231 ASP cc_start: 0.9121 (OUTLIER) cc_final: 0.8860 (t70) REVERT: A 251 LEU cc_start: 0.9556 (tp) cc_final: 0.9254 (tp) REVERT: A 259 ASN cc_start: 0.8852 (m-40) cc_final: 0.8618 (m-40) REVERT: A 263 ASP cc_start: 0.8663 (m-30) cc_final: 0.8419 (m-30) REVERT: A 321 GLU cc_start: 0.9031 (tp30) cc_final: 0.8730 (tp30) REVERT: A 322 MET cc_start: 0.8817 (mmp) cc_final: 0.8613 (mmm) REVERT: A 348 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.7859 (tmm) REVERT: A 400 GLU cc_start: 0.8342 (pp20) cc_final: 0.7793 (pp20) REVERT: A 402 GLU cc_start: 0.8595 (mm-30) cc_final: 0.7846 (mm-30) REVERT: A 406 ASP cc_start: 0.8353 (m-30) cc_final: 0.7946 (m-30) REVERT: A 407 ILE cc_start: 0.9338 (mt) cc_final: 0.8836 (mt) REVERT: A 493 MET cc_start: 0.9386 (tmm) cc_final: 0.9100 (tmm) REVERT: A 505 GLU cc_start: 0.9127 (mt-10) cc_final: 0.8782 (mp0) REVERT: A 515 ASP cc_start: 0.9002 (m-30) cc_final: 0.8541 (m-30) REVERT: A 598 MET cc_start: 0.8831 (mtp) cc_final: 0.8443 (mtp) REVERT: A 615 MET cc_start: 0.9083 (mmp) cc_final: 0.8671 (mmp) REVERT: A 640 MET cc_start: 0.9502 (OUTLIER) cc_final: 0.9101 (tpp) REVERT: A 647 HIS cc_start: 0.9325 (m-70) cc_final: 0.9030 (m-70) REVERT: A 659 LYS cc_start: 0.9148 (mttt) cc_final: 0.8844 (mmtp) REVERT: A 668 ASN cc_start: 0.9630 (m-40) cc_final: 0.9309 (m-40) REVERT: A 686 ARG cc_start: 0.8554 (mtp85) cc_final: 0.8033 (mtp-110) REVERT: B 12 LEU cc_start: 0.9571 (mt) cc_final: 0.9265 (mp) REVERT: B 15 GLU cc_start: 0.9040 (mt-10) cc_final: 0.8801 (mt-10) REVERT: B 27 ASP cc_start: 0.9381 (OUTLIER) cc_final: 0.9094 (p0) REVERT: B 31 GLU cc_start: 0.8931 (mp0) cc_final: 0.8557 (mp0) REVERT: B 65 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8106 (mm-30) REVERT: B 99 LYS cc_start: 0.9397 (mmtt) cc_final: 0.8893 (mmmm) REVERT: B 109 ASN cc_start: 0.9234 (m-40) cc_final: 0.9024 (m-40) REVERT: B 128 PHE cc_start: 0.9547 (t80) cc_final: 0.9202 (t80) REVERT: B 147 GLN cc_start: 0.9442 (mt0) cc_final: 0.9189 (mt0) REVERT: B 149 TYR cc_start: 0.9303 (t80) cc_final: 0.8313 (t80) REVERT: B 157 LEU cc_start: 0.9358 (tp) cc_final: 0.9102 (tp) REVERT: B 161 ARG cc_start: 0.8166 (ttm110) cc_final: 0.6983 (ttm110) REVERT: B 175 VAL cc_start: 0.9616 (t) cc_final: 0.9263 (p) REVERT: B 202 ASN cc_start: 0.9436 (t0) cc_final: 0.9147 (t0) REVERT: B 214 LYS cc_start: 0.8831 (ttmm) cc_final: 0.8472 (mmtt) REVERT: B 236 TYR cc_start: 0.9298 (t80) cc_final: 0.9067 (t80) REVERT: B 296 LYS cc_start: 0.9006 (mttt) cc_final: 0.8803 (mmmt) REVERT: B 333 LYS cc_start: 0.8730 (tttt) cc_final: 0.8314 (ttmm) REVERT: B 348 MET cc_start: 0.8965 (ptp) cc_final: 0.8401 (ptp) REVERT: B 361 GLN cc_start: 0.9082 (tt0) cc_final: 0.8768 (tt0) REVERT: B 362 ASP cc_start: 0.8957 (m-30) cc_final: 0.8248 (m-30) REVERT: B 376 VAL cc_start: 0.9662 (t) cc_final: 0.9308 (t) REVERT: B 389 SER cc_start: 0.9219 (p) cc_final: 0.8947 (p) REVERT: B 392 SER cc_start: 0.9565 (m) cc_final: 0.9326 (p) REVERT: B 415 ASN cc_start: 0.9580 (t0) cc_final: 0.9341 (t0) REVERT: B 447 ASN cc_start: 0.8529 (m-40) cc_final: 0.8283 (m-40) REVERT: B 459 LYS cc_start: 0.9412 (OUTLIER) cc_final: 0.8790 (mtmm) REVERT: B 467 ASN cc_start: 0.9597 (t0) cc_final: 0.9188 (m-40) REVERT: B 483 GLU cc_start: 0.9339 (mp0) cc_final: 0.8969 (mp0) REVERT: B 493 MET cc_start: 0.9681 (tmm) cc_final: 0.9276 (tmm) REVERT: B 515 ASP cc_start: 0.9234 (m-30) cc_final: 0.9015 (m-30) REVERT: B 615 MET cc_start: 0.9315 (mmp) cc_final: 0.8867 (mmm) REVERT: B 634 MET cc_start: 0.9317 (mmm) cc_final: 0.8992 (mmt) REVERT: B 665 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8603 (ttt-90) REVERT: B 667 LEU cc_start: 0.9139 (tp) cc_final: 0.8872 (tp) REVERT: C 30 TRP cc_start: 0.6464 (p-90) cc_final: 0.5605 (p-90) REVERT: C 31 LEU cc_start: 0.8861 (mt) cc_final: 0.8616 (mm) REVERT: C 96 MET cc_start: 0.6694 (mmm) cc_final: 0.6155 (mmm) REVERT: C 245 ASP cc_start: 0.8598 (t70) cc_final: 0.8359 (m-30) REVERT: C 246 LEU cc_start: 0.8322 (mp) cc_final: 0.7858 (mp) REVERT: D 72 THR cc_start: 0.8599 (p) cc_final: 0.8268 (p) REVERT: D 90 LEU cc_start: 0.7873 (mt) cc_final: 0.7635 (mt) REVERT: D 109 PHE cc_start: 0.8647 (m-10) cc_final: 0.8432 (m-80) REVERT: D 127 GLN cc_start: 0.9202 (mm-40) cc_final: 0.8984 (mp10) REVERT: D 185 MET cc_start: 0.6757 (mmm) cc_final: 0.6499 (mmm) REVERT: D 223 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8817 (pt0) REVERT: D 224 LEU cc_start: 0.9213 (mt) cc_final: 0.8848 (mt) REVERT: D 236 TYR cc_start: 0.8817 (t80) cc_final: 0.8597 (t80) REVERT: D 266 LYS cc_start: 0.8833 (mmmm) cc_final: 0.8612 (mmmm) REVERT: D 268 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7918 (mm) REVERT: D 316 LYS cc_start: 0.9141 (tmmt) cc_final: 0.8761 (ttpp) outliers start: 101 outliers final: 58 residues processed: 736 average time/residue: 0.1065 time to fit residues: 119.2242 Evaluate side-chains 695 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 629 time to evaluate : 0.457 ------------------------------------------------------------------------------- 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 80 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 153 THR 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 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 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 27 ASP Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 158 ASN 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 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 587 VAL Chi-restraints excluded: chain B residue 589 SER 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 665 ARG 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 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 193 LEU 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: 10.0000 chunk 131 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 182 optimal weight: 5.9990 chunk 159 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 150 optimal weight: 20.0000 chunk 63 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 158 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 HIS B 361 GLN B 668 ASN C 24 GLN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.132446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.091176 restraints weight = 36087.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.094669 restraints weight = 17344.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.096899 restraints weight = 10374.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.098404 restraints weight = 7203.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.099314 restraints weight = 5523.679| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (11 function evaluations) r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.5530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16386 Z= 0.177 Angle : 0.653 9.611 22134 Z= 0.346 Chirality : 0.044 0.230 2360 Planarity : 0.004 0.036 2818 Dihedral : 9.489 130.386 2299 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.72 % Allowed : 24.36 % Favored : 70.92 % 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: 1.08 (0.18), residues: 1932 helix: 1.20 (0.15), residues: 1121 sheet: -0.54 (0.37), residues: 158 loop : 0.43 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 600 TYR 0.045 0.002 TYR D 142 PHE 0.039 0.002 PHE D 227 TRP 0.029 0.002 TRP C 124 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.18 (16386) covalent geometry : angle 0.65294 / 0.35 (22134) hydrogen bonds : bond 0.04350 / 2.76 ( 871) hydrogen bonds : angle 5.05165 / 3.62 ( 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 751 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 670 time to evaluate : 0.445 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 40 TYR cc_start: 0.9435 (t80) cc_final: 0.9181 (t80) REVERT: A 107 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8813 (mmmm) REVERT: A 147 GLN cc_start: 0.9032 (mt0) cc_final: 0.7895 (mm-40) REVERT: A 161 ARG cc_start: 0.8641 (ttm110) cc_final: 0.8340 (ttm110) REVERT: A 172 LEU cc_start: 0.9553 (mp) cc_final: 0.8990 (mp) REVERT: A 202 ASN cc_start: 0.9609 (t0) cc_final: 0.9246 (t0) REVERT: A 228 LYS cc_start: 0.9452 (mmmm) cc_final: 0.8820 (tppt) REVERT: A 243 ARG cc_start: 0.7340 (tmt-80) cc_final: 0.7076 (tmt-80) REVERT: A 251 LEU cc_start: 0.9518 (tp) cc_final: 0.9115 (tp) REVERT: A 286 ASP cc_start: 0.8747 (m-30) cc_final: 0.8359 (m-30) REVERT: A 290 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8352 (tm-30) REVERT: A 301 PHE cc_start: 0.9469 (m-80) cc_final: 0.9258 (m-10) REVERT: A 321 GLU cc_start: 0.9016 (tp30) cc_final: 0.8628 (tp30) REVERT: A 322 MET cc_start: 0.8855 (mmp) cc_final: 0.8642 (mmm) REVERT: A 341 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8867 (mmtm) REVERT: A 345 LYS cc_start: 0.9536 (tttt) cc_final: 0.9314 (ttpt) REVERT: A 348 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8094 (tmm) REVERT: A 362 ASP cc_start: 0.8471 (m-30) cc_final: 0.7914 (m-30) REVERT: A 384 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7636 (pm20) REVERT: A 400 GLU cc_start: 0.8305 (pp20) cc_final: 0.7938 (pp20) REVERT: A 402 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8063 (mm-30) REVERT: A 406 ASP cc_start: 0.8411 (m-30) cc_final: 0.8031 (m-30) REVERT: A 407 ILE cc_start: 0.9297 (mt) cc_final: 0.8854 (mt) REVERT: A 436 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9261 (mm) REVERT: A 493 MET cc_start: 0.9387 (tmm) cc_final: 0.9163 (tmm) REVERT: A 515 ASP cc_start: 0.9008 (m-30) cc_final: 0.8511 (m-30) REVERT: A 570 MET cc_start: 0.9331 (mtp) cc_final: 0.8990 (mtp) REVERT: A 583 SER cc_start: 0.9381 (m) cc_final: 0.9099 (t) REVERT: A 590 SER cc_start: 0.9435 (t) cc_final: 0.9011 (m) REVERT: A 602 GLU cc_start: 0.8414 (pt0) cc_final: 0.7161 (tm-30) REVERT: A 604 ARG cc_start: 0.8986 (mmp80) cc_final: 0.8686 (mpp-170) REVERT: A 615 MET cc_start: 0.9185 (mmp) cc_final: 0.8583 (mmp) REVERT: A 634 MET cc_start: 0.9173 (mmm) cc_final: 0.8919 (mmt) REVERT: A 640 MET cc_start: 0.9587 (OUTLIER) cc_final: 0.9030 (tpp) REVERT: A 646 GLN cc_start: 0.8924 (pt0) cc_final: 0.8656 (pt0) REVERT: A 647 HIS cc_start: 0.9211 (m-70) cc_final: 0.8846 (m170) REVERT: A 654 PHE cc_start: 0.8799 (t80) cc_final: 0.8355 (t80) REVERT: A 668 ASN cc_start: 0.9638 (m-40) cc_final: 0.9299 (m-40) REVERT: A 686 ARG cc_start: 0.8589 (mtp85) cc_final: 0.8156 (mtp-110) REVERT: B 31 GLU cc_start: 0.8885 (mp0) cc_final: 0.8623 (mt-10) REVERT: B 95 MET cc_start: 0.9346 (tpp) cc_final: 0.8950 (tpp) REVERT: B 112 LYS cc_start: 0.9598 (mmmt) cc_final: 0.9246 (mmtp) REVERT: B 128 PHE cc_start: 0.9527 (t80) cc_final: 0.9129 (t80) REVERT: B 149 TYR cc_start: 0.9345 (t80) cc_final: 0.8517 (t80) REVERT: B 161 ARG cc_start: 0.8050 (ttm110) cc_final: 0.6874 (ttm110) REVERT: B 202 ASN cc_start: 0.9467 (t0) cc_final: 0.9128 (t0) REVERT: B 214 LYS cc_start: 0.8856 (ttmm) cc_final: 0.8431 (mmtm) REVERT: B 236 TYR cc_start: 0.9234 (t80) cc_final: 0.8859 (t80) REVERT: B 296 LYS cc_start: 0.9101 (mttt) cc_final: 0.8883 (mmmt) REVERT: B 321 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8765 (tm-30) REVERT: B 333 LYS cc_start: 0.8749 (tttt) cc_final: 0.8230 (ttmm) REVERT: B 362 ASP cc_start: 0.8889 (m-30) cc_final: 0.8276 (m-30) REVERT: B 389 SER cc_start: 0.9137 (p) cc_final: 0.8877 (p) REVERT: B 392 SER cc_start: 0.9540 (m) cc_final: 0.8689 (p) REVERT: B 415 ASN cc_start: 0.9464 (t0) cc_final: 0.9239 (t0) REVERT: B 447 ASN cc_start: 0.8355 (m-40) cc_final: 0.8129 (m-40) REVERT: B 459 LYS cc_start: 0.9343 (OUTLIER) cc_final: 0.8783 (mtmm) REVERT: B 467 ASN cc_start: 0.9461 (t0) cc_final: 0.9235 (m-40) REVERT: B 493 MET cc_start: 0.9635 (tmm) cc_final: 0.9116 (tmm) REVERT: B 615 MET cc_start: 0.9212 (mmp) cc_final: 0.8756 (mmm) REVERT: B 634 MET cc_start: 0.9306 (mmm) cc_final: 0.8909 (mmt) REVERT: B 659 LYS cc_start: 0.7999 (tptt) cc_final: 0.7715 (tptt) REVERT: B 667 LEU cc_start: 0.9176 (tp) cc_final: 0.8952 (tp) REVERT: C 96 MET cc_start: 0.7112 (mmm) cc_final: 0.6400 (mmm) REVERT: C 100 VAL cc_start: 0.3078 (t) cc_final: 0.2650 (t) REVERT: C 242 TYR cc_start: 0.3434 (t80) cc_final: 0.3210 (t80) REVERT: C 245 ASP cc_start: 0.8592 (t70) cc_final: 0.8057 (m-30) REVERT: C 246 LEU cc_start: 0.8554 (mp) cc_final: 0.8245 (mt) REVERT: D 96 MET cc_start: 0.7473 (mmt) cc_final: 0.6956 (mmt) REVERT: D 107 ASN cc_start: 0.9632 (t0) cc_final: 0.9127 (t0) REVERT: D 149 ASP cc_start: 0.8155 (t70) cc_final: 0.7941 (t70) REVERT: D 158 VAL cc_start: 0.9572 (t) cc_final: 0.9238 (t) REVERT: D 162 TYR cc_start: 0.9168 (m-10) cc_final: 0.8884 (m-80) REVERT: D 185 MET cc_start: 0.6936 (mmm) cc_final: 0.6612 (mmm) REVERT: D 198 GLU cc_start: 0.8746 (mm-30) cc_final: 0.7689 (mm-30) REVERT: D 219 GLU cc_start: 0.9204 (pp20) cc_final: 0.8976 (pm20) REVERT: D 266 LYS cc_start: 0.8859 (mmmm) cc_final: 0.8561 (mmmm) outliers start: 81 outliers final: 47 residues processed: 715 average time/residue: 0.1115 time to fit residues: 121.3718 Evaluate side-chains 693 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 639 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 341 LYS 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 155 THR Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR 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 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 460 SER Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 590 SER 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 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 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: 3.9990 chunk 157 optimal weight: 10.0000 chunk 168 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 60 optimal weight: 0.8980 chunk 185 optimal weight: 8.9990 chunk 191 optimal weight: 10.0000 chunk 159 optimal weight: 20.0000 chunk 182 optimal weight: 7.9990 chunk 93 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN D 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.132432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.091111 restraints weight = 36282.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.094435 restraints weight = 17647.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.096702 restraints weight = 10626.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.098174 restraints weight = 7357.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.099022 restraints weight = 5689.715| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.6070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 16386 Z= 0.205 Angle : 0.670 9.034 22134 Z= 0.355 Chirality : 0.046 0.238 2360 Planarity : 0.004 0.059 2818 Dihedral : 9.135 133.605 2297 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 17.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 5.36 % Allowed : 24.53 % Favored : 70.10 % 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: 0.98 (0.18), residues: 1932 helix: 1.10 (0.15), residues: 1119 sheet: -0.55 (0.37), residues: 162 loop : 0.40 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 446 TYR 0.031 0.002 TYR D 142 PHE 0.034 0.002 PHE D 168 TRP 0.026 0.002 TRP C 124 HIS 0.005 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.20 (16386) covalent geometry : angle 0.67042 / 0.35 (22134) hydrogen bonds : bond 0.04211 / 2.66 ( 871) hydrogen bonds : angle 5.05471 / 3.63 ( 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 746 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 654 time to evaluate : 0.612 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: A 27 ASP cc_start: 0.9074 (p0) cc_final: 0.8431 (p0) REVERT: A 31 GLU cc_start: 0.9045 (pt0) cc_final: 0.8747 (pm20) REVERT: A 40 TYR cc_start: 0.9465 (t80) cc_final: 0.9262 (t80) REVERT: A 64 TYR cc_start: 0.9219 (m-10) cc_final: 0.8809 (m-10) REVERT: A 65 GLU cc_start: 0.8548 (mm-30) cc_final: 0.7693 (mp0) REVERT: A 119 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8369 (mt-10) REVERT: A 150 GLN cc_start: 0.9129 (tm-30) cc_final: 0.7642 (tm-30) REVERT: A 161 ARG cc_start: 0.8645 (ttm110) cc_final: 0.8050 (ttm110) REVERT: A 172 LEU cc_start: 0.9570 (mp) cc_final: 0.9064 (mp) REVERT: A 228 LYS cc_start: 0.9403 (mmmm) cc_final: 0.8971 (tppt) REVERT: A 251 LEU cc_start: 0.9545 (tp) cc_final: 0.9197 (tp) REVERT: A 286 ASP cc_start: 0.8756 (m-30) cc_final: 0.8329 (m-30) REVERT: A 290 GLU cc_start: 0.8673 (tm-30) cc_final: 0.8446 (tm-30) REVERT: A 321 GLU cc_start: 0.9037 (tp30) cc_final: 0.8684 (tp30) REVERT: A 322 MET cc_start: 0.8882 (mmp) cc_final: 0.8681 (mmm) REVERT: A 341 LYS cc_start: 0.9167 (OUTLIER) cc_final: 0.8862 (mmtm) REVERT: A 348 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.8114 (tmm) REVERT: A 362 ASP cc_start: 0.8455 (m-30) cc_final: 0.7687 (m-30) REVERT: A 384 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.7675 (pm20) REVERT: A 400 GLU cc_start: 0.8389 (pp20) cc_final: 0.8053 (pp20) REVERT: A 402 GLU cc_start: 0.8597 (mm-30) cc_final: 0.8135 (mm-30) REVERT: A 406 ASP cc_start: 0.8399 (m-30) cc_final: 0.8068 (m-30) REVERT: A 407 ILE cc_start: 0.9317 (mt) cc_final: 0.8829 (mt) REVERT: A 458 MET cc_start: 0.8934 (mmp) cc_final: 0.8174 (mmp) REVERT: A 493 MET cc_start: 0.9331 (tmm) cc_final: 0.9099 (tmm) REVERT: A 515 ASP cc_start: 0.9011 (m-30) cc_final: 0.8555 (m-30) REVERT: A 570 MET cc_start: 0.9350 (mtp) cc_final: 0.9004 (mtp) REVERT: A 583 SER cc_start: 0.9434 (OUTLIER) cc_final: 0.9155 (t) REVERT: A 590 SER cc_start: 0.9278 (t) cc_final: 0.8971 (m) REVERT: A 615 MET cc_start: 0.9223 (mmp) cc_final: 0.8600 (mmp) REVERT: A 640 MET cc_start: 0.9649 (OUTLIER) cc_final: 0.9062 (tpp) REVERT: A 647 HIS cc_start: 0.9218 (m-70) cc_final: 0.8846 (m170) REVERT: A 668 ASN cc_start: 0.9643 (m-40) cc_final: 0.9357 (m-40) REVERT: B 31 GLU cc_start: 0.8909 (mp0) cc_final: 0.8593 (mp0) REVERT: B 65 GLU cc_start: 0.8536 (mm-30) cc_final: 0.8116 (mm-30) REVERT: B 95 MET cc_start: 0.9370 (tpp) cc_final: 0.9003 (tpp) REVERT: B 106 LEU cc_start: 0.9235 (tt) cc_final: 0.8957 (tt) REVERT: B 119 GLU cc_start: 0.9064 (mp0) cc_final: 0.8497 (mp0) REVERT: B 128 PHE cc_start: 0.9513 (t80) cc_final: 0.9123 (t80) REVERT: B 149 TYR cc_start: 0.9405 (t80) cc_final: 0.8445 (t80) REVERT: B 161 ARG cc_start: 0.8115 (ttm110) cc_final: 0.7046 (ttm110) REVERT: B 202 ASN cc_start: 0.9463 (t0) cc_final: 0.9150 (t0) REVERT: B 214 LYS cc_start: 0.8926 (ttmm) cc_final: 0.8428 (mmtm) REVERT: B 236 TYR cc_start: 0.9236 (t80) cc_final: 0.8960 (t80) REVERT: B 296 LYS cc_start: 0.9145 (mttt) cc_final: 0.8908 (mmmt) REVERT: B 333 LYS cc_start: 0.8707 (tttt) cc_final: 0.8280 (ttmm) REVERT: B 361 GLN cc_start: 0.9098 (OUTLIER) cc_final: 0.8734 (tp40) REVERT: B 377 LYS cc_start: 0.9280 (mttt) cc_final: 0.8919 (mtmm) REVERT: B 389 SER cc_start: 0.9107 (p) cc_final: 0.8613 (p) REVERT: B 392 SER cc_start: 0.9491 (m) cc_final: 0.9008 (p) REVERT: B 394 TYR cc_start: 0.9418 (m-80) cc_final: 0.9151 (m-80) REVERT: B 415 ASN cc_start: 0.9372 (t0) cc_final: 0.8970 (t0) REVERT: B 447 ASN cc_start: 0.8403 (m-40) cc_final: 0.8163 (m-40) REVERT: B 459 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.8804 (mtmm) REVERT: B 466 MET cc_start: 0.9109 (ptp) cc_final: 0.8853 (ptp) REVERT: B 467 ASN cc_start: 0.9417 (t0) cc_final: 0.9091 (m-40) REVERT: B 483 GLU cc_start: 0.9309 (mp0) cc_final: 0.8937 (mp0) REVERT: B 493 MET cc_start: 0.9658 (tmm) cc_final: 0.9103 (tmm) REVERT: B 527 TYR cc_start: 0.9280 (t80) cc_final: 0.9010 (t80) REVERT: B 604 ARG cc_start: 0.9130 (tpp80) cc_final: 0.8574 (mmm-85) REVERT: B 615 MET cc_start: 0.9187 (mmp) cc_final: 0.8826 (mmp) REVERT: B 645 GLN cc_start: 0.9566 (tp40) cc_final: 0.9143 (tp-100) REVERT: B 659 LYS cc_start: 0.8145 (tptt) cc_final: 0.7791 (tptt) REVERT: C 100 VAL cc_start: 0.2641 (t) cc_final: 0.2400 (t) REVERT: C 124 TRP cc_start: 0.6396 (t60) cc_final: 0.6099 (t60) REVERT: C 245 ASP cc_start: 0.8447 (t70) cc_final: 0.8135 (m-30) REVERT: D 96 MET cc_start: 0.7498 (mmt) cc_final: 0.7071 (mmt) REVERT: D 98 ASN cc_start: 0.8557 (m-40) cc_final: 0.8350 (m110) REVERT: D 110 MET cc_start: 0.8241 (ppp) cc_final: 0.7938 (ptp) REVERT: D 127 GLN cc_start: 0.9245 (mm-40) cc_final: 0.9036 (mp10) REVERT: D 148 ASP cc_start: 0.7535 (t0) cc_final: 0.7265 (t0) REVERT: D 158 VAL cc_start: 0.9647 (t) cc_final: 0.9282 (t) REVERT: D 162 TYR cc_start: 0.9267 (m-10) cc_final: 0.8945 (m-80) REVERT: D 185 MET cc_start: 0.6935 (mmm) cc_final: 0.6577 (mmm) REVERT: D 219 GLU cc_start: 0.9221 (OUTLIER) cc_final: 0.9015 (pm20) REVERT: D 227 PHE cc_start: 0.8682 (m-80) cc_final: 0.8444 (m-80) outliers start: 92 outliers final: 66 residues processed: 693 average time/residue: 0.1133 time to fit residues: 120.2057 Evaluate side-chains 704 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 630 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 183 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 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 414 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 653 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 158 ASN 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 277 THR Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 361 GLN 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 417 LEU 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 546 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 590 SER 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 57 LYS 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 207 LEU Chi-restraints excluded: chain C residue 255 ASP 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 115 THR Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 315 LEU 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: 0.8980 chunk 120 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 168 optimal weight: 6.9990 chunk 157 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 365 ASN A 370 ASN A 588 GLN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN D 136 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.134292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.093642 restraints weight = 36021.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.097245 restraints weight = 17202.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.099550 restraints weight = 10295.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.100955 restraints weight = 7129.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.101791 restraints weight = 5492.715| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3174 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3174 r_free = 0.3174 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (14 function evaluations) r_final: 0.3174 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.6415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16386 Z= 0.162 Angle : 0.666 9.389 22134 Z= 0.350 Chirality : 0.045 0.186 2360 Planarity : 0.004 0.042 2818 Dihedral : 8.778 135.084 2294 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 5.48 % Allowed : 26.34 % Favored : 68.18 % 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: 0.86 (0.18), residues: 1932 helix: 1.05 (0.15), residues: 1125 sheet: -0.49 (0.39), residues: 158 loop : 0.21 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 164 TYR 0.046 0.002 TYR D 142 PHE 0.056 0.002 PHE D 109 TRP 0.024 0.001 TRP C 124 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (16386) covalent geometry : angle 0.66582 / 0.35 (22134) hydrogen bonds : bond 0.04090 / 2.58 ( 871) hydrogen bonds : angle 5.05273 / 3.65 ( 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 754 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 660 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.9050 (p0) cc_final: 0.8514 (p0) REVERT: A 30 LYS cc_start: 0.9316 (ttpp) cc_final: 0.9110 (ttpp) REVERT: A 31 GLU cc_start: 0.9030 (pt0) cc_final: 0.8510 (pm20) REVERT: A 40 TYR cc_start: 0.9475 (t80) cc_final: 0.9263 (t80) REVERT: A 65 GLU cc_start: 0.8599 (mm-30) cc_final: 0.7846 (mp0) REVERT: A 150 GLN cc_start: 0.9157 (tm-30) cc_final: 0.7775 (tm-30) REVERT: A 161 ARG cc_start: 0.8503 (ttm110) cc_final: 0.8102 (ttm110) REVERT: A 172 LEU cc_start: 0.9506 (mp) cc_final: 0.9048 (mp) REVERT: A 243 ARG cc_start: 0.7133 (tmt-80) cc_final: 0.6857 (tmt-80) REVERT: A 286 ASP cc_start: 0.8725 (m-30) cc_final: 0.8292 (m-30) REVERT: A 290 GLU cc_start: 0.8706 (tm-30) cc_final: 0.8466 (tm-30) REVERT: A 321 GLU cc_start: 0.9034 (tp30) cc_final: 0.8688 (tp30) REVERT: A 322 MET cc_start: 0.8913 (mmp) cc_final: 0.8711 (mmm) REVERT: A 341 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8835 (mmtm) REVERT: A 348 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8164 (tmm) REVERT: A 362 ASP cc_start: 0.8458 (m-30) cc_final: 0.7609 (m-30) REVERT: A 384 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.7664 (pm20) REVERT: A 389 SER cc_start: 0.9531 (OUTLIER) cc_final: 0.9284 (p) REVERT: A 390 GLN cc_start: 0.9007 (mt0) cc_final: 0.8756 (mt0) REVERT: A 400 GLU cc_start: 0.8340 (pp20) cc_final: 0.8013 (pp20) REVERT: A 402 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8126 (mm-30) REVERT: A 406 ASP cc_start: 0.8217 (m-30) cc_final: 0.8004 (m-30) REVERT: A 407 ILE cc_start: 0.9053 (mt) cc_final: 0.8724 (mt) REVERT: A 515 ASP cc_start: 0.9035 (m-30) cc_final: 0.8607 (m-30) REVERT: A 570 MET cc_start: 0.9384 (mtp) cc_final: 0.9061 (mtp) REVERT: A 583 SER cc_start: 0.9457 (OUTLIER) cc_final: 0.9197 (t) REVERT: A 590 SER cc_start: 0.9170 (t) cc_final: 0.8573 (p) REVERT: A 610 LYS cc_start: 0.9214 (ttpp) cc_final: 0.8965 (ttmm) REVERT: A 615 MET cc_start: 0.9296 (mmp) cc_final: 0.8819 (mmp) REVERT: A 640 MET cc_start: 0.9677 (OUTLIER) cc_final: 0.9128 (tpp) REVERT: A 668 ASN cc_start: 0.9655 (m-40) cc_final: 0.9350 (m-40) REVERT: B 30 LYS cc_start: 0.9521 (tptt) cc_final: 0.9317 (tptt) REVERT: B 31 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8614 (mp0) REVERT: B 65 GLU cc_start: 0.8317 (mm-30) cc_final: 0.8031 (mm-30) REVERT: B 95 MET cc_start: 0.9353 (tpp) cc_final: 0.8975 (tpp) REVERT: B 106 LEU cc_start: 0.9305 (tt) cc_final: 0.9000 (tt) REVERT: B 112 LYS cc_start: 0.9546 (mmmt) cc_final: 0.9233 (mmmt) REVERT: B 119 GLU cc_start: 0.9040 (mp0) cc_final: 0.8443 (mp0) REVERT: B 128 PHE cc_start: 0.9519 (t80) cc_final: 0.9162 (t80) REVERT: B 149 TYR cc_start: 0.9394 (t80) cc_final: 0.8379 (t80) REVERT: B 158 ASN cc_start: 0.9317 (OUTLIER) cc_final: 0.7934 (t0) REVERT: B 161 ARG cc_start: 0.8077 (ttm110) cc_final: 0.7057 (ttm110) REVERT: B 184 ARG cc_start: 0.9337 (mmm-85) cc_final: 0.9128 (mmm-85) REVERT: B 202 ASN cc_start: 0.9414 (t0) cc_final: 0.9033 (t0) REVERT: B 214 LYS cc_start: 0.8892 (ttmm) cc_final: 0.8367 (mmtp) REVERT: B 221 LYS cc_start: 0.9309 (mmtp) cc_final: 0.9016 (mttp) REVERT: B 263 ASP cc_start: 0.9205 (m-30) cc_final: 0.8778 (m-30) REVERT: B 267 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.9086 (pp) REVERT: B 296 LYS cc_start: 0.9233 (mttt) cc_final: 0.8986 (mmmt) REVERT: B 322 MET cc_start: 0.9654 (mmm) cc_final: 0.9392 (tpp) REVERT: B 333 LYS cc_start: 0.8698 (tttt) cc_final: 0.8274 (ttmm) REVERT: B 377 LYS cc_start: 0.9202 (mttt) cc_final: 0.8796 (mttp) REVERT: B 389 SER cc_start: 0.9086 (p) cc_final: 0.8222 (p) REVERT: B 392 SER cc_start: 0.9524 (m) cc_final: 0.8886 (p) REVERT: B 394 TYR cc_start: 0.9431 (m-80) cc_final: 0.9145 (m-80) REVERT: B 403 ILE cc_start: 0.9195 (mp) cc_final: 0.8989 (mm) REVERT: B 415 ASN cc_start: 0.9270 (t0) cc_final: 0.8867 (t0) REVERT: B 447 ASN cc_start: 0.8289 (m-40) cc_final: 0.7988 (m-40) REVERT: B 459 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.8757 (mtmm) REVERT: B 466 MET cc_start: 0.9089 (ptp) cc_final: 0.8755 (ptp) REVERT: B 467 ASN cc_start: 0.9311 (t0) cc_final: 0.8616 (t0) REVERT: B 493 MET cc_start: 0.9639 (tmm) cc_final: 0.9063 (tmm) REVERT: B 527 TYR cc_start: 0.9286 (t80) cc_final: 0.9022 (t80) REVERT: B 548 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8320 (mm-30) REVERT: B 550 MET cc_start: 0.8310 (mtm) cc_final: 0.8077 (mtt) REVERT: B 615 MET cc_start: 0.9241 (mmp) cc_final: 0.8893 (mmp) REVERT: B 645 GLN cc_start: 0.9533 (tp40) cc_final: 0.9147 (tp-100) REVERT: B 659 LYS cc_start: 0.7982 (tptt) cc_final: 0.7644 (tptt) REVERT: D 96 MET cc_start: 0.7512 (mmt) cc_final: 0.7114 (mmt) REVERT: D 100 VAL cc_start: 0.8230 (OUTLIER) cc_final: 0.7937 (p) REVERT: D 110 MET cc_start: 0.8233 (ppp) cc_final: 0.7731 (ptp) REVERT: D 158 VAL cc_start: 0.9643 (OUTLIER) cc_final: 0.9249 (t) REVERT: D 162 TYR cc_start: 0.9223 (m-10) cc_final: 0.8869 (m-80) REVERT: D 185 MET cc_start: 0.6935 (mmm) cc_final: 0.6654 (mmm) REVERT: D 227 PHE cc_start: 0.8770 (m-80) cc_final: 0.8427 (m-80) outliers start: 94 outliers final: 60 residues processed: 693 average time/residue: 0.1104 time to fit residues: 116.5545 Evaluate side-chains 700 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 628 time to evaluate : 0.604 ------------------------------------------------------------------------------- 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 58 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 199 VAL 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 381 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 SER 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 583 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 653 SER 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 155 THR Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 314 MET 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 417 LEU 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 B residue 687 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 142 TYR 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 100 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 0.9990 chunk 183 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 172 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 136 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 646 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN D 25 ASN ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.137935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.096884 restraints weight = 36133.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.100339 restraints weight = 17695.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.102647 restraints weight = 10727.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.104159 restraints weight = 7425.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.105073 restraints weight = 5708.588| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 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 = 0.3191 r_free = 0.3191 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (11 function evaluations) r_final: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.6687 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= 0.154 Angle : 0.693 9.697 22134 Z= 0.360 Chirality : 0.046 0.269 2360 Planarity : 0.004 0.040 2818 Dihedral : 8.585 133.888 2294 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.13 % Allowed : 27.86 % Favored : 67.02 % 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: 0.76 (0.18), residues: 1932 helix: 0.98 (0.15), residues: 1127 sheet: -0.56 (0.38), residues: 158 loop : 0.16 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 485 TYR 0.039 0.002 TYR D 142 PHE 0.036 0.002 PHE B 261 TRP 0.032 0.002 TRP C 124 HIS 0.011 0.001 HIS D 101 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.15 (16386) covalent geometry : angle 0.69257 / 0.36 (22134) hydrogen bonds : bond 0.04123 / 2.61 ( 871) hydrogen bonds : angle 5.09621 / 3.69 ( 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 739 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 651 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8987 (p0) cc_final: 0.8250 (p0) REVERT: A 30 LYS cc_start: 0.9278 (ttpp) cc_final: 0.9011 (ttpp) REVERT: A 31 GLU cc_start: 0.9025 (pt0) cc_final: 0.8451 (pm20) REVERT: A 40 TYR cc_start: 0.9463 (t80) cc_final: 0.9245 (t80) REVERT: A 65 GLU cc_start: 0.8656 (mm-30) cc_final: 0.7862 (mp0) REVERT: A 144 MET cc_start: 0.8948 (mtm) cc_final: 0.8479 (mtt) REVERT: A 150 GLN cc_start: 0.9156 (tm-30) cc_final: 0.8789 (tm-30) REVERT: A 161 ARG cc_start: 0.8454 (ttm110) cc_final: 0.8113 (ttm110) REVERT: A 228 LYS cc_start: 0.9363 (mmmm) cc_final: 0.8880 (mmtm) REVERT: A 231 ASP cc_start: 0.8916 (t70) cc_final: 0.8630 (t0) REVERT: A 252 ASN cc_start: 0.8972 (t0) cc_final: 0.8667 (t0) REVERT: A 286 ASP cc_start: 0.8726 (m-30) cc_final: 0.8296 (m-30) REVERT: A 290 GLU cc_start: 0.8702 (tm-30) cc_final: 0.8434 (tm-30) REVERT: A 321 GLU cc_start: 0.9040 (tp30) cc_final: 0.8699 (tp30) REVERT: A 341 LYS cc_start: 0.9132 (OUTLIER) cc_final: 0.8830 (mmtm) REVERT: A 348 MET cc_start: 0.8545 (OUTLIER) cc_final: 0.8189 (tmm) REVERT: A 361 GLN cc_start: 0.9084 (OUTLIER) cc_final: 0.8697 (tp40) REVERT: A 362 ASP cc_start: 0.8364 (m-30) cc_final: 0.7310 (m-30) REVERT: A 384 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.7723 (pm20) REVERT: A 390 GLN cc_start: 0.9015 (mt0) cc_final: 0.8770 (mt0) REVERT: A 400 GLU cc_start: 0.8303 (pp20) cc_final: 0.7987 (pp20) REVERT: A 402 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8114 (mm-30) REVERT: A 406 ASP cc_start: 0.8165 (m-30) cc_final: 0.7865 (m-30) REVERT: A 441 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8484 (mm-30) REVERT: A 459 LYS cc_start: 0.8956 (mtmm) cc_final: 0.8485 (ttmm) REVERT: A 515 ASP cc_start: 0.9021 (m-30) cc_final: 0.8599 (m-30) REVERT: A 570 MET cc_start: 0.9369 (mtp) cc_final: 0.8992 (mtp) REVERT: A 583 SER cc_start: 0.9478 (OUTLIER) cc_final: 0.9218 (t) REVERT: A 615 MET cc_start: 0.9301 (mmp) cc_final: 0.8798 (mmp) REVERT: A 640 MET cc_start: 0.9673 (OUTLIER) cc_final: 0.9112 (tpp) REVERT: A 646 GLN cc_start: 0.9367 (pt0) cc_final: 0.8568 (pm20) REVERT: A 668 ASN cc_start: 0.9664 (m-40) cc_final: 0.9345 (m-40) REVERT: B 31 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8571 (mp0) REVERT: B 65 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8097 (mm-30) REVERT: B 95 MET cc_start: 0.9347 (tpp) cc_final: 0.8947 (tpp) REVERT: B 106 LEU cc_start: 0.9298 (tt) cc_final: 0.8962 (tt) REVERT: B 112 LYS cc_start: 0.9515 (mmmt) cc_final: 0.9188 (mmmt) REVERT: B 119 GLU cc_start: 0.9013 (mp0) cc_final: 0.8451 (mp0) REVERT: B 128 PHE cc_start: 0.9530 (t80) cc_final: 0.9161 (t80) REVERT: B 149 TYR cc_start: 0.9368 (t80) cc_final: 0.8369 (t80) REVERT: B 158 ASN cc_start: 0.9195 (OUTLIER) cc_final: 0.7986 (t0) REVERT: B 161 ARG cc_start: 0.8153 (ttm110) cc_final: 0.7191 (ttm110) REVERT: B 202 ASN cc_start: 0.9305 (t0) cc_final: 0.8983 (t0) REVERT: B 214 LYS cc_start: 0.8876 (ttmm) cc_final: 0.8361 (mmtp) REVERT: B 263 ASP cc_start: 0.9178 (m-30) cc_final: 0.8793 (m-30) REVERT: B 267 ILE cc_start: 0.9288 (OUTLIER) cc_final: 0.9064 (pp) REVERT: B 296 LYS cc_start: 0.9274 (mttt) cc_final: 0.9021 (mmmt) REVERT: B 322 MET cc_start: 0.9658 (mmm) cc_final: 0.9435 (tpp) REVERT: B 333 LYS cc_start: 0.8716 (tttt) cc_final: 0.8296 (ttmm) REVERT: B 348 MET cc_start: 0.9028 (ptp) cc_final: 0.8579 (ptp) REVERT: B 361 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8660 (tp40) REVERT: B 377 LYS cc_start: 0.9256 (mttt) cc_final: 0.8796 (mtmm) REVERT: B 389 SER cc_start: 0.9073 (p) cc_final: 0.8511 (p) REVERT: B 392 SER cc_start: 0.9392 (m) cc_final: 0.8862 (p) REVERT: B 394 TYR cc_start: 0.9389 (m-80) cc_final: 0.9091 (m-80) REVERT: B 396 ASP cc_start: 0.8376 (p0) cc_final: 0.7881 (p0) REVERT: B 415 ASN cc_start: 0.9243 (t0) cc_final: 0.8950 (t0) REVERT: B 459 LYS cc_start: 0.9345 (OUTLIER) cc_final: 0.8759 (mtmm) REVERT: B 466 MET cc_start: 0.9018 (ptp) cc_final: 0.8808 (ptp) REVERT: B 471 TYR cc_start: 0.9205 (t80) cc_final: 0.8622 (t80) REVERT: B 493 MET cc_start: 0.9641 (tmm) cc_final: 0.9060 (tmm) REVERT: B 494 MET cc_start: 0.9267 (ttm) cc_final: 0.9019 (mmt) REVERT: B 527 TYR cc_start: 0.9238 (t80) cc_final: 0.8977 (t80) REVERT: B 548 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8355 (mm-30) REVERT: B 585 SER cc_start: 0.9341 (p) cc_final: 0.8744 (t) REVERT: B 615 MET cc_start: 0.9247 (mmp) cc_final: 0.8899 (mmp) REVERT: B 640 MET cc_start: 0.9504 (tpp) cc_final: 0.9000 (tpp) REVERT: B 645 GLN cc_start: 0.9503 (tp40) cc_final: 0.9052 (tp-100) REVERT: B 659 LYS cc_start: 0.7891 (tptt) cc_final: 0.7592 (tptt) REVERT: C 96 MET cc_start: 0.7191 (mmm) cc_final: 0.6573 (mmm) REVERT: C 117 THR cc_start: 0.7098 (m) cc_final: 0.6831 (p) REVERT: C 174 TYR cc_start: 0.4288 (OUTLIER) cc_final: 0.3991 (t80) REVERT: C 242 TYR cc_start: 0.3677 (t80) cc_final: 0.3403 (t80) REVERT: C 245 ASP cc_start: 0.8354 (t70) cc_final: 0.8019 (m-30) REVERT: D 46 TYR cc_start: 0.9477 (m-80) cc_final: 0.8927 (m-10) REVERT: D 95 MET cc_start: 0.7801 (tmm) cc_final: 0.7051 (tmm) REVERT: D 100 VAL cc_start: 0.8222 (OUTLIER) cc_final: 0.7869 (p) REVERT: D 110 MET cc_start: 0.8206 (ppp) cc_final: 0.7660 (ptp) REVERT: D 158 VAL cc_start: 0.9621 (OUTLIER) cc_final: 0.9231 (t) REVERT: D 162 TYR cc_start: 0.9189 (m-10) cc_final: 0.8817 (m-80) REVERT: D 185 MET cc_start: 0.7090 (mmm) cc_final: 0.6838 (mmm) REVERT: D 198 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8176 (mm-30) REVERT: D 227 PHE cc_start: 0.8851 (m-80) cc_final: 0.8483 (m-80) REVERT: D 315 LEU cc_start: 0.9241 (OUTLIER) cc_final: 0.8978 (mp) outliers start: 88 outliers final: 58 residues processed: 686 average time/residue: 0.1113 time to fit residues: 116.3313 Evaluate side-chains 698 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 625 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 58 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 141 VAL 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 408 SER Chi-restraints excluded: chain A residue 409 CYS 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 443 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE 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 31 GLU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 158 ASN Chi-restraints excluded: chain B residue 168 VAL 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 246 SER 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 361 GLN 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 417 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 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 B residue 687 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 142 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 25 ASN 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 158 VAL Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 0.1980 chunk 51 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN B 158 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.138520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.097278 restraints weight = 36029.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.100897 restraints weight = 17373.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.103276 restraints weight = 10424.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.104773 restraints weight = 7202.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.105669 restraints weight = 5555.853| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.6989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16386 Z= 0.148 Angle : 0.733 17.442 22134 Z= 0.373 Chirality : 0.047 0.277 2360 Planarity : 0.004 0.042 2818 Dihedral : 8.464 134.281 2294 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.01 % Allowed : 29.90 % Favored : 65.09 % 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: 0.68 (0.18), residues: 1932 helix: 0.89 (0.15), residues: 1140 sheet: -0.48 (0.39), residues: 160 loop : 0.14 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 665 TYR 0.036 0.002 TYR D 142 PHE 0.038 0.002 PHE B 261 TRP 0.026 0.001 TRP C 124 HIS 0.010 0.001 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (16386) covalent geometry : angle 0.73263 / 0.37 (22134) hydrogen bonds : bond 0.04127 / 2.62 ( 871) hydrogen bonds : angle 5.12819 / 3.72 ( 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 751 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 665 time to evaluate : 0.576 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 27 ASP cc_start: 0.8954 (p0) cc_final: 0.8219 (p0) REVERT: A 31 GLU cc_start: 0.9012 (pt0) cc_final: 0.8411 (pm20) REVERT: A 40 TYR cc_start: 0.9464 (t80) cc_final: 0.9211 (t80) REVERT: A 144 MET cc_start: 0.8945 (mtm) cc_final: 0.8360 (mtt) REVERT: A 161 ARG cc_start: 0.8432 (ttm110) cc_final: 0.8181 (ttm110) REVERT: A 184 ARG cc_start: 0.9226 (mmm-85) cc_final: 0.8823 (tpt90) REVERT: A 286 ASP cc_start: 0.8718 (m-30) cc_final: 0.8246 (m-30) REVERT: A 290 GLU cc_start: 0.8674 (tm-30) cc_final: 0.8412 (tm-30) REVERT: A 321 GLU cc_start: 0.9028 (tp30) cc_final: 0.8690 (tp30) REVERT: A 341 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8834 (mmtm) REVERT: A 348 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8171 (tmm) REVERT: A 361 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8665 (tp40) REVERT: A 362 ASP cc_start: 0.8366 (m-30) cc_final: 0.7290 (m-30) REVERT: A 384 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7721 (pm20) REVERT: A 390 GLN cc_start: 0.8925 (mt0) cc_final: 0.8689 (mt0) REVERT: A 400 GLU cc_start: 0.8376 (pp20) cc_final: 0.8090 (pp20) REVERT: A 402 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8161 (mm-30) REVERT: A 441 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8424 (mm-30) REVERT: A 458 MET cc_start: 0.8546 (mmp) cc_final: 0.7981 (mmp) REVERT: A 459 LYS cc_start: 0.8737 (mtmm) cc_final: 0.8318 (ttmm) REVERT: A 493 MET cc_start: 0.8967 (tmm) cc_final: 0.8643 (tmm) REVERT: A 515 ASP cc_start: 0.9020 (m-30) cc_final: 0.8527 (m-30) REVERT: A 570 MET cc_start: 0.9346 (mtp) cc_final: 0.8953 (mtp) REVERT: A 583 SER cc_start: 0.9495 (m) cc_final: 0.8967 (t) REVERT: A 604 ARG cc_start: 0.8483 (ttm110) cc_final: 0.8160 (ttm110) REVERT: A 615 MET cc_start: 0.9283 (mmp) cc_final: 0.8758 (mmp) REVERT: A 636 LYS cc_start: 0.9604 (mmtp) cc_final: 0.9296 (mmmt) REVERT: A 640 MET cc_start: 0.9687 (OUTLIER) cc_final: 0.8949 (tpp) REVERT: A 646 GLN cc_start: 0.9325 (pt0) cc_final: 0.8604 (pm20) REVERT: A 668 ASN cc_start: 0.9637 (m-40) cc_final: 0.9354 (m-40) REVERT: B 31 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8540 (mp0) REVERT: B 65 GLU cc_start: 0.8320 (mm-30) cc_final: 0.8119 (mm-30) REVERT: B 95 MET cc_start: 0.9290 (tpp) cc_final: 0.8721 (tpp) REVERT: B 106 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8895 (tt) REVERT: B 112 LYS cc_start: 0.9476 (mmmt) cc_final: 0.9157 (mmmt) REVERT: B 119 GLU cc_start: 0.8980 (mp0) cc_final: 0.8458 (mp0) REVERT: B 128 PHE cc_start: 0.9537 (t80) cc_final: 0.9163 (t80) REVERT: B 147 GLN cc_start: 0.9565 (mt0) cc_final: 0.9136 (mm110) REVERT: B 149 TYR cc_start: 0.9258 (t80) cc_final: 0.8512 (t80) REVERT: B 161 ARG cc_start: 0.8028 (ttm110) cc_final: 0.7230 (ttm110) REVERT: B 214 LYS cc_start: 0.8879 (ttmm) cc_final: 0.8369 (mmtp) REVERT: B 257 ASP cc_start: 0.9188 (m-30) cc_final: 0.8659 (m-30) REVERT: B 263 ASP cc_start: 0.9166 (m-30) cc_final: 0.8784 (m-30) REVERT: B 267 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.9012 (pp) REVERT: B 296 LYS cc_start: 0.9216 (mttt) cc_final: 0.8967 (mmmt) REVERT: B 322 MET cc_start: 0.9688 (mmm) cc_final: 0.8889 (mpp) REVERT: B 333 LYS cc_start: 0.8725 (tttt) cc_final: 0.8304 (ttmm) REVERT: B 348 MET cc_start: 0.9034 (ptp) cc_final: 0.8586 (ptp) REVERT: B 357 TYR cc_start: 0.8547 (m-10) cc_final: 0.8146 (m-10) REVERT: B 389 SER cc_start: 0.9046 (p) cc_final: 0.8478 (p) REVERT: B 392 SER cc_start: 0.9390 (m) cc_final: 0.8857 (p) REVERT: B 394 TYR cc_start: 0.9392 (m-80) cc_final: 0.9068 (m-80) REVERT: B 396 ASP cc_start: 0.8225 (p0) cc_final: 0.7871 (p0) REVERT: B 415 ASN cc_start: 0.9195 (t0) cc_final: 0.8919 (t0) REVERT: B 443 THR cc_start: 0.9358 (OUTLIER) cc_final: 0.9143 (m) REVERT: B 447 ASN cc_start: 0.9048 (m-40) cc_final: 0.8232 (m-40) REVERT: B 459 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.8740 (mtmm) REVERT: B 466 MET cc_start: 0.8962 (ptp) cc_final: 0.8729 (ptp) REVERT: B 467 ASN cc_start: 0.8989 (t0) cc_final: 0.8673 (m-40) REVERT: B 471 TYR cc_start: 0.9116 (t80) cc_final: 0.8564 (t80) REVERT: B 493 MET cc_start: 0.9616 (tmm) cc_final: 0.9058 (tmm) REVERT: B 516 GLN cc_start: 0.9430 (mt0) cc_final: 0.9099 (mt0) REVERT: B 548 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8302 (mm-30) REVERT: B 585 SER cc_start: 0.9298 (p) cc_final: 0.8684 (t) REVERT: B 586 TYR cc_start: 0.9069 (m-80) cc_final: 0.8823 (m-10) REVERT: B 615 MET cc_start: 0.9295 (mmp) cc_final: 0.9018 (mmm) REVERT: B 632 MET cc_start: 0.8918 (mtp) cc_final: 0.8705 (mtp) REVERT: B 640 MET cc_start: 0.9526 (tpp) cc_final: 0.9230 (tpp) REVERT: B 645 GLN cc_start: 0.9526 (tp40) cc_final: 0.9121 (tp-100) REVERT: B 659 LYS cc_start: 0.7718 (tptt) cc_final: 0.7467 (tptt) REVERT: C 44 TRP cc_start: 0.7187 (t-100) cc_final: 0.6544 (t-100) REVERT: C 96 MET cc_start: 0.7129 (mmm) cc_final: 0.6459 (mmm) REVERT: C 174 TYR cc_start: 0.4467 (OUTLIER) cc_final: 0.4109 (t80) REVERT: C 242 TYR cc_start: 0.3645 (t80) cc_final: 0.3213 (t80) REVERT: C 245 ASP cc_start: 0.8379 (t70) cc_final: 0.8070 (m-30) REVERT: D 46 TYR cc_start: 0.9475 (m-80) cc_final: 0.8920 (m-10) REVERT: D 80 HIS cc_start: 0.8149 (m90) cc_final: 0.7268 (t-90) REVERT: D 95 MET cc_start: 0.7870 (tmm) cc_final: 0.7265 (tmm) REVERT: D 96 MET cc_start: 0.6922 (mmt) cc_final: 0.6678 (mmt) REVERT: D 100 VAL cc_start: 0.8094 (OUTLIER) cc_final: 0.7824 (p) REVERT: D 110 MET cc_start: 0.8196 (ppp) cc_final: 0.7641 (ptp) REVERT: D 162 TYR cc_start: 0.9071 (m-10) cc_final: 0.8691 (m-80) REVERT: D 174 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.8379 (t80) REVERT: D 185 MET cc_start: 0.7135 (mmm) cc_final: 0.6912 (mmm) REVERT: D 227 PHE cc_start: 0.8926 (m-80) cc_final: 0.8504 (m-80) outliers start: 86 outliers final: 60 residues processed: 696 average time/residue: 0.1071 time to fit residues: 113.6874 Evaluate side-chains 698 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 625 time to evaluate : 0.680 ------------------------------------------------------------------------------- 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 58 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 317 MET 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 409 CYS 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 584 ILE Chi-restraints excluded: chain A residue 597 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 267 ILE Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 361 GLN 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 417 LEU 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 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 204 TYR 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 129 LYS Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 150 GLU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 315 LEU 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: 4.9990 chunk 61 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 153 optimal weight: 9.9990 chunk 11 optimal weight: 0.4980 chunk 158 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 chunk 151 optimal weight: 20.0000 chunk 81 optimal weight: 0.9980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN D 132 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.134071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.092884 restraints weight = 37029.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.096344 restraints weight = 17865.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.098567 restraints weight = 10843.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.099956 restraints weight = 7617.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.100930 restraints weight = 5991.715| |-----------------------------------------------------------------------------| r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.7202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 16386 Z= 0.236 Angle : 0.796 14.017 22134 Z= 0.411 Chirality : 0.050 0.327 2360 Planarity : 0.004 0.051 2818 Dihedral : 8.439 136.598 2294 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.90 % Allowed : 31.35 % Favored : 63.75 % 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: 0.59 (0.18), residues: 1932 helix: 0.76 (0.15), residues: 1136 sheet: 0.30 (0.44), residues: 130 loop : -0.04 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 164 TYR 0.036 0.002 TYR B 613 PHE 0.039 0.002 PHE B 261 TRP 0.031 0.002 TRP C 124 HIS 0.015 0.002 HIS A 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.24 (16386) covalent geometry : angle 0.79569 / 0.41 (22134) hydrogen bonds : bond 0.04277 / 2.71 ( 871) hydrogen bonds : angle 5.29403 / 3.82 ( 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: 84 poor density : 631 time to evaluate : 0.593 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 27 ASP cc_start: 0.8957 (p0) cc_final: 0.8324 (p0) REVERT: A 31 GLU cc_start: 0.8906 (pt0) cc_final: 0.8371 (pm20) REVERT: A 64 TYR cc_start: 0.9289 (m-10) cc_final: 0.8987 (m-10) REVERT: A 65 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8093 (mp0) REVERT: A 119 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8124 (mt-10) REVERT: A 161 ARG cc_start: 0.8518 (ttm110) cc_final: 0.8188 (ttm110) REVERT: A 172 LEU cc_start: 0.9396 (mp) cc_final: 0.9075 (mp) REVERT: A 184 ARG cc_start: 0.9247 (mmm-85) cc_final: 0.8845 (tpt90) REVERT: A 290 GLU cc_start: 0.8717 (tm-30) cc_final: 0.8482 (tm-30) REVERT: A 321 GLU cc_start: 0.9082 (tp30) cc_final: 0.8768 (tp30) REVERT: A 341 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8838 (mmtm) REVERT: A 348 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.8142 (tmm) REVERT: A 361 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8677 (tp40) REVERT: A 384 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.7717 (pm20) REVERT: A 390 GLN cc_start: 0.8903 (mt0) cc_final: 0.8649 (mt0) REVERT: A 400 GLU cc_start: 0.8428 (pp20) cc_final: 0.8126 (pp20) REVERT: A 402 GLU cc_start: 0.8679 (mm-30) cc_final: 0.8257 (mm-30) REVERT: A 406 ASP cc_start: 0.8049 (m-30) cc_final: 0.7775 (m-30) REVERT: A 459 LYS cc_start: 0.8924 (mtmm) cc_final: 0.8466 (ttmm) REVERT: A 479 TYR cc_start: 0.9083 (t80) cc_final: 0.8865 (t80) REVERT: A 515 ASP cc_start: 0.9003 (m-30) cc_final: 0.8616 (m-30) REVERT: A 583 SER cc_start: 0.9346 (m) cc_final: 0.8979 (t) REVERT: A 604 ARG cc_start: 0.8447 (ttm110) cc_final: 0.8133 (tpp80) REVERT: A 615 MET cc_start: 0.9278 (mmp) cc_final: 0.8747 (mmp) REVERT: A 636 LYS cc_start: 0.9612 (mmtp) cc_final: 0.9290 (mmmt) REVERT: A 640 MET cc_start: 0.9667 (OUTLIER) cc_final: 0.8883 (tpp) REVERT: A 668 ASN cc_start: 0.9642 (m-40) cc_final: 0.9372 (m-40) REVERT: B 11 GLN cc_start: 0.9366 (OUTLIER) cc_final: 0.9163 (mp10) REVERT: B 31 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8567 (mp0) REVERT: B 65 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8175 (mm-30) REVERT: B 95 MET cc_start: 0.9317 (tpp) cc_final: 0.8883 (tpp) REVERT: B 106 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.8584 (tt) REVERT: B 112 LYS cc_start: 0.9497 (mmmt) cc_final: 0.9156 (mmmt) REVERT: B 119 GLU cc_start: 0.9043 (mp0) cc_final: 0.8534 (mp0) REVERT: B 128 PHE cc_start: 0.9589 (t80) cc_final: 0.9246 (t80) REVERT: B 129 PHE cc_start: 0.9566 (m-10) cc_final: 0.9344 (m-10) REVERT: B 147 GLN cc_start: 0.9566 (mt0) cc_final: 0.9180 (mm-40) REVERT: B 149 TYR cc_start: 0.9363 (t80) cc_final: 0.8359 (t80) REVERT: B 157 LEU cc_start: 0.9382 (tp) cc_final: 0.9175 (tp) REVERT: B 161 ARG cc_start: 0.8286 (ttm110) cc_final: 0.7234 (ttm110) REVERT: B 211 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7723 (mm-30) REVERT: B 214 LYS cc_start: 0.8917 (ttmm) cc_final: 0.8411 (mmtp) REVERT: B 263 ASP cc_start: 0.9168 (m-30) cc_final: 0.8797 (m-30) REVERT: B 267 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.9048 (pp) REVERT: B 296 LYS cc_start: 0.9266 (mttt) cc_final: 0.8991 (mmmt) REVERT: B 312 GLN cc_start: 0.8951 (mp10) cc_final: 0.8647 (pm20) REVERT: B 322 MET cc_start: 0.9641 (mmm) cc_final: 0.8764 (mpp) REVERT: B 333 LYS cc_start: 0.8813 (tttt) cc_final: 0.8337 (ttmm) REVERT: B 357 TYR cc_start: 0.9003 (m-10) cc_final: 0.8730 (m-10) REVERT: B 389 SER cc_start: 0.8883 (p) cc_final: 0.8672 (p) REVERT: B 392 SER cc_start: 0.9408 (m) cc_final: 0.8993 (p) REVERT: B 394 TYR cc_start: 0.9447 (m-80) cc_final: 0.9154 (m-80) REVERT: B 396 ASP cc_start: 0.8415 (p0) cc_final: 0.8037 (p0) REVERT: B 415 ASN cc_start: 0.9238 (t0) cc_final: 0.8910 (t0) REVERT: B 459 LYS cc_start: 0.9362 (OUTLIER) cc_final: 0.8783 (mtmm) REVERT: B 466 MET cc_start: 0.9044 (ptp) cc_final: 0.8798 (ptp) REVERT: B 467 ASN cc_start: 0.8918 (t0) cc_final: 0.8669 (m-40) REVERT: B 471 TYR cc_start: 0.9219 (t80) cc_final: 0.8666 (t80) REVERT: B 483 GLU cc_start: 0.9347 (mp0) cc_final: 0.8586 (mm-30) REVERT: B 493 MET cc_start: 0.9612 (tmm) cc_final: 0.9039 (tmm) REVERT: B 585 SER cc_start: 0.9346 (p) cc_final: 0.8792 (t) REVERT: B 588 GLN cc_start: 0.9556 (mm-40) cc_final: 0.9084 (mm-40) REVERT: B 610 LYS cc_start: 0.9160 (ptpt) cc_final: 0.8740 (ptmm) REVERT: B 615 MET cc_start: 0.9386 (mmp) cc_final: 0.9091 (mmm) REVERT: B 640 MET cc_start: 0.9493 (tpp) cc_final: 0.9175 (tpp) REVERT: B 659 LYS cc_start: 0.7776 (tptt) cc_final: 0.7435 (tptt) REVERT: C 44 TRP cc_start: 0.7505 (t-100) cc_final: 0.7181 (t-100) REVERT: C 96 MET cc_start: 0.6874 (mmm) cc_final: 0.6209 (mmm) REVERT: C 174 TYR cc_start: 0.4634 (OUTLIER) cc_final: 0.4320 (t80) REVERT: C 242 TYR cc_start: 0.3481 (t80) cc_final: 0.3110 (t80) REVERT: C 245 ASP cc_start: 0.8409 (t70) cc_final: 0.8093 (m-30) REVERT: D 46 TYR cc_start: 0.9443 (m-80) cc_final: 0.8878 (m-10) REVERT: D 80 HIS cc_start: 0.8235 (m90) cc_final: 0.7402 (t-90) REVERT: D 93 MET cc_start: 0.7640 (ppp) cc_final: 0.6929 (pmm) REVERT: D 95 MET cc_start: 0.8052 (tmm) cc_final: 0.7333 (tmm) REVERT: D 96 MET cc_start: 0.7161 (mmt) cc_final: 0.6825 (mmt) REVERT: D 98 ASN cc_start: 0.8361 (m-40) cc_final: 0.7988 (m110) REVERT: D 100 VAL cc_start: 0.8123 (OUTLIER) cc_final: 0.7792 (p) REVERT: D 110 MET cc_start: 0.8298 (ppp) cc_final: 0.7717 (ptp) REVERT: D 162 TYR cc_start: 0.9092 (m-10) cc_final: 0.8648 (m-80) REVERT: D 173 TYR cc_start: 0.7625 (t80) cc_final: 0.6775 (t80) REVERT: D 174 TYR cc_start: 0.8770 (OUTLIER) cc_final: 0.8374 (t80) REVERT: D 185 MET cc_start: 0.7134 (mmm) cc_final: 0.6876 (mmm) REVERT: D 196 ARG cc_start: 0.8548 (ptp-170) cc_final: 0.8173 (ptp-170) REVERT: D 227 PHE cc_start: 0.8929 (m-80) cc_final: 0.8574 (m-80) REVERT: D 242 TYR cc_start: 0.8701 (OUTLIER) cc_final: 0.8365 (m-80) outliers start: 84 outliers final: 58 residues processed: 668 average time/residue: 0.1133 time to fit residues: 115.7045 Evaluate side-chains 681 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 609 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 124 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 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 384 GLU Chi-restraints excluded: chain A residue 409 CYS 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 597 ILE Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 11 GLN Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 106 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 246 SER Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 314 MET 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 417 LEU 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 B residue 687 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 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 89 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 107 ASN 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 150 GLU Chi-restraints excluded: chain D residue 174 TYR 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 Chi-restraints excluded: chain D residue 315 LEU 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: 2.9990 chunk 149 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 114 optimal weight: 0.6980 chunk 86 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN B 11 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN D 107 ASN D 127 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.138279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.097595 restraints weight = 36030.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.101203 restraints weight = 17308.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.103521 restraints weight = 10385.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.104957 restraints weight = 7219.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.105943 restraints weight = 5615.415| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.7429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16386 Z= 0.159 Angle : 0.805 14.294 22134 Z= 0.409 Chirality : 0.050 0.357 2360 Planarity : 0.004 0.081 2818 Dihedral : 8.224 136.114 2294 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.43 % Allowed : 32.11 % Favored : 63.46 % 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: 0.41 (0.18), residues: 1932 helix: 0.62 (0.15), residues: 1153 sheet: -0.49 (0.42), residues: 150 loop : 0.09 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 164 TYR 0.058 0.002 TYR D 22 PHE 0.039 0.002 PHE D 168 TRP 0.030 0.002 TRP C 124 HIS 0.013 0.002 HIS A 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (16386) covalent geometry : angle 0.80522 / 0.41 (22134) hydrogen bonds : bond 0.04344 / 2.78 ( 871) hydrogen bonds : angle 5.29127 / 3.82 ( 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 700 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 624 time to evaluate : 0.633 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: A 65 GLU cc_start: 0.8703 (mm-30) cc_final: 0.7981 (mp0) REVERT: A 119 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8101 (mt-10) REVERT: A 144 MET cc_start: 0.8909 (mtm) cc_final: 0.8441 (mtt) REVERT: A 161 ARG cc_start: 0.8467 (ttm110) cc_final: 0.8184 (ttm110) REVERT: A 184 ARG cc_start: 0.9161 (mmm-85) cc_final: 0.8884 (tpt90) REVERT: A 221 LYS cc_start: 0.9460 (mmtp) cc_final: 0.8801 (mptt) REVERT: A 228 LYS cc_start: 0.9262 (mmmm) cc_final: 0.8415 (mmmt) REVERT: A 232 ASN cc_start: 0.9431 (m-40) cc_final: 0.8683 (m-40) REVERT: A 286 ASP cc_start: 0.8731 (m-30) cc_final: 0.8470 (m-30) REVERT: A 290 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8368 (tm-30) REVERT: A 321 GLU cc_start: 0.9066 (tp30) cc_final: 0.8760 (tp30) REVERT: A 341 LYS cc_start: 0.9153 (OUTLIER) cc_final: 0.8827 (mmtm) REVERT: A 348 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8087 (tmm) REVERT: A 361 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8661 (tp40) REVERT: A 362 ASP cc_start: 0.8437 (m-30) cc_final: 0.8073 (m-30) REVERT: A 384 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7554 (pm20) REVERT: A 390 GLN cc_start: 0.8931 (mt0) cc_final: 0.8697 (mt0) REVERT: A 400 GLU cc_start: 0.8388 (pp20) cc_final: 0.8115 (pp20) REVERT: A 402 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8223 (mm-30) REVERT: A 441 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8478 (mm-30) REVERT: A 459 LYS cc_start: 0.8827 (mtmm) cc_final: 0.8398 (ttmm) REVERT: A 515 ASP cc_start: 0.9025 (m-30) cc_final: 0.8668 (m-30) REVERT: A 570 MET cc_start: 0.9321 (mtp) cc_final: 0.8953 (mtp) REVERT: A 576 LEU cc_start: 0.9013 (mt) cc_final: 0.8701 (mt) REVERT: A 604 ARG cc_start: 0.8379 (ttm110) cc_final: 0.8094 (tpp80) REVERT: A 615 MET cc_start: 0.9271 (mmp) cc_final: 0.8737 (mmp) REVERT: A 636 LYS cc_start: 0.9583 (mmtp) cc_final: 0.9247 (mmmt) REVERT: A 640 MET cc_start: 0.9679 (OUTLIER) cc_final: 0.8942 (tpp) REVERT: A 646 GLN cc_start: 0.9366 (pt0) cc_final: 0.8639 (pm20) REVERT: A 668 ASN cc_start: 0.9646 (m-40) cc_final: 0.9334 (m-40) REVERT: B 31 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8502 (mp0) REVERT: B 65 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8176 (mm-30) REVERT: B 95 MET cc_start: 0.9157 (tpp) cc_final: 0.8686 (tpp) REVERT: B 112 LYS cc_start: 0.9465 (mmmt) cc_final: 0.9136 (mmmt) REVERT: B 116 GLU cc_start: 0.8837 (mt-10) cc_final: 0.8548 (mt-10) REVERT: B 119 GLU cc_start: 0.8995 (mp0) cc_final: 0.8365 (mp0) REVERT: B 128 PHE cc_start: 0.9566 (t80) cc_final: 0.9244 (t80) REVERT: B 147 GLN cc_start: 0.9538 (mt0) cc_final: 0.9032 (mm-40) REVERT: B 149 TYR cc_start: 0.9311 (t80) cc_final: 0.8469 (t80) REVERT: B 157 LEU cc_start: 0.9355 (tp) cc_final: 0.9129 (tp) REVERT: B 161 ARG cc_start: 0.8324 (ttm110) cc_final: 0.7260 (ttm110) REVERT: B 166 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8678 (mm-30) REVERT: B 211 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7654 (mm-30) REVERT: B 214 LYS cc_start: 0.8892 (ttmm) cc_final: 0.8274 (mmtp) REVERT: B 257 ASP cc_start: 0.9169 (m-30) cc_final: 0.8632 (m-30) REVERT: B 263 ASP cc_start: 0.9134 (m-30) cc_final: 0.8753 (m-30) REVERT: B 267 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.8997 (pp) REVERT: B 290 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8456 (pp20) REVERT: B 296 LYS cc_start: 0.9281 (mttt) cc_final: 0.8955 (mmmt) REVERT: B 312 GLN cc_start: 0.8873 (mp10) cc_final: 0.8602 (pm20) REVERT: B 322 MET cc_start: 0.9656 (mmm) cc_final: 0.9436 (tpp) REVERT: B 333 LYS cc_start: 0.8820 (tttt) cc_final: 0.8421 (ttmm) REVERT: B 359 MET cc_start: 0.9106 (ttt) cc_final: 0.8772 (tmm) REVERT: B 392 SER cc_start: 0.9407 (m) cc_final: 0.8972 (p) REVERT: B 394 TYR cc_start: 0.9420 (m-80) cc_final: 0.9096 (m-80) REVERT: B 396 ASP cc_start: 0.8221 (p0) cc_final: 0.7838 (p0) REVERT: B 415 ASN cc_start: 0.9218 (t0) cc_final: 0.8956 (t0) REVERT: B 443 THR cc_start: 0.9438 (OUTLIER) cc_final: 0.9180 (m) REVERT: B 459 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8657 (mtmm) REVERT: B 466 MET cc_start: 0.8995 (ptp) cc_final: 0.8702 (ptp) REVERT: B 467 ASN cc_start: 0.8851 (t0) cc_final: 0.8632 (m-40) REVERT: B 471 TYR cc_start: 0.9091 (t80) cc_final: 0.8504 (t80) REVERT: B 483 GLU cc_start: 0.9338 (mp0) cc_final: 0.8953 (mp0) REVERT: B 493 MET cc_start: 0.9599 (tmm) cc_final: 0.9230 (tmm) REVERT: B 585 SER cc_start: 0.9361 (p) cc_final: 0.8779 (t) REVERT: B 610 LYS cc_start: 0.9151 (ptpt) cc_final: 0.8715 (ptmm) REVERT: B 615 MET cc_start: 0.9401 (mmp) cc_final: 0.9088 (mmm) REVERT: B 632 MET cc_start: 0.8860 (mtp) cc_final: 0.8264 (mtp) REVERT: B 633 ASP cc_start: 0.8774 (t0) cc_final: 0.8471 (t0) REVERT: B 640 MET cc_start: 0.9487 (tpp) cc_final: 0.9262 (tpp) REVERT: B 659 LYS cc_start: 0.7552 (tptt) cc_final: 0.7272 (tptt) REVERT: B 664 THR cc_start: 0.9221 (p) cc_final: 0.8943 (p) REVERT: C 44 TRP cc_start: 0.7325 (t-100) cc_final: 0.6781 (t-100) REVERT: C 96 MET cc_start: 0.6941 (mmm) cc_final: 0.6318 (mmm) REVERT: C 174 TYR cc_start: 0.4624 (OUTLIER) cc_final: 0.4268 (t80) REVERT: C 242 TYR cc_start: 0.3402 (t80) cc_final: 0.3034 (t80) REVERT: C 245 ASP cc_start: 0.8430 (t70) cc_final: 0.8106 (m-30) REVERT: D 46 TYR cc_start: 0.9417 (m-10) cc_final: 0.8856 (m-10) REVERT: D 80 HIS cc_start: 0.8212 (m90) cc_final: 0.7497 (t-90) REVERT: D 93 MET cc_start: 0.7395 (ppp) cc_final: 0.6307 (pmm) REVERT: D 95 MET cc_start: 0.8000 (tmm) cc_final: 0.6981 (tmm) REVERT: D 96 MET cc_start: 0.7036 (mmt) cc_final: 0.6783 (mmt) REVERT: D 100 VAL cc_start: 0.8206 (OUTLIER) cc_final: 0.7890 (p) REVERT: D 110 MET cc_start: 0.8273 (ppp) cc_final: 0.7719 (ptp) REVERT: D 162 TYR cc_start: 0.9053 (m-10) cc_final: 0.8616 (m-80) REVERT: D 173 TYR cc_start: 0.7693 (t80) cc_final: 0.7000 (t80) REVERT: D 174 TYR cc_start: 0.8702 (OUTLIER) cc_final: 0.8171 (t80) REVERT: D 185 MET cc_start: 0.7119 (mmm) cc_final: 0.6915 (mmm) REVERT: D 196 ARG cc_start: 0.8540 (ptp-170) cc_final: 0.8110 (ptp-170) REVERT: D 214 ASN cc_start: 0.9468 (m-40) cc_final: 0.9099 (p0) REVERT: D 227 PHE cc_start: 0.8953 (m-80) cc_final: 0.8546 (m-80) REVERT: D 242 TYR cc_start: 0.8694 (OUTLIER) cc_final: 0.8387 (m-80) outliers start: 76 outliers final: 54 residues processed: 656 average time/residue: 0.1160 time to fit residues: 115.9182 Evaluate side-chains 667 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 600 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 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 317 MET 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 409 CYS 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 597 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 193 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 417 LEU 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 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 250 VAL Chi-restraints excluded: chain C residue 312 VAL 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 127 GLN Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 198 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 Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 4.9990 chunk 62 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 189 optimal weight: 0.5980 chunk 181 optimal weight: 10.0000 chunk 165 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 54 optimal weight: 0.0980 chunk 132 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN C 214 ASN ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN D 127 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.140258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.099075 restraints weight = 35871.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.102594 restraints weight = 17865.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.104951 restraints weight = 10835.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.106492 restraints weight = 7569.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.107438 restraints weight = 5872.117| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3280 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.7694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16386 Z= 0.157 Angle : 0.823 14.597 22134 Z= 0.416 Chirality : 0.051 0.376 2360 Planarity : 0.004 0.061 2818 Dihedral : 8.184 136.929 2294 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.85 % Allowed : 33.16 % Favored : 63.00 % 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: 0.42 (0.18), residues: 1932 helix: 0.66 (0.15), residues: 1136 sheet: -0.21 (0.43), residues: 144 loop : -0.06 (0.23), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 164 TYR 0.064 0.002 TYR D 22 PHE 0.038 0.002 PHE D 168 TRP 0.026 0.001 TRP C 124 HIS 0.016 0.002 HIS A 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.16 (16386) covalent geometry : angle 0.82292 / 0.42 (22134) hydrogen bonds : bond 0.04342 / 2.77 ( 871) hydrogen bonds : angle 5.36587 / 3.87 ( 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 706 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 640 time to evaluate : 0.523 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: A 31 GLU cc_start: 0.8970 (pt0) cc_final: 0.8769 (pm20) REVERT: A 65 GLU cc_start: 0.8757 (mm-30) cc_final: 0.8038 (mp0) REVERT: A 95 MET cc_start: 0.9420 (tpp) cc_final: 0.9173 (tpp) REVERT: A 109 ASN cc_start: 0.9022 (m-40) cc_final: 0.8722 (m-40) REVERT: A 119 GLU cc_start: 0.8531 (mt-10) cc_final: 0.8134 (mt-10) REVERT: A 144 MET cc_start: 0.8867 (mtm) cc_final: 0.8374 (mtt) REVERT: A 184 ARG cc_start: 0.9162 (mmm-85) cc_final: 0.8871 (tpt90) REVERT: A 221 LYS cc_start: 0.9466 (mmtp) cc_final: 0.8842 (mttp) REVERT: A 228 LYS cc_start: 0.9265 (mmmm) cc_final: 0.8398 (mmmt) REVERT: A 232 ASN cc_start: 0.9417 (m-40) cc_final: 0.8702 (m-40) REVERT: A 250 TYR cc_start: 0.8653 (m-10) cc_final: 0.8425 (m-10) REVERT: A 290 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8311 (tm-30) REVERT: A 318 ASP cc_start: 0.8857 (t0) cc_final: 0.8494 (p0) REVERT: A 341 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8815 (mmtm) REVERT: A 348 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8067 (tmm) REVERT: A 362 ASP cc_start: 0.8357 (m-30) cc_final: 0.8140 (m-30) REVERT: A 384 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7719 (pm20) REVERT: A 390 GLN cc_start: 0.8981 (mt0) cc_final: 0.8732 (mt0) REVERT: A 399 GLU cc_start: 0.8112 (tp30) cc_final: 0.7003 (tp30) REVERT: A 420 MET cc_start: 0.9261 (mmm) cc_final: 0.8886 (mmm) REVERT: A 436 LEU cc_start: 0.9392 (mm) cc_final: 0.9116 (mm) REVERT: A 441 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8569 (mt-10) REVERT: A 458 MET cc_start: 0.8546 (mmp) cc_final: 0.7914 (mmp) REVERT: A 459 LYS cc_start: 0.8822 (mtmm) cc_final: 0.8471 (ttmm) REVERT: A 515 ASP cc_start: 0.9020 (m-30) cc_final: 0.8634 (m-30) REVERT: A 552 ILE cc_start: 0.8070 (mm) cc_final: 0.7793 (tp) REVERT: A 576 LEU cc_start: 0.9084 (mt) cc_final: 0.8762 (mt) REVERT: A 604 ARG cc_start: 0.8250 (ttm110) cc_final: 0.7987 (tpp80) REVERT: A 610 LYS cc_start: 0.9271 (ttpp) cc_final: 0.8820 (ttmm) REVERT: A 615 MET cc_start: 0.9253 (mmp) cc_final: 0.8726 (mmp) REVERT: A 636 LYS cc_start: 0.9575 (mmtp) cc_final: 0.9240 (mmmt) REVERT: A 640 MET cc_start: 0.9639 (OUTLIER) cc_final: 0.8979 (tpp) REVERT: A 668 ASN cc_start: 0.9620 (m-40) cc_final: 0.9323 (m-40) REVERT: B 31 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8486 (mt-10) REVERT: B 65 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8201 (mm-30) REVERT: B 95 MET cc_start: 0.9163 (tpp) cc_final: 0.8245 (tpp) REVERT: B 99 LYS cc_start: 0.9339 (mmtt) cc_final: 0.8601 (tppp) REVERT: B 112 LYS cc_start: 0.9437 (mmmt) cc_final: 0.9151 (mmmt) REVERT: B 116 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8562 (mt-10) REVERT: B 119 GLU cc_start: 0.8985 (mp0) cc_final: 0.8357 (mp0) REVERT: B 128 PHE cc_start: 0.9546 (t80) cc_final: 0.9214 (t80) REVERT: B 147 GLN cc_start: 0.9549 (mt0) cc_final: 0.9059 (mm-40) REVERT: B 149 TYR cc_start: 0.9299 (t80) cc_final: 0.8473 (t80) REVERT: B 157 LEU cc_start: 0.9368 (tp) cc_final: 0.9112 (tp) REVERT: B 161 ARG cc_start: 0.8431 (ttm110) cc_final: 0.7417 (ttm110) REVERT: B 214 LYS cc_start: 0.8913 (ttmm) cc_final: 0.8311 (mmtp) REVERT: B 257 ASP cc_start: 0.9157 (m-30) cc_final: 0.8693 (m-30) REVERT: B 263 ASP cc_start: 0.9113 (m-30) cc_final: 0.8731 (m-30) REVERT: B 267 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8959 (pp) REVERT: B 290 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8465 (pp20) REVERT: B 296 LYS cc_start: 0.9287 (mttt) cc_final: 0.8970 (mmmt) REVERT: B 312 GLN cc_start: 0.8799 (mp10) cc_final: 0.8489 (pm20) REVERT: B 322 MET cc_start: 0.9674 (mmm) cc_final: 0.9431 (tpp) REVERT: B 333 LYS cc_start: 0.8831 (tttt) cc_final: 0.8462 (ttmm) REVERT: B 357 TYR cc_start: 0.8443 (m-10) cc_final: 0.8088 (m-10) REVERT: B 359 MET cc_start: 0.9075 (ttt) cc_final: 0.8803 (tmm) REVERT: B 361 GLN cc_start: 0.9002 (tt0) cc_final: 0.8782 (tt0) REVERT: B 392 SER cc_start: 0.9397 (m) cc_final: 0.8796 (p) REVERT: B 394 TYR cc_start: 0.9381 (m-80) cc_final: 0.9030 (m-80) REVERT: B 396 ASP cc_start: 0.8114 (p0) cc_final: 0.7733 (p0) REVERT: B 415 ASN cc_start: 0.9239 (t0) cc_final: 0.8988 (t0) REVERT: B 459 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.8669 (mtmm) REVERT: B 466 MET cc_start: 0.8974 (ptp) cc_final: 0.8659 (ptp) REVERT: B 467 ASN cc_start: 0.8834 (t0) cc_final: 0.8632 (m-40) REVERT: B 471 TYR cc_start: 0.8995 (t80) cc_final: 0.8447 (t80) REVERT: B 493 MET cc_start: 0.9598 (tmm) cc_final: 0.9255 (tmm) REVERT: B 494 MET cc_start: 0.9321 (mmt) cc_final: 0.9007 (mmp) REVERT: B 548 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8381 (mm-30) REVERT: B 615 MET cc_start: 0.9377 (mmp) cc_final: 0.9034 (mmm) REVERT: B 633 ASP cc_start: 0.8699 (t0) cc_final: 0.8261 (t0) REVERT: C 96 MET cc_start: 0.6669 (mmm) cc_final: 0.6091 (mmm) REVERT: C 174 TYR cc_start: 0.4610 (OUTLIER) cc_final: 0.4276 (t80) REVERT: C 242 TYR cc_start: 0.3372 (t80) cc_final: 0.2976 (t80) REVERT: C 245 ASP cc_start: 0.8459 (t70) cc_final: 0.8136 (m-30) REVERT: D 46 TYR cc_start: 0.9374 (m-10) cc_final: 0.8847 (m-10) REVERT: D 80 HIS cc_start: 0.8172 (m90) cc_final: 0.7329 (t-90) REVERT: D 93 MET cc_start: 0.6810 (ppp) cc_final: 0.6069 (pmm) REVERT: D 95 MET cc_start: 0.7851 (tmm) cc_final: 0.6849 (tmm) REVERT: D 98 ASN cc_start: 0.7726 (m-40) cc_final: 0.7482 (m110) REVERT: D 100 VAL cc_start: 0.8158 (OUTLIER) cc_final: 0.7892 (p) REVERT: D 110 MET cc_start: 0.8296 (ppp) cc_final: 0.7743 (ptp) REVERT: D 162 TYR cc_start: 0.8932 (m-10) cc_final: 0.8484 (m-80) REVERT: D 173 TYR cc_start: 0.7654 (t80) cc_final: 0.6911 (t80) REVERT: D 174 TYR cc_start: 0.8736 (OUTLIER) cc_final: 0.8080 (t80) REVERT: D 214 ASN cc_start: 0.9467 (m-40) cc_final: 0.9131 (p0) REVERT: D 227 PHE cc_start: 0.8973 (m-80) cc_final: 0.8699 (m-80) REVERT: D 242 TYR cc_start: 0.8719 (OUTLIER) cc_final: 0.8436 (m-80) outliers start: 66 outliers final: 47 residues processed: 667 average time/residue: 0.1199 time to fit residues: 121.5321 Evaluate side-chains 668 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 610 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 93 SER 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 317 MET 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 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 550 MET Chi-restraints excluded: chain A residue 597 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 193 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 611 THR 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 142 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 43 THR 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 107 ASN Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 198 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 Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 148 optimal weight: 6.9990 chunk 125 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 127 GLN C 214 ASN ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.136694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.095943 restraints weight = 36311.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.099411 restraints weight = 17637.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.101676 restraints weight = 10695.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 61)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.103133 restraints weight = 7483.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.104056 restraints weight = 5804.176| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3216 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (11 function evaluations) r_final: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.7787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 16386 Z= 0.212 Angle : 0.857 12.830 22134 Z= 0.439 Chirality : 0.052 0.304 2360 Planarity : 0.005 0.064 2818 Dihedral : 8.244 138.814 2291 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.90 % Allowed : 33.39 % Favored : 62.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.27 (0.18), residues: 1932 helix: 0.59 (0.15), residues: 1138 sheet: -0.66 (0.41), residues: 160 loop : -0.10 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 207 TYR 0.060 0.002 TYR D 22 PHE 0.039 0.002 PHE B 261 TRP 0.053 0.003 TRP C 44 HIS 0.018 0.002 HIS A 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 (16386) covalent geometry : angle 0.85732 / 0.44 (22134) hydrogen bonds : bond 0.04462 / 2.82 ( 871) hydrogen bonds : angle 5.41117 / 3.92 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3401.90 seconds wall clock time: 59 minutes 39.06 seconds (3579.06 seconds total)