Starting phenix.real_space_refine on Fri Jul 3 19:45:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz9_45057/07_2026/9bz9_45057_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz9_45057/07_2026/9bz9_45057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bz9_45057/07_2026/9bz9_45057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz9_45057/07_2026/9bz9_45057.map" model { file = "/net/cci-nas-00/data/ceres_data/9bz9_45057/07_2026/9bz9_45057_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz9_45057/07_2026/9bz9_45057_neut.cif" } resolution = 4.64 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 68 residue(s): 0.02s 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: 3.54, per 1000 atoms: 0.22 Number of scatterers: 16038 At special positions: 0 Unit cell: (93.288, 124.722, 129.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 670.0 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 64.1% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 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: 3.954A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.665A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.947A 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: 4.851A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.627A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A 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: 3.878A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.026A 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: 3.634A 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: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 181 removed outlier: 4.936A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix removed outlier: 3.576A pdb=" N GLN C 181 " --> pdb=" O TYR C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.567A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.668A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.359A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.425A 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: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A 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 605 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.478A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.184A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.048A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.907A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.345A 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: 7.806A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 871 hydrogen bonds defined for protein. 2568 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: 2.88 Time building geometry restraints manager: 1.55 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: 4857 1.34 - 1.46: 3044 1.46 - 1.58: 8304 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 4.80e+01 bond pdb=" O3B TTP A 803 " pdb=" PG TTP A 803 " ideal model delta sigma weight residual 1.748 1.610 0.138 2.00e-02 2.50e+03 4.77e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.600 -0.060 1.25e-02 6.40e+03 2.33e+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 1.19e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.608 0.067 2.00e-02 2.50e+03 1.12e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21515 2.09 - 4.19: 527 4.19 - 6.28: 71 6.28 - 8.38: 11 8.38 - 10.47: 10 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N SER A 609 " pdb=" CA SER A 609 " pdb=" C SER A 609 " ideal model delta sigma weight residual 110.41 119.07 -8.66 1.23e+00 6.61e-01 4.96e+01 angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.59 -6.05 1.36e+00 5.41e-01 1.98e+01 angle pdb=" C ASN A 608 " pdb=" N SER A 609 " pdb=" CA SER A 609 " ideal model delta sigma weight residual 121.06 129.21 -8.15 1.88e+00 2.83e-01 1.88e+01 angle pdb=" N ASN C 288 " pdb=" CA ASN C 288 " pdb=" CB ASN C 288 " ideal model delta sigma weight residual 110.39 103.68 6.71 1.66e+00 3.63e-01 1.63e+01 angle pdb=" N SER A 609 " pdb=" CA SER A 609 " pdb=" CB SER A 609 " ideal model delta sigma weight residual 110.38 104.92 5.46 1.37e+00 5.33e-01 1.59e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.04: 9090 25.04 - 50.08: 654 50.08 - 75.12: 126 75.12 - 100.16: 26 100.16 - 125.20: 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 -98.18 125.20 1 2.00e+01 2.50e-03 3.78e+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 -95.55 122.57 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 -134.25 12.25 0 2.50e+00 1.60e-01 2.40e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2145 0.094 - 0.187: 183 0.187 - 0.281: 28 0.281 - 0.374: 2 0.374 - 0.468: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.47e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.58e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 288 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.58e+00 pdb=" C ASN C 288 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN C 288 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY C 289 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 609 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.23e+00 pdb=" C SER A 609 " -0.040 2.00e-02 2.50e+03 pdb=" O SER A 609 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS A 610 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 608 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" CG ASN A 608 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN A 608 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 608 " 0.010 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 130 2.51 - 3.11: 11584 3.11 - 3.70: 27097 3.70 - 4.30: 41576 4.30 - 4.90: 65504 Nonbonded interactions: 145891 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 1.961 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.964 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 145886 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.560 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5824 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= 0.336 Angle : 0.800 10.473 22134 Z= 0.480 Chirality : 0.058 0.468 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.663 125.204 6202 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: 0.59 (0.14), residues: 1151 sheet: 0.45 (0.41), residues: 128 loop : 0.21 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 168 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 0.00598 / 0.34 (16386) covalent geometry : angle 0.80017 / 0.48 (22134) hydrogen bonds : bond 0.15437 / 9.58 ( 869) hydrogen bonds : angle 6.52098 / 4.65 ( 2568) *********************** 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 926 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 902 time to evaluate : 0.662 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: A 33 VAL cc_start: 0.8856 (t) cc_final: 0.8411 (t) REVERT: A 51 LEU cc_start: 0.8122 (tp) cc_final: 0.7517 (tp) REVERT: A 81 PHE cc_start: 0.7597 (m-80) cc_final: 0.7373 (m-80) REVERT: A 125 VAL cc_start: 0.9045 (t) cc_final: 0.7561 (t) REVERT: A 143 LEU cc_start: 0.9043 (tp) cc_final: 0.8603 (tp) REVERT: A 166 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8065 (mm-30) REVERT: A 181 ASP cc_start: 0.8496 (m-30) cc_final: 0.8081 (m-30) REVERT: A 213 ILE cc_start: 0.8120 (mt) cc_final: 0.7582 (mp) REVERT: A 224 VAL cc_start: 0.8883 (t) cc_final: 0.7943 (p) REVERT: A 283 VAL cc_start: 0.8505 (t) cc_final: 0.7257 (t) REVERT: A 288 PHE cc_start: 0.7249 (t80) cc_final: 0.6809 (t80) REVERT: A 300 VAL cc_start: 0.7424 (m) cc_final: 0.7081 (m) REVERT: A 322 MET cc_start: 0.7645 (mmp) cc_final: 0.6459 (mmm) REVERT: A 342 LEU cc_start: 0.9170 (tp) cc_final: 0.8685 (tp) REVERT: A 348 MET cc_start: 0.8437 (tmm) cc_final: 0.8148 (tmm) REVERT: A 360 PHE cc_start: 0.7566 (m-80) cc_final: 0.7296 (m-10) REVERT: A 362 ASP cc_start: 0.6185 (m-30) cc_final: 0.4945 (m-30) REVERT: A 367 VAL cc_start: 0.8092 (m) cc_final: 0.7842 (m) REVERT: A 370 ASN cc_start: 0.7524 (m-40) cc_final: 0.6769 (m-40) REVERT: A 416 ILE cc_start: 0.8779 (mt) cc_final: 0.8556 (mt) REVERT: A 431 LEU cc_start: 0.8996 (mt) cc_final: 0.8657 (mm) REVERT: A 436 LEU cc_start: 0.9252 (mt) cc_final: 0.8890 (mt) REVERT: A 500 ILE cc_start: 0.9201 (mt) cc_final: 0.8593 (mt) REVERT: A 550 MET cc_start: 0.6900 (mtm) cc_final: 0.6695 (mtp) REVERT: A 634 MET cc_start: 0.8337 (mmp) cc_final: 0.7981 (mpp) REVERT: A 641 ILE cc_start: 0.9277 (mm) cc_final: 0.9031 (mm) REVERT: A 652 ILE cc_start: 0.8789 (mt) cc_final: 0.8486 (mt) REVERT: A 653 SER cc_start: 0.9052 (OUTLIER) cc_final: 0.8703 (p) REVERT: A 682 ILE cc_start: 0.8321 (mt) cc_final: 0.8049 (mt) REVERT: B 41 ILE cc_start: 0.8853 (mm) cc_final: 0.8168 (mt) REVERT: B 51 LEU cc_start: 0.8561 (tp) cc_final: 0.8189 (tp) REVERT: B 95 MET cc_start: 0.7883 (tpp) cc_final: 0.7677 (tpp) REVERT: B 98 PHE cc_start: 0.7798 (t80) cc_final: 0.7464 (t80) REVERT: B 99 LYS cc_start: 0.9167 (mmtt) cc_final: 0.8345 (mmmm) REVERT: B 100 PHE cc_start: 0.7911 (t80) cc_final: 0.7617 (t80) REVERT: B 101 TYR cc_start: 0.7554 (m-80) cc_final: 0.7060 (m-80) REVERT: B 143 LEU cc_start: 0.9038 (tp) cc_final: 0.8825 (tp) REVERT: B 149 TYR cc_start: 0.8345 (t80) cc_final: 0.7632 (t80) REVERT: B 179 LEU cc_start: 0.8607 (tp) cc_final: 0.7581 (tp) REVERT: B 191 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8176 (mm-40) REVERT: B 213 ILE cc_start: 0.8783 (mt) cc_final: 0.8573 (tp) REVERT: B 232 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.8049 (m-40) REVERT: B 240 MET cc_start: 0.6884 (mpt) cc_final: 0.6327 (mpt) REVERT: B 288 PHE cc_start: 0.7313 (t80) cc_final: 0.6320 (t80) REVERT: B 322 MET cc_start: 0.7357 (mmm) cc_final: 0.5747 (tpp) REVERT: B 337 ILE cc_start: 0.8308 (pt) cc_final: 0.8013 (pt) REVERT: B 361 GLN cc_start: 0.6689 (tt0) cc_final: 0.6386 (tt0) REVERT: B 362 ASP cc_start: 0.6252 (m-30) cc_final: 0.5525 (m-30) REVERT: B 373 ILE cc_start: 0.9065 (mt) cc_final: 0.8326 (mt) REVERT: B 415 ASN cc_start: 0.8552 (t0) cc_final: 0.7839 (t0) REVERT: B 418 ASN cc_start: 0.7652 (m-40) cc_final: 0.6534 (m-40) REVERT: B 425 ILE cc_start: 0.9268 (mt) cc_final: 0.8740 (mt) REVERT: B 436 LEU cc_start: 0.9378 (mt) cc_final: 0.9100 (mt) REVERT: B 493 MET cc_start: 0.7437 (tmm) cc_final: 0.7141 (tmm) REVERT: B 494 MET cc_start: 0.7842 (mtp) cc_final: 0.7587 (mtp) REVERT: B 496 ASN cc_start: 0.7072 (t0) cc_final: 0.5334 (t0) REVERT: B 565 VAL cc_start: 0.9293 (t) cc_final: 0.9093 (p) REVERT: B 575 ARG cc_start: 0.7594 (mtm110) cc_final: 0.6953 (mtm180) REVERT: B 588 GLN cc_start: 0.7455 (mm-40) cc_final: 0.6997 (mm-40) REVERT: B 601 ILE cc_start: 0.7785 (mt) cc_final: 0.7236 (mt) REVERT: B 613 TYR cc_start: 0.7838 (t80) cc_final: 0.7531 (t80) REVERT: B 641 ILE cc_start: 0.9444 (mm) cc_final: 0.9126 (mm) REVERT: B 656 LEU cc_start: 0.8212 (mt) cc_final: 0.7882 (mt) REVERT: C 85 GLN cc_start: 0.5803 (mt0) cc_final: 0.4903 (tt0) REVERT: C 90 LEU cc_start: 0.5509 (mt) cc_final: 0.4962 (mt) REVERT: C 137 MET cc_start: 0.4147 (mtp) cc_final: 0.3338 (mtt) REVERT: C 194 ILE cc_start: 0.7431 (mt) cc_final: 0.7175 (mp) REVERT: C 205 VAL cc_start: 0.7608 (t) cc_final: 0.7316 (t) REVERT: C 275 PRO cc_start: 0.5456 (Cg_endo) cc_final: 0.4948 (Cg_exo) REVERT: D 31 LEU cc_start: 0.8392 (mt) cc_final: 0.8033 (mt) REVERT: D 100 VAL cc_start: 0.3534 (t) cc_final: 0.3147 (t) REVERT: D 205 VAL cc_start: 0.7168 (t) cc_final: 0.6763 (t) REVERT: D 317 ASP cc_start: 0.6461 (t0) cc_final: 0.5765 (t70) outliers start: 24 outliers final: 5 residues processed: 915 average time/residue: 0.1341 time to fit residues: 177.2933 Evaluate side-chains 631 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 624 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.0370 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 overall best weight: 3.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 GLN A 43 GLN A 147 GLN A 239 GLN A 320 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 232 ASN B 304 HIS ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN C 25 ASN C 84 HIS C 119 ASN C 132 GLN D 71 ASN D 80 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.109756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.076401 restraints weight = 51461.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.079284 restraints weight = 30598.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.081300 restraints weight = 21322.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.082766 restraints weight = 16386.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.083724 restraints weight = 13391.079| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 13 (19 function evaluations) r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16386 Z= 0.255 Angle : 0.693 9.035 22134 Z= 0.376 Chirality : 0.044 0.312 2360 Planarity : 0.004 0.040 2818 Dihedral : 9.802 126.888 2290 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.29 % Allowed : 3.03 % Favored : 96.68 % 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: 1.14 (0.18), residues: 1932 helix: 1.17 (0.15), residues: 1116 sheet: 0.02 (0.40), residues: 126 loop : 0.43 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 452 TYR 0.028 0.002 TYR C 247 PHE 0.043 0.003 PHE D 178 TRP 0.014 0.002 TRP A 558 HIS 0.007 0.002 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.26 (16386) covalent geometry : angle 0.69299 / 0.38 (22134) hydrogen bonds : bond 0.04729 / 2.97 ( 869) hydrogen bonds : angle 5.22534 / 3.74 ( 2568) *********************** 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 703 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 698 time to evaluate : 0.578 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 18 ILE cc_start: 0.9734 (mm) cc_final: 0.9247 (mt) REVERT: A 65 GLU cc_start: 0.8404 (mm-30) cc_final: 0.8124 (mm-30) REVERT: A 87 LYS cc_start: 0.9218 (tptm) cc_final: 0.8949 (tptm) REVERT: A 107 LYS cc_start: 0.9398 (mttm) cc_final: 0.9163 (mmmt) REVERT: A 136 LYS cc_start: 0.9759 (mmpt) cc_final: 0.9467 (ttpt) REVERT: A 143 LEU cc_start: 0.9249 (tp) cc_final: 0.8989 (tp) REVERT: A 144 MET cc_start: 0.9324 (mtm) cc_final: 0.8853 (mtm) REVERT: A 145 ILE cc_start: 0.9431 (tp) cc_final: 0.9226 (tp) REVERT: A 194 LYS cc_start: 0.9447 (ttpt) cc_final: 0.9186 (ttpp) REVERT: A 236 TYR cc_start: 0.8864 (t80) cc_final: 0.8600 (t80) REVERT: A 252 ASN cc_start: 0.8567 (t0) cc_final: 0.8130 (t0) REVERT: A 254 PHE cc_start: 0.8381 (m-10) cc_final: 0.7966 (m-10) REVERT: A 279 SER cc_start: 0.7717 (m) cc_final: 0.7496 (p) REVERT: A 286 ASP cc_start: 0.9083 (m-30) cc_final: 0.8664 (m-30) REVERT: A 362 ASP cc_start: 0.8579 (m-30) cc_final: 0.8365 (m-30) REVERT: A 385 VAL cc_start: 0.9619 (t) cc_final: 0.9418 (t) REVERT: A 387 GLN cc_start: 0.8671 (mt0) cc_final: 0.8282 (mt0) REVERT: A 421 GLU cc_start: 0.9480 (tm-30) cc_final: 0.9267 (tm-30) REVERT: A 436 LEU cc_start: 0.9626 (mt) cc_final: 0.9402 (mt) REVERT: A 502 ARG cc_start: 0.9493 (tpt170) cc_final: 0.9234 (tpt90) REVERT: A 510 LYS cc_start: 0.9688 (mmmt) cc_final: 0.9057 (mmtm) REVERT: A 550 MET cc_start: 0.6468 (mtm) cc_final: 0.5334 (ptp) REVERT: A 571 TYR cc_start: 0.8902 (t80) cc_final: 0.8608 (t80) REVERT: A 572 HIS cc_start: 0.9516 (m90) cc_final: 0.9150 (m90) REVERT: A 598 MET cc_start: 0.8389 (ttt) cc_final: 0.7193 (ttm) REVERT: A 615 MET cc_start: 0.8915 (mmp) cc_final: 0.8512 (mmp) REVERT: A 626 TYR cc_start: 0.9133 (m-80) cc_final: 0.8750 (m-10) REVERT: A 634 MET cc_start: 0.9338 (mmp) cc_final: 0.9097 (mpp) REVERT: A 655 THR cc_start: 0.9442 (t) cc_final: 0.9089 (t) REVERT: A 667 LEU cc_start: 0.9453 (tt) cc_final: 0.9210 (tt) REVERT: A 683 TYR cc_start: 0.8494 (t80) cc_final: 0.7790 (t80) REVERT: B 19 GLN cc_start: 0.9349 (mt0) cc_final: 0.8876 (pp30) REVERT: B 51 LEU cc_start: 0.9462 (tp) cc_final: 0.9086 (tp) REVERT: B 77 ILE cc_start: 0.9765 (mt) cc_final: 0.9452 (mt) REVERT: B 87 LYS cc_start: 0.9298 (tptp) cc_final: 0.8981 (tptp) REVERT: B 89 PHE cc_start: 0.9279 (t80) cc_final: 0.9025 (t80) REVERT: B 95 MET cc_start: 0.9506 (tpp) cc_final: 0.8603 (tpp) REVERT: B 99 LYS cc_start: 0.9463 (mmmt) cc_final: 0.8755 (mmmt) REVERT: B 115 LEU cc_start: 0.9036 (mp) cc_final: 0.8799 (mp) REVERT: B 144 MET cc_start: 0.9639 (mtm) cc_final: 0.9031 (mtm) REVERT: B 149 TYR cc_start: 0.8975 (t80) cc_final: 0.8636 (t80) REVERT: B 150 GLN cc_start: 0.9052 (tp40) cc_final: 0.8742 (tp40) REVERT: B 161 ARG cc_start: 0.8819 (ttm110) cc_final: 0.8610 (mtt-85) REVERT: B 162 LYS cc_start: 0.9327 (tppt) cc_final: 0.8889 (mttm) REVERT: B 168 VAL cc_start: 0.9162 (t) cc_final: 0.8812 (p) REVERT: B 211 GLU cc_start: 0.8982 (mm-30) cc_final: 0.8087 (mt-10) REVERT: B 220 THR cc_start: 0.8153 (p) cc_final: 0.7463 (p) REVERT: B 236 TYR cc_start: 0.8830 (t80) cc_final: 0.8587 (t80) REVERT: B 259 ASN cc_start: 0.8911 (m-40) cc_final: 0.8703 (m-40) REVERT: B 267 ILE cc_start: 0.8799 (pt) cc_final: 0.8484 (pt) REVERT: B 286 ASP cc_start: 0.8979 (m-30) cc_final: 0.8249 (m-30) REVERT: B 317 MET cc_start: 0.8619 (pmm) cc_final: 0.8263 (pmm) REVERT: B 319 MET cc_start: 0.9214 (tpp) cc_final: 0.8893 (tpp) REVERT: B 321 GLU cc_start: 0.8703 (tm-30) cc_final: 0.8391 (tm-30) REVERT: B 322 MET cc_start: 0.8701 (mmm) cc_final: 0.7770 (mmm) REVERT: B 355 TYR cc_start: 0.9291 (m-10) cc_final: 0.8882 (m-10) REVERT: B 362 ASP cc_start: 0.8664 (m-30) cc_final: 0.7907 (m-30) REVERT: B 396 ASP cc_start: 0.7853 (p0) cc_final: 0.7507 (p0) REVERT: B 415 ASN cc_start: 0.9003 (t0) cc_final: 0.7733 (t0) REVERT: B 418 ASN cc_start: 0.9324 (m-40) cc_final: 0.8684 (m-40) REVERT: B 458 MET cc_start: 0.9445 (mmm) cc_final: 0.9024 (mmm) REVERT: B 467 ASN cc_start: 0.9278 (m-40) cc_final: 0.8931 (m110) REVERT: B 492 PHE cc_start: 0.9756 (m-80) cc_final: 0.9533 (m-80) REVERT: B 494 MET cc_start: 0.9424 (mtp) cc_final: 0.8629 (mtp) REVERT: B 496 ASN cc_start: 0.9726 (t0) cc_final: 0.9025 (t0) REVERT: B 499 SER cc_start: 0.9919 (t) cc_final: 0.9699 (p) REVERT: B 500 ILE cc_start: 0.9726 (mt) cc_final: 0.9471 (mt) REVERT: B 501 GLN cc_start: 0.9096 (tp-100) cc_final: 0.8568 (tp-100) REVERT: B 515 ASP cc_start: 0.9082 (m-30) cc_final: 0.8770 (m-30) REVERT: B 570 MET cc_start: 0.9248 (tpp) cc_final: 0.8687 (tpp) REVERT: B 574 TYR cc_start: 0.8342 (m-80) cc_final: 0.8091 (m-80) REVERT: B 575 ARG cc_start: 0.8828 (mtm110) cc_final: 0.8219 (mtm110) REVERT: B 588 GLN cc_start: 0.9363 (mm-40) cc_final: 0.8775 (mm-40) REVERT: B 601 ILE cc_start: 0.9262 (mt) cc_final: 0.8738 (mp) REVERT: B 615 MET cc_start: 0.9038 (mmp) cc_final: 0.8132 (mmp) REVERT: B 618 LEU cc_start: 0.8879 (mt) cc_final: 0.8582 (mt) REVERT: B 631 ASP cc_start: 0.9388 (t0) cc_final: 0.9172 (t0) REVERT: B 645 GLN cc_start: 0.8953 (tp40) cc_final: 0.8710 (tp-100) REVERT: C 21 PHE cc_start: 0.8778 (m-80) cc_final: 0.8131 (m-80) REVERT: C 46 TYR cc_start: 0.7797 (m-80) cc_final: 0.7528 (m-80) REVERT: C 89 VAL cc_start: 0.7545 (t) cc_final: 0.7301 (t) REVERT: C 96 MET cc_start: 0.6788 (mmt) cc_final: 0.6216 (mmt) REVERT: C 139 VAL cc_start: 0.8804 (p) cc_final: 0.8543 (t) REVERT: C 204 TYR cc_start: 0.9534 (t80) cc_final: 0.9082 (t80) REVERT: C 315 LEU cc_start: 0.8388 (mt) cc_final: 0.7917 (mt) REVERT: D 33 GLU cc_start: 0.9383 (mp0) cc_final: 0.9156 (mp0) REVERT: D 46 TYR cc_start: 0.8826 (m-80) cc_final: 0.8429 (m-80) REVERT: D 96 MET cc_start: 0.8429 (mmt) cc_final: 0.7802 (mmm) REVERT: D 109 PHE cc_start: 0.7539 (OUTLIER) cc_final: 0.7045 (m-80) REVERT: D 185 MET cc_start: 0.6685 (mmm) cc_final: 0.5955 (mmp) REVERT: D 259 PHE cc_start: 0.7792 (t80) cc_final: 0.7279 (t80) REVERT: D 317 ASP cc_start: 0.9309 (t0) cc_final: 0.8200 (t0) outliers start: 5 outliers final: 1 residues processed: 701 average time/residue: 0.1239 time to fit residues: 127.1989 Evaluate side-chains 563 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 561 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 164 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 182 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 GLN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 HIS C 28 GLN C 84 HIS D 25 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 186 GLN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 263 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.107371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.075073 restraints weight = 53192.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.077695 restraints weight = 31875.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.079777 restraints weight = 22119.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.080749 restraints weight = 17168.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.081942 restraints weight = 14410.677| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.5946 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= 0.214 Angle : 0.643 8.865 22134 Z= 0.346 Chirality : 0.043 0.212 2360 Planarity : 0.004 0.056 2818 Dihedral : 9.481 129.356 2290 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.12 % Allowed : 2.91 % Favored : 96.97 % 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: 0.91 (0.19), residues: 1932 helix: 0.99 (0.15), residues: 1147 sheet: -0.47 (0.39), residues: 144 loop : 0.40 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 243 TYR 0.031 0.002 TYR A 606 PHE 0.037 0.002 PHE D 109 TRP 0.009 0.001 TRP C 30 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.21 (16386) covalent geometry : angle 0.64338 / 0.35 (22134) hydrogen bonds : bond 0.04263 / 2.68 ( 869) hydrogen bonds : angle 5.02445 / 3.56 ( 2568) *********************** 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 682 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 680 time to evaluate : 0.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ILE cc_start: 0.9571 (mm) cc_final: 0.9370 (mm) REVERT: A 65 GLU cc_start: 0.8674 (mm-30) cc_final: 0.8172 (mm-30) REVERT: A 87 LYS cc_start: 0.9289 (tptm) cc_final: 0.8936 (tptm) REVERT: A 95 MET cc_start: 0.9780 (tpt) cc_final: 0.9438 (tpp) REVERT: A 99 LYS cc_start: 0.9493 (mmtp) cc_final: 0.9055 (mmtp) REVERT: A 104 TYR cc_start: 0.8975 (m-80) cc_final: 0.8150 (m-80) REVERT: A 107 LYS cc_start: 0.9403 (mttm) cc_final: 0.9098 (mmmt) REVERT: A 117 ARG cc_start: 0.9247 (mtp85) cc_final: 0.8825 (mmt180) REVERT: A 119 GLU cc_start: 0.9170 (mt-10) cc_final: 0.8842 (mt-10) REVERT: A 129 PHE cc_start: 0.9477 (m-80) cc_final: 0.9169 (m-80) REVERT: A 136 LYS cc_start: 0.9770 (mmpt) cc_final: 0.9457 (ttpt) REVERT: A 144 MET cc_start: 0.9092 (mtm) cc_final: 0.8659 (mtm) REVERT: A 150 GLN cc_start: 0.9209 (tp40) cc_final: 0.9002 (tp40) REVERT: A 168 VAL cc_start: 0.9242 (m) cc_final: 0.8937 (p) REVERT: A 176 ASN cc_start: 0.8744 (t0) cc_final: 0.8539 (t0) REVERT: A 194 LYS cc_start: 0.9499 (ttpt) cc_final: 0.9135 (ttpp) REVERT: A 195 LEU cc_start: 0.9632 (mt) cc_final: 0.9326 (mt) REVERT: A 224 VAL cc_start: 0.8822 (t) cc_final: 0.8509 (t) REVERT: A 227 MET cc_start: 0.9351 (mtp) cc_final: 0.8818 (mtp) REVERT: A 252 ASN cc_start: 0.8592 (t0) cc_final: 0.8250 (t0) REVERT: A 254 PHE cc_start: 0.8356 (m-10) cc_final: 0.8111 (m-10) REVERT: A 286 ASP cc_start: 0.9123 (m-30) cc_final: 0.8639 (m-30) REVERT: A 362 ASP cc_start: 0.9198 (m-30) cc_final: 0.8573 (m-30) REVERT: A 370 ASN cc_start: 0.9380 (m-40) cc_final: 0.8959 (m110) REVERT: A 387 GLN cc_start: 0.8653 (mt0) cc_final: 0.8434 (mt0) REVERT: A 396 ASP cc_start: 0.9067 (p0) cc_final: 0.8789 (p0) REVERT: A 493 MET cc_start: 0.9374 (tmm) cc_final: 0.9158 (tmm) REVERT: A 522 TYR cc_start: 0.9061 (m-80) cc_final: 0.8719 (m-80) REVERT: A 583 SER cc_start: 0.9385 (t) cc_final: 0.9014 (t) REVERT: A 602 GLU cc_start: 0.8662 (pt0) cc_final: 0.8399 (pt0) REVERT: A 604 ARG cc_start: 0.8573 (mmp-170) cc_final: 0.8352 (mmp-170) REVERT: A 615 MET cc_start: 0.8910 (mmp) cc_final: 0.8643 (mmp) REVERT: A 626 TYR cc_start: 0.9289 (m-80) cc_final: 0.8911 (m-10) REVERT: A 637 VAL cc_start: 0.9802 (t) cc_final: 0.9517 (t) REVERT: A 645 GLN cc_start: 0.8506 (tp-100) cc_final: 0.7319 (tp-100) REVERT: A 659 LYS cc_start: 0.9319 (mttt) cc_final: 0.9112 (mmmt) REVERT: A 680 LYS cc_start: 0.8379 (mttt) cc_final: 0.7846 (mttt) REVERT: B 19 GLN cc_start: 0.9307 (mt0) cc_final: 0.8900 (pp30) REVERT: B 51 LEU cc_start: 0.9526 (tp) cc_final: 0.9232 (tp) REVERT: B 77 ILE cc_start: 0.9724 (mt) cc_final: 0.9398 (mt) REVERT: B 87 LYS cc_start: 0.9358 (tptp) cc_final: 0.9053 (tptp) REVERT: B 89 PHE cc_start: 0.9200 (t80) cc_final: 0.8636 (t80) REVERT: B 95 MET cc_start: 0.9562 (tpp) cc_final: 0.8630 (tpp) REVERT: B 99 LYS cc_start: 0.9507 (mmmt) cc_final: 0.8779 (mmmt) REVERT: B 118 TYR cc_start: 0.9265 (t80) cc_final: 0.9048 (t80) REVERT: B 144 MET cc_start: 0.9559 (mtm) cc_final: 0.8939 (mtm) REVERT: B 149 TYR cc_start: 0.9072 (t80) cc_final: 0.8673 (t80) REVERT: B 150 GLN cc_start: 0.9122 (tp40) cc_final: 0.8858 (tp40) REVERT: B 161 ARG cc_start: 0.8767 (ttm110) cc_final: 0.8471 (mtt-85) REVERT: B 162 LYS cc_start: 0.9383 (tppt) cc_final: 0.9092 (mttt) REVERT: B 164 ARG cc_start: 0.9220 (ptt90) cc_final: 0.8908 (ttp80) REVERT: B 191 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8826 (mm-40) REVERT: B 211 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8165 (mt-10) REVERT: B 250 TYR cc_start: 0.8725 (m-80) cc_final: 0.8292 (m-80) REVERT: B 257 ASP cc_start: 0.8358 (m-30) cc_final: 0.8100 (m-30) REVERT: B 286 ASP cc_start: 0.9086 (m-30) cc_final: 0.8398 (m-30) REVERT: B 317 MET cc_start: 0.8561 (pmm) cc_final: 0.7457 (pmm) REVERT: B 319 MET cc_start: 0.9007 (tpp) cc_final: 0.8794 (tpp) REVERT: B 333 LYS cc_start: 0.9183 (tptm) cc_final: 0.8953 (tptp) REVERT: B 350 ARG cc_start: 0.8895 (tpp80) cc_final: 0.8157 (tpp80) REVERT: B 355 TYR cc_start: 0.9228 (m-10) cc_final: 0.8977 (m-10) REVERT: B 362 ASP cc_start: 0.8777 (m-30) cc_final: 0.7977 (m-30) REVERT: B 373 ILE cc_start: 0.9788 (mt) cc_final: 0.8894 (mt) REVERT: B 390 GLN cc_start: 0.9240 (mm-40) cc_final: 0.8938 (mm-40) REVERT: B 396 ASP cc_start: 0.7965 (p0) cc_final: 0.7295 (p0) REVERT: B 399 GLU cc_start: 0.9476 (mm-30) cc_final: 0.9248 (mm-30) REVERT: B 415 ASN cc_start: 0.9016 (t0) cc_final: 0.7642 (t0) REVERT: B 418 ASN cc_start: 0.9164 (m-40) cc_final: 0.8638 (m-40) REVERT: B 426 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8751 (tm-30) REVERT: B 467 ASN cc_start: 0.9313 (m-40) cc_final: 0.9033 (m110) REVERT: B 496 ASN cc_start: 0.9663 (t0) cc_final: 0.8352 (t0) REVERT: B 499 SER cc_start: 0.9917 (t) cc_final: 0.9567 (p) REVERT: B 500 ILE cc_start: 0.9746 (mt) cc_final: 0.9469 (mt) REVERT: B 501 GLN cc_start: 0.8979 (tp-100) cc_final: 0.8426 (tp-100) REVERT: B 515 ASP cc_start: 0.9169 (m-30) cc_final: 0.8814 (m-30) REVERT: B 570 MET cc_start: 0.9068 (tpp) cc_final: 0.8724 (tpp) REVERT: B 575 ARG cc_start: 0.8911 (mtm110) cc_final: 0.7308 (mtm180) REVERT: B 588 GLN cc_start: 0.9438 (mm-40) cc_final: 0.8809 (mm-40) REVERT: B 601 ILE cc_start: 0.9152 (mt) cc_final: 0.8751 (mp) REVERT: B 602 GLU cc_start: 0.8305 (mp0) cc_final: 0.7501 (mp0) REVERT: B 618 LEU cc_start: 0.9012 (mt) cc_final: 0.8539 (mt) REVERT: B 667 LEU cc_start: 0.9512 (tt) cc_final: 0.9170 (tt) REVERT: C 204 TYR cc_start: 0.9639 (t80) cc_final: 0.9355 (t80) REVERT: D 96 MET cc_start: 0.8352 (mmt) cc_final: 0.7798 (mmm) REVERT: D 179 TYR cc_start: 0.9208 (t80) cc_final: 0.9006 (t80) REVERT: D 185 MET cc_start: 0.7424 (mmm) cc_final: 0.6584 (mmm) REVERT: D 189 GLU cc_start: 0.9068 (tp30) cc_final: 0.8656 (pt0) REVERT: D 239 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7195 (pm20) REVERT: D 259 PHE cc_start: 0.7489 (t80) cc_final: 0.7191 (t80) REVERT: D 317 ASP cc_start: 0.9248 (t0) cc_final: 0.8504 (t0) outliers start: 2 outliers final: 0 residues processed: 682 average time/residue: 0.1167 time to fit residues: 117.6226 Evaluate side-chains 571 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 570 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 chunk 168 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 127 optimal weight: 3.9990 chunk 60 optimal weight: 10.0000 chunk 185 optimal weight: 7.9990 chunk 191 optimal weight: 2.9990 chunk 159 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN C 238 ASN D 23 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 ASN D 238 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.102853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.071701 restraints weight = 55861.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.074446 restraints weight = 33210.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.076275 restraints weight = 22915.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.077522 restraints weight = 17512.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.078453 restraints weight = 14329.551| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7430 moved from start: 0.6972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 16386 Z= 0.296 Angle : 0.729 8.670 22134 Z= 0.389 Chirality : 0.045 0.236 2360 Planarity : 0.005 0.053 2818 Dihedral : 9.667 132.096 2290 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 22.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.06 % Allowed : 3.15 % Favored : 96.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.30 (0.18), residues: 1932 helix: 0.54 (0.15), residues: 1135 sheet: -0.63 (0.43), residues: 134 loop : 0.05 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 665 TYR 0.030 0.002 TYR D 174 PHE 0.035 0.003 PHE D 166 TRP 0.014 0.002 TRP A 623 HIS 0.008 0.002 HIS A 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.30 (16386) covalent geometry : angle 0.72907 / 0.39 (22134) hydrogen bonds : bond 0.04351 / 2.75 ( 869) hydrogen bonds : angle 5.24814 / 3.71 ( 2568) *********************** 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 637 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 636 time to evaluate : 0.403 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 65 GLU cc_start: 0.8754 (mm-30) cc_final: 0.8231 (mm-30) REVERT: A 89 PHE cc_start: 0.9186 (t80) cc_final: 0.8960 (t80) REVERT: A 95 MET cc_start: 0.9670 (tpt) cc_final: 0.8892 (tpp) REVERT: A 99 LYS cc_start: 0.9559 (mmtp) cc_final: 0.9108 (mmmm) REVERT: A 104 TYR cc_start: 0.9046 (m-80) cc_final: 0.8339 (m-80) REVERT: A 107 LYS cc_start: 0.9398 (mttm) cc_final: 0.8956 (tptt) REVERT: A 117 ARG cc_start: 0.9262 (mtp85) cc_final: 0.8881 (mmt180) REVERT: A 119 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8622 (pm20) REVERT: A 120 ASP cc_start: 0.9371 (m-30) cc_final: 0.8337 (m-30) REVERT: A 129 PHE cc_start: 0.9565 (m-80) cc_final: 0.9185 (m-80) REVERT: A 144 MET cc_start: 0.9068 (mtm) cc_final: 0.8694 (mtm) REVERT: A 150 GLN cc_start: 0.9090 (tp40) cc_final: 0.8674 (tm-30) REVERT: A 168 VAL cc_start: 0.9243 (m) cc_final: 0.9042 (p) REVERT: A 191 GLN cc_start: 0.8993 (mm110) cc_final: 0.8790 (mp10) REVERT: A 194 LYS cc_start: 0.9491 (ttpt) cc_final: 0.9232 (ttpp) REVERT: A 224 VAL cc_start: 0.8906 (t) cc_final: 0.8692 (t) REVERT: A 227 MET cc_start: 0.9300 (mtp) cc_final: 0.8945 (mtp) REVERT: A 235 ARG cc_start: 0.8437 (ttp-110) cc_final: 0.8120 (ttp-110) REVERT: A 252 ASN cc_start: 0.8922 (t0) cc_final: 0.8643 (t0) REVERT: A 286 ASP cc_start: 0.9160 (m-30) cc_final: 0.8544 (m-30) REVERT: A 317 MET cc_start: 0.9184 (mtm) cc_final: 0.8947 (mtm) REVERT: A 322 MET cc_start: 0.9238 (mmm) cc_final: 0.8681 (mmm) REVERT: A 335 GLU cc_start: 0.9315 (tp30) cc_final: 0.9088 (tm-30) REVERT: A 337 ILE cc_start: 0.9683 (pt) cc_final: 0.9141 (pt) REVERT: A 350 ARG cc_start: 0.8471 (mtp85) cc_final: 0.7764 (mtp85) REVERT: A 362 ASP cc_start: 0.9248 (m-30) cc_final: 0.9013 (m-30) REVERT: A 366 LYS cc_start: 0.9468 (ptpp) cc_final: 0.8950 (ptpp) REVERT: A 375 LYS cc_start: 0.9493 (mttt) cc_final: 0.9058 (mttt) REVERT: A 396 ASP cc_start: 0.9118 (p0) cc_final: 0.8843 (p0) REVERT: A 399 GLU cc_start: 0.9498 (tp30) cc_final: 0.9253 (tp30) REVERT: A 402 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8779 (tm-30) REVERT: A 468 LEU cc_start: 0.9621 (tp) cc_final: 0.9360 (tp) REVERT: A 493 MET cc_start: 0.9292 (tmm) cc_final: 0.9013 (tmm) REVERT: A 500 ILE cc_start: 0.9866 (mt) cc_final: 0.9551 (mt) REVERT: A 501 GLN cc_start: 0.9647 (mm-40) cc_final: 0.8879 (tp-100) REVERT: A 515 ASP cc_start: 0.9488 (m-30) cc_final: 0.9214 (m-30) REVERT: A 583 SER cc_start: 0.9470 (t) cc_final: 0.9207 (t) REVERT: A 584 ILE cc_start: 0.9604 (pt) cc_final: 0.9215 (pt) REVERT: A 586 TYR cc_start: 0.9207 (m-80) cc_final: 0.8962 (m-80) REVERT: A 602 GLU cc_start: 0.8889 (pt0) cc_final: 0.8155 (pt0) REVERT: A 615 MET cc_start: 0.8867 (mmp) cc_final: 0.8582 (mmp) REVERT: A 632 MET cc_start: 0.9036 (mtp) cc_final: 0.8552 (mtp) REVERT: B 87 LYS cc_start: 0.9362 (tptp) cc_final: 0.8994 (tptp) REVERT: B 95 MET cc_start: 0.9628 (tpp) cc_final: 0.9271 (tpp) REVERT: B 99 LYS cc_start: 0.9556 (mmmt) cc_final: 0.9074 (mmmm) REVERT: B 144 MET cc_start: 0.9546 (mtm) cc_final: 0.8955 (mtm) REVERT: B 161 ARG cc_start: 0.8912 (ttm110) cc_final: 0.8223 (mtt180) REVERT: B 162 LYS cc_start: 0.9437 (tppt) cc_final: 0.9171 (mttt) REVERT: B 164 ARG cc_start: 0.9351 (ptt90) cc_final: 0.9051 (ptt-90) REVERT: B 190 MET cc_start: 0.9667 (mtm) cc_final: 0.9313 (mmp) REVERT: B 235 ARG cc_start: 0.8417 (mtm-85) cc_final: 0.8162 (mtm-85) REVERT: B 252 ASN cc_start: 0.8903 (t0) cc_final: 0.8695 (t0) REVERT: B 286 ASP cc_start: 0.9179 (m-30) cc_final: 0.8549 (m-30) REVERT: B 319 MET cc_start: 0.9042 (tpp) cc_final: 0.8840 (tpp) REVERT: B 333 LYS cc_start: 0.9133 (tptm) cc_final: 0.8880 (tptp) REVERT: B 362 ASP cc_start: 0.8827 (m-30) cc_final: 0.7972 (m-30) REVERT: B 387 GLN cc_start: 0.8872 (mt0) cc_final: 0.8572 (mp10) REVERT: B 396 ASP cc_start: 0.8247 (p0) cc_final: 0.7781 (p0) REVERT: B 399 GLU cc_start: 0.9481 (mm-30) cc_final: 0.9193 (mp0) REVERT: B 407 ILE cc_start: 0.8874 (mt) cc_final: 0.8536 (mt) REVERT: B 415 ASN cc_start: 0.8963 (t0) cc_final: 0.8370 (t0) REVERT: B 418 ASN cc_start: 0.9102 (m-40) cc_final: 0.8790 (m110) REVERT: B 427 LYS cc_start: 0.9715 (ptpp) cc_final: 0.9244 (ptpt) REVERT: B 480 GLU cc_start: 0.9290 (pm20) cc_final: 0.9069 (pm20) REVERT: B 496 ASN cc_start: 0.9672 (t0) cc_final: 0.8517 (t0) REVERT: B 499 SER cc_start: 0.9874 (t) cc_final: 0.9654 (p) REVERT: B 500 ILE cc_start: 0.9785 (mt) cc_final: 0.9540 (mt) REVERT: B 505 GLU cc_start: 0.9132 (mt-10) cc_final: 0.8750 (mt-10) REVERT: B 515 ASP cc_start: 0.9137 (m-30) cc_final: 0.8706 (m-30) REVERT: B 570 MET cc_start: 0.9076 (tpp) cc_final: 0.8555 (tpt) REVERT: B 575 ARG cc_start: 0.8809 (mtm110) cc_final: 0.7348 (mtm180) REVERT: B 602 GLU cc_start: 0.8284 (mp0) cc_final: 0.7974 (mp0) REVERT: B 615 MET cc_start: 0.9053 (mmp) cc_final: 0.8790 (mmp) REVERT: B 618 LEU cc_start: 0.9035 (mt) cc_final: 0.8695 (mt) REVERT: B 632 MET cc_start: 0.8888 (mmp) cc_final: 0.8685 (mmm) REVERT: B 634 MET cc_start: 0.9402 (mmm) cc_final: 0.9041 (mmm) REVERT: B 667 LEU cc_start: 0.9495 (tt) cc_final: 0.9209 (tt) REVERT: C 157 MET cc_start: 0.5109 (ptt) cc_final: 0.4812 (ptt) REVERT: C 183 LYS cc_start: 0.7745 (mttt) cc_final: 0.7539 (mtpt) REVERT: C 204 TYR cc_start: 0.9677 (t80) cc_final: 0.9197 (t80) REVERT: C 278 GLU cc_start: 0.9271 (pm20) cc_final: 0.9003 (pm20) REVERT: D 101 HIS cc_start: 0.8928 (m90) cc_final: 0.8612 (m90) REVERT: D 179 TYR cc_start: 0.9239 (t80) cc_final: 0.8950 (t80) REVERT: D 185 MET cc_start: 0.7753 (mmm) cc_final: 0.7029 (mmm) REVERT: D 259 PHE cc_start: 0.7784 (t80) cc_final: 0.7366 (t80) outliers start: 1 outliers final: 0 residues processed: 637 average time/residue: 0.1169 time to fit residues: 110.2692 Evaluate side-chains 547 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 547 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 0.5980 chunk 46 optimal weight: 0.8980 chunk 120 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 126 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 32 optimal weight: 0.0980 chunk 122 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 168 optimal weight: 6.9990 chunk 157 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 HIS B 11 GLN ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN B 410 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.108397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.076241 restraints weight = 52941.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.078891 restraints weight = 31868.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.080837 restraints weight = 22455.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.082291 restraints weight = 17111.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.083282 restraints weight = 13799.097| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3134 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3134 r_free = 0.3134 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-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: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.7162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16386 Z= 0.143 Angle : 0.612 12.211 22134 Z= 0.324 Chirality : 0.042 0.181 2360 Planarity : 0.004 0.055 2818 Dihedral : 9.224 130.912 2290 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.06 % Allowed : 2.10 % Favored : 97.84 % 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: 0.70 (0.19), residues: 1932 helix: 0.84 (0.15), residues: 1163 sheet: -0.67 (0.43), residues: 142 loop : 0.30 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 161 TYR 0.029 0.002 TYR D 174 PHE 0.023 0.002 PHE D 227 TRP 0.007 0.001 TRP D 124 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (16386) covalent geometry : angle 0.61199 / 0.32 (22134) hydrogen bonds : bond 0.03883 / 2.46 ( 869) hydrogen bonds : angle 5.00503 / 3.55 ( 2568) *********************** 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 654 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 653 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9298 (tptp) cc_final: 0.9093 (tppt) REVERT: A 29 ASP cc_start: 0.9546 (t0) cc_final: 0.9218 (t70) REVERT: A 95 MET cc_start: 0.9711 (tpt) cc_final: 0.9223 (mmm) REVERT: A 104 TYR cc_start: 0.8927 (m-80) cc_final: 0.8276 (m-80) REVERT: A 117 ARG cc_start: 0.9228 (mtp85) cc_final: 0.9015 (mmt180) REVERT: A 119 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8572 (pm20) REVERT: A 120 ASP cc_start: 0.9324 (m-30) cc_final: 0.8423 (m-30) REVERT: A 129 PHE cc_start: 0.9529 (m-80) cc_final: 0.9152 (m-80) REVERT: A 136 LYS cc_start: 0.9790 (mmtt) cc_final: 0.9461 (ttpt) REVERT: A 144 MET cc_start: 0.8993 (mtm) cc_final: 0.8484 (mtm) REVERT: A 168 VAL cc_start: 0.9347 (m) cc_final: 0.9101 (p) REVERT: A 180 ASN cc_start: 0.8907 (m110) cc_final: 0.8563 (m-40) REVERT: A 194 LYS cc_start: 0.9362 (ttpt) cc_final: 0.9023 (ttpp) REVERT: A 195 LEU cc_start: 0.9571 (mt) cc_final: 0.9339 (mt) REVERT: A 224 VAL cc_start: 0.8916 (t) cc_final: 0.8698 (t) REVERT: A 227 MET cc_start: 0.9314 (mtp) cc_final: 0.8829 (mtp) REVERT: A 235 ARG cc_start: 0.8798 (ttp-110) cc_final: 0.7991 (mtm110) REVERT: A 252 ASN cc_start: 0.8854 (t0) cc_final: 0.8549 (t0) REVERT: A 254 PHE cc_start: 0.8707 (m-10) cc_final: 0.8283 (m-10) REVERT: A 286 ASP cc_start: 0.9112 (m-30) cc_final: 0.8584 (m-30) REVERT: A 307 TYR cc_start: 0.9402 (t80) cc_final: 0.9178 (t80) REVERT: A 322 MET cc_start: 0.9200 (mmm) cc_final: 0.8986 (mmm) REVERT: A 350 ARG cc_start: 0.8534 (mtp85) cc_final: 0.7841 (mtp85) REVERT: A 359 MET cc_start: 0.9110 (ttp) cc_final: 0.8906 (ttp) REVERT: A 362 ASP cc_start: 0.9196 (m-30) cc_final: 0.8923 (m-30) REVERT: A 366 LYS cc_start: 0.9453 (ptpp) cc_final: 0.9049 (pttp) REVERT: A 370 ASN cc_start: 0.9468 (m-40) cc_final: 0.9188 (m110) REVERT: A 375 LYS cc_start: 0.9499 (mttt) cc_final: 0.9073 (mttt) REVERT: A 385 VAL cc_start: 0.9648 (t) cc_final: 0.9376 (m) REVERT: A 396 ASP cc_start: 0.8977 (p0) cc_final: 0.8773 (p0) REVERT: A 399 GLU cc_start: 0.9484 (tp30) cc_final: 0.9276 (tp30) REVERT: A 402 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8861 (tm-30) REVERT: A 414 LEU cc_start: 0.9584 (mt) cc_final: 0.9374 (mt) REVERT: A 468 LEU cc_start: 0.9544 (tp) cc_final: 0.9252 (tp) REVERT: A 493 MET cc_start: 0.9311 (tmm) cc_final: 0.8999 (tmm) REVERT: A 506 ILE cc_start: 0.9787 (mm) cc_final: 0.9435 (mm) REVERT: A 515 ASP cc_start: 0.9495 (m-30) cc_final: 0.9221 (m-30) REVERT: A 522 TYR cc_start: 0.9242 (m-80) cc_final: 0.8894 (m-80) REVERT: A 562 LYS cc_start: 0.9665 (pttp) cc_final: 0.9449 (pttp) REVERT: A 583 SER cc_start: 0.9373 (t) cc_final: 0.9058 (t) REVERT: A 585 SER cc_start: 0.9634 (p) cc_final: 0.9207 (t) REVERT: A 591 THR cc_start: 0.9150 (p) cc_final: 0.8809 (p) REVERT: A 602 GLU cc_start: 0.8895 (pt0) cc_final: 0.8418 (pt0) REVERT: A 615 MET cc_start: 0.8844 (mmp) cc_final: 0.8499 (mmp) REVERT: A 653 SER cc_start: 0.8976 (p) cc_final: 0.8682 (p) REVERT: A 667 LEU cc_start: 0.9601 (tt) cc_final: 0.9387 (tt) REVERT: B 51 LEU cc_start: 0.9496 (tp) cc_final: 0.9162 (tp) REVERT: B 77 ILE cc_start: 0.9727 (mt) cc_final: 0.9358 (mt) REVERT: B 87 LYS cc_start: 0.9370 (tptp) cc_final: 0.9021 (tptp) REVERT: B 95 MET cc_start: 0.9571 (tpp) cc_final: 0.9077 (tpp) REVERT: B 99 LYS cc_start: 0.9588 (mmmt) cc_final: 0.9120 (mmmm) REVERT: B 114 ILE cc_start: 0.9519 (mt) cc_final: 0.9218 (pt) REVERT: B 144 MET cc_start: 0.9247 (mtm) cc_final: 0.8803 (mtm) REVERT: B 147 GLN cc_start: 0.9140 (tt0) cc_final: 0.8841 (tt0) REVERT: B 149 TYR cc_start: 0.9393 (t80) cc_final: 0.8863 (t80) REVERT: B 162 LYS cc_start: 0.9426 (tppt) cc_final: 0.9212 (mttt) REVERT: B 164 ARG cc_start: 0.9290 (ptt90) cc_final: 0.9039 (ttp80) REVERT: B 179 LEU cc_start: 0.9488 (tp) cc_final: 0.9280 (tp) REVERT: B 191 GLN cc_start: 0.9319 (mm-40) cc_final: 0.8854 (mm-40) REVERT: B 211 GLU cc_start: 0.9074 (mm-30) cc_final: 0.8156 (mt-10) REVERT: B 252 ASN cc_start: 0.8849 (t0) cc_final: 0.8616 (t0) REVERT: B 263 ASP cc_start: 0.9416 (m-30) cc_final: 0.9181 (m-30) REVERT: B 286 ASP cc_start: 0.9199 (m-30) cc_final: 0.8528 (m-30) REVERT: B 350 ARG cc_start: 0.9201 (tpp80) cc_final: 0.8859 (tpp80) REVERT: B 355 TYR cc_start: 0.9421 (m-10) cc_final: 0.9217 (m-10) REVERT: B 362 ASP cc_start: 0.8792 (m-30) cc_final: 0.7939 (m-30) REVERT: B 373 ILE cc_start: 0.9677 (mt) cc_final: 0.9035 (mt) REVERT: B 387 GLN cc_start: 0.8754 (mt0) cc_final: 0.8416 (mp10) REVERT: B 390 GLN cc_start: 0.9223 (mm110) cc_final: 0.8962 (mm-40) REVERT: B 396 ASP cc_start: 0.8105 (p0) cc_final: 0.7513 (p0) REVERT: B 399 GLU cc_start: 0.9497 (mm-30) cc_final: 0.9170 (mp0) REVERT: B 407 ILE cc_start: 0.8692 (mt) cc_final: 0.8322 (mt) REVERT: B 415 ASN cc_start: 0.9183 (t0) cc_final: 0.7871 (t0) REVERT: B 418 ASN cc_start: 0.9310 (m-40) cc_final: 0.8886 (m-40) REVERT: B 426 GLU cc_start: 0.9280 (pm20) cc_final: 0.8951 (pm20) REVERT: B 427 LYS cc_start: 0.9691 (ptpp) cc_final: 0.9274 (ptpp) REVERT: B 466 MET cc_start: 0.9128 (ptp) cc_final: 0.8589 (ptp) REVERT: B 467 ASN cc_start: 0.9180 (m-40) cc_final: 0.8416 (m-40) REVERT: B 480 GLU cc_start: 0.9254 (pm20) cc_final: 0.8905 (mt-10) REVERT: B 496 ASN cc_start: 0.9629 (t0) cc_final: 0.8587 (t0) REVERT: B 499 SER cc_start: 0.9884 (t) cc_final: 0.9635 (p) REVERT: B 501 GLN cc_start: 0.8858 (tp-100) cc_final: 0.8316 (tp-100) REVERT: B 515 ASP cc_start: 0.9155 (m-30) cc_final: 0.8754 (m-30) REVERT: B 516 GLN cc_start: 0.9086 (tt0) cc_final: 0.8708 (tt0) REVERT: B 570 MET cc_start: 0.9066 (tpp) cc_final: 0.8646 (tpp) REVERT: B 575 ARG cc_start: 0.8586 (mtm110) cc_final: 0.7268 (mtm180) REVERT: B 601 ILE cc_start: 0.9300 (mp) cc_final: 0.9042 (mp) REVERT: B 602 GLU cc_start: 0.8357 (mp0) cc_final: 0.7984 (mp0) REVERT: B 618 LEU cc_start: 0.9064 (mt) cc_final: 0.8826 (mt) REVERT: B 632 MET cc_start: 0.9008 (mmp) cc_final: 0.8697 (mmm) REVERT: B 634 MET cc_start: 0.9394 (mmm) cc_final: 0.9131 (mmm) REVERT: B 656 LEU cc_start: 0.9524 (mt) cc_final: 0.9306 (mt) REVERT: B 667 LEU cc_start: 0.9603 (tt) cc_final: 0.9379 (tt) REVERT: C 76 ILE cc_start: 0.5579 (tt) cc_final: 0.5206 (pt) REVERT: C 157 MET cc_start: 0.4995 (ptt) cc_final: 0.4541 (ptt) REVERT: C 183 LYS cc_start: 0.7609 (mttt) cc_final: 0.7399 (mtmt) REVERT: C 204 TYR cc_start: 0.9641 (t80) cc_final: 0.9338 (t80) REVERT: C 278 GLU cc_start: 0.9227 (pm20) cc_final: 0.8988 (pm20) REVERT: D 46 TYR cc_start: 0.9054 (m-80) cc_final: 0.8805 (m-10) REVERT: D 69 GLN cc_start: 0.7690 (tm-30) cc_final: 0.7387 (pp30) REVERT: D 179 TYR cc_start: 0.9153 (t80) cc_final: 0.8830 (t80) REVERT: D 185 MET cc_start: 0.7779 (mmm) cc_final: 0.6818 (mmm) REVERT: D 189 GLU cc_start: 0.8947 (tp30) cc_final: 0.8717 (pt0) REVERT: D 201 HIS cc_start: 0.9478 (m170) cc_final: 0.9197 (m170) REVERT: D 259 PHE cc_start: 0.7684 (t80) cc_final: 0.7152 (t80) outliers start: 1 outliers final: 0 residues processed: 653 average time/residue: 0.1266 time to fit residues: 122.0199 Evaluate side-chains 575 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 575 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 20.0000 chunk 72 optimal weight: 0.3980 chunk 172 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 136 optimal weight: 0.5980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 645 GLN ** D 28 GLN ** 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 = 0.3588 r_free = 0.3588 target = 0.111785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.080044 restraints weight = 50905.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.082909 restraints weight = 29860.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.084784 restraints weight = 20705.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.086136 restraints weight = 15759.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.087099 restraints weight = 12820.961| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (5 function evaluations) r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.7395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16386 Z= 0.128 Angle : 0.601 7.585 22134 Z= 0.318 Chirality : 0.042 0.264 2360 Planarity : 0.004 0.049 2818 Dihedral : 9.075 131.498 2290 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.12 % Allowed : 1.22 % Favored : 98.66 % 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: 0.70 (0.19), residues: 1932 helix: 0.85 (0.15), residues: 1158 sheet: -0.66 (0.44), residues: 142 loop : 0.30 (0.24), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 163 TYR 0.025 0.001 TYR B 683 PHE 0.040 0.002 PHE D 109 TRP 0.006 0.001 TRP D 124 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (16386) covalent geometry : angle 0.60069 / 0.32 (22134) hydrogen bonds : bond 0.03848 / 2.40 ( 869) hydrogen bonds : angle 4.90734 / 3.50 ( 2568) *********************** 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 647 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 645 time to evaluate : 0.451 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: A 8 LYS cc_start: 0.9292 (tptp) cc_final: 0.9083 (tppt) REVERT: A 29 ASP cc_start: 0.9515 (t0) cc_final: 0.9187 (t70) REVERT: A 65 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8421 (mm-30) REVERT: A 104 TYR cc_start: 0.8858 (m-80) cc_final: 0.8192 (m-80) REVERT: A 107 LYS cc_start: 0.9476 (mttm) cc_final: 0.9230 (mmmt) REVERT: A 117 ARG cc_start: 0.9203 (mtp85) cc_final: 0.8934 (mmt180) REVERT: A 120 ASP cc_start: 0.9223 (m-30) cc_final: 0.8308 (m-30) REVERT: A 129 PHE cc_start: 0.9528 (m-80) cc_final: 0.9087 (m-80) REVERT: A 136 LYS cc_start: 0.9785 (mmtt) cc_final: 0.9470 (ttpt) REVERT: A 144 MET cc_start: 0.8960 (mtm) cc_final: 0.8439 (mtm) REVERT: A 168 VAL cc_start: 0.9340 (m) cc_final: 0.9110 (p) REVERT: A 191 GLN cc_start: 0.9042 (mm110) cc_final: 0.8420 (mm-40) REVERT: A 195 LEU cc_start: 0.9539 (mt) cc_final: 0.9309 (mt) REVERT: A 227 MET cc_start: 0.9134 (mtp) cc_final: 0.8813 (mtp) REVERT: A 235 ARG cc_start: 0.8878 (ttp-110) cc_final: 0.8076 (mtm110) REVERT: A 252 ASN cc_start: 0.8877 (t0) cc_final: 0.8555 (t0) REVERT: A 254 PHE cc_start: 0.8796 (m-10) cc_final: 0.8413 (m-10) REVERT: A 286 ASP cc_start: 0.9100 (m-30) cc_final: 0.8568 (m-30) REVERT: A 313 HIS cc_start: 0.8787 (m90) cc_final: 0.8515 (m170) REVERT: A 317 MET cc_start: 0.8798 (mtm) cc_final: 0.8097 (mpp) REVERT: A 322 MET cc_start: 0.9190 (mmm) cc_final: 0.8940 (mmm) REVERT: A 350 ARG cc_start: 0.8549 (mtp85) cc_final: 0.7835 (mtp85) REVERT: A 362 ASP cc_start: 0.9156 (m-30) cc_final: 0.8889 (m-30) REVERT: A 366 LYS cc_start: 0.9465 (ptpp) cc_final: 0.9071 (pttp) REVERT: A 370 ASN cc_start: 0.9487 (m-40) cc_final: 0.9046 (m110) REVERT: A 375 LYS cc_start: 0.9497 (mttt) cc_final: 0.9148 (mttt) REVERT: A 385 VAL cc_start: 0.9684 (t) cc_final: 0.9463 (m) REVERT: A 393 SER cc_start: 0.9557 (m) cc_final: 0.9326 (m) REVERT: A 399 GLU cc_start: 0.9461 (tp30) cc_final: 0.9255 (tp30) REVERT: A 402 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8812 (tm-30) REVERT: A 405 LEU cc_start: 0.9118 (mt) cc_final: 0.8628 (mt) REVERT: A 437 THR cc_start: 0.9484 (m) cc_final: 0.9277 (m) REVERT: A 468 LEU cc_start: 0.9514 (tp) cc_final: 0.9243 (tp) REVERT: A 493 MET cc_start: 0.9288 (tmm) cc_final: 0.9015 (tmm) REVERT: A 515 ASP cc_start: 0.9479 (m-30) cc_final: 0.9195 (m-30) REVERT: A 522 TYR cc_start: 0.9254 (m-80) cc_final: 0.8912 (m-80) REVERT: A 562 LYS cc_start: 0.9681 (pttp) cc_final: 0.9455 (pttp) REVERT: A 571 TYR cc_start: 0.9109 (t80) cc_final: 0.8488 (t80) REVERT: A 583 SER cc_start: 0.9313 (t) cc_final: 0.8933 (t) REVERT: A 585 SER cc_start: 0.9625 (p) cc_final: 0.9101 (t) REVERT: A 591 THR cc_start: 0.8972 (p) cc_final: 0.8511 (p) REVERT: A 595 MET cc_start: 0.9061 (tpp) cc_final: 0.8757 (tpp) REVERT: A 602 GLU cc_start: 0.8876 (pt0) cc_final: 0.8491 (pt0) REVERT: A 615 MET cc_start: 0.8933 (mmp) cc_final: 0.8583 (mmp) REVERT: A 618 LEU cc_start: 0.9280 (tt) cc_final: 0.9078 (tt) REVERT: A 653 SER cc_start: 0.8977 (p) cc_final: 0.8514 (p) REVERT: A 654 PHE cc_start: 0.9150 (t80) cc_final: 0.8928 (t80) REVERT: A 667 LEU cc_start: 0.9619 (tt) cc_final: 0.9416 (tt) REVERT: A 677 ARG cc_start: 0.9468 (mmm-85) cc_final: 0.8361 (mmm-85) REVERT: B 51 LEU cc_start: 0.9493 (tp) cc_final: 0.9087 (tp) REVERT: B 77 ILE cc_start: 0.9592 (mt) cc_final: 0.9338 (mt) REVERT: B 81 PHE cc_start: 0.9505 (m-10) cc_final: 0.9156 (m-10) REVERT: B 87 LYS cc_start: 0.9365 (tptp) cc_final: 0.9038 (tptp) REVERT: B 95 MET cc_start: 0.9557 (tpp) cc_final: 0.8589 (tpp) REVERT: B 99 LYS cc_start: 0.9600 (mmmt) cc_final: 0.8819 (mmmt) REVERT: B 114 ILE cc_start: 0.9555 (mt) cc_final: 0.9201 (pt) REVERT: B 143 LEU cc_start: 0.9627 (tp) cc_final: 0.9334 (tp) REVERT: B 144 MET cc_start: 0.9098 (mtm) cc_final: 0.8625 (mtm) REVERT: B 147 GLN cc_start: 0.9110 (tt0) cc_final: 0.8683 (tt0) REVERT: B 148 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8729 (mm-30) REVERT: B 149 TYR cc_start: 0.9446 (t80) cc_final: 0.8811 (t80) REVERT: B 162 LYS cc_start: 0.9415 (tppt) cc_final: 0.9157 (mttt) REVERT: B 211 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8528 (mm-30) REVERT: B 240 MET cc_start: 0.8236 (mpp) cc_final: 0.7779 (mpp) REVERT: B 252 ASN cc_start: 0.8847 (t0) cc_final: 0.8618 (t0) REVERT: B 257 ASP cc_start: 0.8454 (m-30) cc_final: 0.8160 (m-30) REVERT: B 263 ASP cc_start: 0.9375 (m-30) cc_final: 0.9133 (m-30) REVERT: B 286 ASP cc_start: 0.9135 (m-30) cc_final: 0.8405 (m-30) REVERT: B 322 MET cc_start: 0.8440 (ttt) cc_final: 0.7873 (ttt) REVERT: B 333 LYS cc_start: 0.9200 (tptp) cc_final: 0.8812 (tptp) REVERT: B 335 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8081 (mt-10) REVERT: B 350 ARG cc_start: 0.9195 (tpp80) cc_final: 0.8924 (tpp80) REVERT: B 362 ASP cc_start: 0.8865 (m-30) cc_final: 0.8012 (m-30) REVERT: B 373 ILE cc_start: 0.9651 (mt) cc_final: 0.8986 (mt) REVERT: B 375 LYS cc_start: 0.9188 (mmmm) cc_final: 0.8895 (mmtt) REVERT: B 387 GLN cc_start: 0.8705 (mt0) cc_final: 0.8421 (mp10) REVERT: B 390 GLN cc_start: 0.9212 (mm110) cc_final: 0.8931 (mm-40) REVERT: B 396 ASP cc_start: 0.7973 (p0) cc_final: 0.7456 (p0) REVERT: B 399 GLU cc_start: 0.9497 (mm-30) cc_final: 0.9144 (mp0) REVERT: B 407 ILE cc_start: 0.8547 (mt) cc_final: 0.7890 (mt) REVERT: B 415 ASN cc_start: 0.9205 (t0) cc_final: 0.7937 (t0) REVERT: B 416 ILE cc_start: 0.9791 (mt) cc_final: 0.9450 (mt) REVERT: B 418 ASN cc_start: 0.9284 (m-40) cc_final: 0.8735 (m-40) REVERT: B 420 MET cc_start: 0.9151 (mmm) cc_final: 0.8618 (mmm) REVERT: B 426 GLU cc_start: 0.9214 (pm20) cc_final: 0.8842 (pm20) REVERT: B 427 LYS cc_start: 0.9698 (ptpp) cc_final: 0.9199 (ptpp) REVERT: B 466 MET cc_start: 0.9006 (ptp) cc_final: 0.8421 (ptp) REVERT: B 467 ASN cc_start: 0.9220 (m-40) cc_final: 0.8288 (m110) REVERT: B 496 ASN cc_start: 0.9632 (t0) cc_final: 0.9161 (t0) REVERT: B 501 GLN cc_start: 0.8874 (tp-100) cc_final: 0.8406 (tp-100) REVERT: B 515 ASP cc_start: 0.9136 (m-30) cc_final: 0.8721 (m-30) REVERT: B 516 GLN cc_start: 0.9083 (tt0) cc_final: 0.8749 (tt0) REVERT: B 570 MET cc_start: 0.9119 (tpp) cc_final: 0.8462 (tpt) REVERT: B 575 ARG cc_start: 0.8436 (mtm110) cc_final: 0.8102 (mtm110) REVERT: B 601 ILE cc_start: 0.9247 (mp) cc_final: 0.8961 (mp) REVERT: B 618 LEU cc_start: 0.9139 (mt) cc_final: 0.8912 (mt) REVERT: B 632 MET cc_start: 0.9095 (mmp) cc_final: 0.8638 (mmm) REVERT: B 654 PHE cc_start: 0.9488 (t80) cc_final: 0.9136 (t80) REVERT: B 675 HIS cc_start: 0.9421 (t70) cc_final: 0.9182 (t70) REVERT: C 108 ILE cc_start: 0.9208 (mt) cc_final: 0.8998 (mt) REVERT: C 157 MET cc_start: 0.4809 (ptt) cc_final: 0.4435 (ptt) REVERT: C 179 TYR cc_start: 0.9505 (t80) cc_final: 0.9269 (t80) REVERT: C 185 MET cc_start: 0.8856 (mpp) cc_final: 0.8611 (mpp) REVERT: C 204 TYR cc_start: 0.9613 (t80) cc_final: 0.9314 (t80) REVERT: C 276 TYR cc_start: 0.9191 (t80) cc_final: 0.8979 (t80) REVERT: C 278 GLU cc_start: 0.9136 (pm20) cc_final: 0.8919 (pm20) REVERT: D 46 TYR cc_start: 0.9068 (m-80) cc_final: 0.8829 (m-10) REVERT: D 179 TYR cc_start: 0.9140 (t80) cc_final: 0.8796 (t80) REVERT: D 185 MET cc_start: 0.7887 (mmm) cc_final: 0.7024 (mmm) REVERT: D 189 GLU cc_start: 0.8968 (tp30) cc_final: 0.8758 (pt0) REVERT: D 201 HIS cc_start: 0.9422 (m170) cc_final: 0.9189 (m170) REVERT: D 259 PHE cc_start: 0.7440 (t80) cc_final: 0.7211 (t80) outliers start: 2 outliers final: 0 residues processed: 647 average time/residue: 0.1235 time to fit residues: 117.6508 Evaluate side-chains 562 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 562 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 0.0170 chunk 51 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 186 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 0.6980 chunk 45 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 overall best weight: 1.9022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS ** A 131 ASN ** 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 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.111884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.080671 restraints weight = 52200.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.083380 restraints weight = 30903.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.085455 restraints weight = 21129.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.086783 restraints weight = 16275.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.087732 restraints weight = 13143.308| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3159 r_free = 0.3159 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3159 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.7658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16386 Z= 0.157 Angle : 0.607 7.415 22134 Z= 0.327 Chirality : 0.042 0.222 2360 Planarity : 0.004 0.059 2818 Dihedral : 9.090 133.204 2290 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.06 % Allowed : 1.28 % Favored : 98.66 % 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: 0.58 (0.19), residues: 1932 helix: 0.78 (0.15), residues: 1153 sheet: -0.93 (0.43), residues: 144 loop : 0.22 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 243 TYR 0.030 0.002 TYR D 142 PHE 0.030 0.002 PHE D 109 TRP 0.009 0.001 TRP A 623 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (16386) covalent geometry : angle 0.60702 / 0.33 (22134) hydrogen bonds : bond 0.03890 / 2.44 ( 869) hydrogen bonds : angle 4.99852 / 3.55 ( 2568) *********************** 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 629 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 628 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8716 (mm-30) cc_final: 0.8345 (mp0) REVERT: A 95 MET cc_start: 0.9622 (tpt) cc_final: 0.8829 (tpp) REVERT: A 99 LYS cc_start: 0.9602 (mmtp) cc_final: 0.9258 (mmtp) REVERT: A 104 TYR cc_start: 0.8912 (m-80) cc_final: 0.8315 (m-80) REVERT: A 117 ARG cc_start: 0.9359 (mtp85) cc_final: 0.8908 (mmt180) REVERT: A 129 PHE cc_start: 0.9543 (m-80) cc_final: 0.9107 (m-80) REVERT: A 136 LYS cc_start: 0.9786 (mmtt) cc_final: 0.9533 (ttpt) REVERT: A 144 MET cc_start: 0.8935 (mtm) cc_final: 0.8462 (mtm) REVERT: A 168 VAL cc_start: 0.9335 (m) cc_final: 0.9095 (p) REVERT: A 227 MET cc_start: 0.9349 (mtp) cc_final: 0.8788 (mtp) REVERT: A 235 ARG cc_start: 0.8900 (ttp-110) cc_final: 0.8514 (ttp-110) REVERT: A 252 ASN cc_start: 0.8897 (t0) cc_final: 0.8609 (t0) REVERT: A 254 PHE cc_start: 0.8556 (m-10) cc_final: 0.8170 (m-10) REVERT: A 286 ASP cc_start: 0.9107 (m-30) cc_final: 0.8601 (m-30) REVERT: A 314 MET cc_start: 0.8720 (ptp) cc_final: 0.8164 (ptp) REVERT: A 317 MET cc_start: 0.8748 (mtm) cc_final: 0.7891 (mpp) REVERT: A 322 MET cc_start: 0.9195 (mmm) cc_final: 0.8812 (mmm) REVERT: A 335 GLU cc_start: 0.9272 (tp30) cc_final: 0.9051 (tm-30) REVERT: A 350 ARG cc_start: 0.8427 (mtp85) cc_final: 0.7781 (mtp85) REVERT: A 362 ASP cc_start: 0.9159 (m-30) cc_final: 0.8868 (m-30) REVERT: A 366 LYS cc_start: 0.9441 (ptpp) cc_final: 0.9076 (pttp) REVERT: A 370 ASN cc_start: 0.9443 (m-40) cc_final: 0.8951 (m110) REVERT: A 375 LYS cc_start: 0.9498 (mttt) cc_final: 0.9128 (mttt) REVERT: A 385 VAL cc_start: 0.9647 (t) cc_final: 0.9416 (m) REVERT: A 396 ASP cc_start: 0.8978 (p0) cc_final: 0.8724 (p0) REVERT: A 402 GLU cc_start: 0.9084 (tm-30) cc_final: 0.8865 (tm-30) REVERT: A 414 LEU cc_start: 0.9609 (mt) cc_final: 0.9366 (mt) REVERT: A 426 GLU cc_start: 0.9343 (tm-30) cc_final: 0.9066 (tm-30) REVERT: A 437 THR cc_start: 0.9491 (m) cc_final: 0.9290 (m) REVERT: A 441 GLU cc_start: 0.9129 (pp20) cc_final: 0.8909 (pp20) REVERT: A 468 LEU cc_start: 0.9535 (tp) cc_final: 0.9264 (tp) REVERT: A 493 MET cc_start: 0.9300 (tmm) cc_final: 0.8951 (tmm) REVERT: A 515 ASP cc_start: 0.9478 (m-30) cc_final: 0.9211 (m-30) REVERT: A 522 TYR cc_start: 0.9248 (m-80) cc_final: 0.8826 (m-80) REVERT: A 562 LYS cc_start: 0.9678 (pttp) cc_final: 0.9460 (pttp) REVERT: A 570 MET cc_start: 0.8860 (ptp) cc_final: 0.8254 (pmm) REVERT: A 583 SER cc_start: 0.9337 (t) cc_final: 0.8974 (t) REVERT: A 585 SER cc_start: 0.9699 (p) cc_final: 0.9309 (t) REVERT: A 591 THR cc_start: 0.9047 (p) cc_final: 0.8649 (p) REVERT: A 595 MET cc_start: 0.9085 (tpp) cc_final: 0.8733 (tpp) REVERT: A 598 MET cc_start: 0.8227 (tpt) cc_final: 0.8022 (tpt) REVERT: A 615 MET cc_start: 0.8897 (mmp) cc_final: 0.8614 (mmp) REVERT: A 618 LEU cc_start: 0.9300 (tt) cc_final: 0.9065 (tt) REVERT: A 627 LYS cc_start: 0.9493 (tttt) cc_final: 0.9151 (tttm) REVERT: A 653 SER cc_start: 0.9060 (p) cc_final: 0.8656 (p) REVERT: A 677 ARG cc_start: 0.9458 (mmm-85) cc_final: 0.8302 (mmm-85) REVERT: B 27 ASP cc_start: 0.9095 (p0) cc_final: 0.8794 (p0) REVERT: B 51 LEU cc_start: 0.9499 (tp) cc_final: 0.9082 (tp) REVERT: B 77 ILE cc_start: 0.9566 (mt) cc_final: 0.9331 (mt) REVERT: B 81 PHE cc_start: 0.9516 (m-10) cc_final: 0.9157 (m-10) REVERT: B 87 LYS cc_start: 0.9362 (tptp) cc_final: 0.9028 (tptp) REVERT: B 95 MET cc_start: 0.9601 (tpp) cc_final: 0.9190 (tpp) REVERT: B 114 ILE cc_start: 0.9526 (mt) cc_final: 0.9211 (pt) REVERT: B 143 LEU cc_start: 0.9663 (tp) cc_final: 0.9454 (tp) REVERT: B 144 MET cc_start: 0.9002 (mtm) cc_final: 0.8532 (mtm) REVERT: B 147 GLN cc_start: 0.9027 (tt0) cc_final: 0.8711 (tt0) REVERT: B 148 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8556 (mm-30) REVERT: B 149 TYR cc_start: 0.9459 (t80) cc_final: 0.8912 (t80) REVERT: B 162 LYS cc_start: 0.9366 (tppt) cc_final: 0.9150 (mttt) REVERT: B 164 ARG cc_start: 0.9273 (ptt90) cc_final: 0.8828 (ttp80) REVERT: B 211 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8519 (mm-30) REVERT: B 240 MET cc_start: 0.8253 (mpp) cc_final: 0.7764 (mpp) REVERT: B 252 ASN cc_start: 0.8857 (t0) cc_final: 0.8652 (t0) REVERT: B 257 ASP cc_start: 0.8468 (m-30) cc_final: 0.8152 (m-30) REVERT: B 286 ASP cc_start: 0.9219 (m-30) cc_final: 0.8599 (m-30) REVERT: B 287 LYS cc_start: 0.9453 (mmtt) cc_final: 0.8970 (mmtp) REVERT: B 317 MET cc_start: 0.8006 (pmm) cc_final: 0.7750 (pmm) REVERT: B 318 ASP cc_start: 0.9271 (t70) cc_final: 0.9025 (t0) REVERT: B 333 LYS cc_start: 0.9191 (tptp) cc_final: 0.8798 (tptp) REVERT: B 335 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8080 (mt-10) REVERT: B 350 ARG cc_start: 0.9157 (tpp80) cc_final: 0.8954 (tpp80) REVERT: B 362 ASP cc_start: 0.8853 (m-30) cc_final: 0.8017 (m-30) REVERT: B 375 LYS cc_start: 0.9231 (mmmm) cc_final: 0.8973 (mmmm) REVERT: B 381 LEU cc_start: 0.9121 (pt) cc_final: 0.8914 (pt) REVERT: B 396 ASP cc_start: 0.8119 (p0) cc_final: 0.7538 (p0) REVERT: B 399 GLU cc_start: 0.9480 (mm-30) cc_final: 0.9135 (mp0) REVERT: B 407 ILE cc_start: 0.8658 (mt) cc_final: 0.8241 (mt) REVERT: B 415 ASN cc_start: 0.9230 (t0) cc_final: 0.8064 (t0) REVERT: B 416 ILE cc_start: 0.9791 (mt) cc_final: 0.9462 (mt) REVERT: B 418 ASN cc_start: 0.9263 (m-40) cc_final: 0.8825 (m-40) REVERT: B 420 MET cc_start: 0.9221 (mmm) cc_final: 0.8733 (mmm) REVERT: B 426 GLU cc_start: 0.9213 (pm20) cc_final: 0.8916 (pm20) REVERT: B 427 LYS cc_start: 0.9695 (ptpp) cc_final: 0.9237 (ptpp) REVERT: B 466 MET cc_start: 0.8999 (ptp) cc_final: 0.8260 (ptp) REVERT: B 467 ASN cc_start: 0.9234 (m-40) cc_final: 0.8301 (m110) REVERT: B 468 LEU cc_start: 0.9500 (tp) cc_final: 0.9296 (tp) REVERT: B 480 GLU cc_start: 0.9294 (pm20) cc_final: 0.8915 (mt-10) REVERT: B 496 ASN cc_start: 0.9539 (t0) cc_final: 0.9297 (t0) REVERT: B 500 ILE cc_start: 0.9793 (mt) cc_final: 0.9364 (mt) REVERT: B 515 ASP cc_start: 0.9102 (m-30) cc_final: 0.8638 (m-30) REVERT: B 570 MET cc_start: 0.9208 (tpp) cc_final: 0.8292 (tpt) REVERT: B 618 LEU cc_start: 0.9106 (mt) cc_final: 0.8878 (mt) REVERT: B 632 MET cc_start: 0.9170 (mmp) cc_final: 0.8903 (mmm) REVERT: B 675 HIS cc_start: 0.9435 (t70) cc_final: 0.9190 (t70) REVERT: C 185 MET cc_start: 0.8848 (mpp) cc_final: 0.8620 (mpp) REVERT: C 204 TYR cc_start: 0.9647 (t80) cc_final: 0.9329 (t80) REVERT: C 278 GLU cc_start: 0.9140 (pm20) cc_final: 0.8928 (pm20) REVERT: D 46 TYR cc_start: 0.9065 (m-80) cc_final: 0.8807 (m-10) REVERT: D 179 TYR cc_start: 0.9101 (t80) cc_final: 0.8768 (t80) REVERT: D 185 MET cc_start: 0.7869 (mmm) cc_final: 0.6897 (mmm) REVERT: D 189 GLU cc_start: 0.9044 (tp30) cc_final: 0.8839 (pt0) REVERT: D 317 ASP cc_start: 0.9243 (t0) cc_final: 0.8970 (t0) outliers start: 1 outliers final: 0 residues processed: 629 average time/residue: 0.1273 time to fit residues: 118.0733 Evaluate side-chains 542 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 542 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 6.9990 chunk 99 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 19 optimal weight: 9.9990 chunk 134 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 chunk 151 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 HIS ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 HIS ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** 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 = 0.3519 r_free = 0.3519 target = 0.106972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.076469 restraints weight = 54713.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.078929 restraints weight = 33134.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.080848 restraints weight = 23116.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.082129 restraints weight = 17813.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.083019 restraints weight = 14574.808| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.7980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16386 Z= 0.227 Angle : 0.670 7.225 22134 Z= 0.360 Chirality : 0.043 0.184 2360 Planarity : 0.004 0.052 2818 Dihedral : 9.377 138.421 2290 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.38 (0.19), residues: 1932 helix: 0.67 (0.15), residues: 1139 sheet: -1.19 (0.42), residues: 140 loop : 0.11 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 161 TYR 0.026 0.002 TYR A 531 PHE 0.029 0.002 PHE A 360 TRP 0.021 0.002 TRP A 558 HIS 0.007 0.002 HIS A 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00470 / 0.23 (16386) covalent geometry : angle 0.67032 / 0.36 (22134) hydrogen bonds : bond 0.04014 / 2.52 ( 869) hydrogen bonds : angle 5.16667 / 3.68 ( 2568) *********************** 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 616 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 616 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.9280 (m-80) cc_final: 0.8963 (m-80) REVERT: A 65 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8333 (mp0) REVERT: A 95 MET cc_start: 0.9688 (tpt) cc_final: 0.8344 (tpp) REVERT: A 99 LYS cc_start: 0.9628 (mmtp) cc_final: 0.9258 (mmtp) REVERT: A 104 TYR cc_start: 0.8959 (m-80) cc_final: 0.8436 (m-80) REVERT: A 107 LYS cc_start: 0.9461 (mttm) cc_final: 0.9015 (tptt) REVERT: A 119 GLU cc_start: 0.9032 (pm20) cc_final: 0.8725 (pm20) REVERT: A 120 ASP cc_start: 0.9313 (m-30) cc_final: 0.8406 (m-30) REVERT: A 129 PHE cc_start: 0.9542 (m-80) cc_final: 0.9124 (m-80) REVERT: A 136 LYS cc_start: 0.9825 (mmtt) cc_final: 0.9554 (mmmm) REVERT: A 144 MET cc_start: 0.8937 (mtm) cc_final: 0.8580 (mtm) REVERT: A 161 ARG cc_start: 0.9186 (ttm110) cc_final: 0.8895 (ttm110) REVERT: A 168 VAL cc_start: 0.9349 (m) cc_final: 0.9089 (p) REVERT: A 227 MET cc_start: 0.9250 (mtp) cc_final: 0.8744 (mtp) REVERT: A 231 ASP cc_start: 0.9040 (t0) cc_final: 0.8802 (t0) REVERT: A 235 ARG cc_start: 0.8739 (ttp-110) cc_final: 0.8358 (mtm-85) REVERT: A 252 ASN cc_start: 0.8893 (t0) cc_final: 0.8556 (t0) REVERT: A 286 ASP cc_start: 0.9127 (m-30) cc_final: 0.8651 (m-30) REVERT: A 317 MET cc_start: 0.8850 (mtm) cc_final: 0.8578 (mtm) REVERT: A 337 ILE cc_start: 0.9691 (pt) cc_final: 0.9164 (pt) REVERT: A 359 MET cc_start: 0.9317 (ptt) cc_final: 0.8606 (ppp) REVERT: A 362 ASP cc_start: 0.9213 (m-30) cc_final: 0.8703 (m-30) REVERT: A 370 ASN cc_start: 0.9469 (m-40) cc_final: 0.9202 (m110) REVERT: A 375 LYS cc_start: 0.9513 (mttt) cc_final: 0.9149 (mttt) REVERT: A 385 VAL cc_start: 0.9610 (t) cc_final: 0.9405 (m) REVERT: A 396 ASP cc_start: 0.9016 (p0) cc_final: 0.8786 (p0) REVERT: A 399 GLU cc_start: 0.9455 (tp30) cc_final: 0.9244 (tp30) REVERT: A 413 SER cc_start: 0.9326 (m) cc_final: 0.9110 (t) REVERT: A 414 LEU cc_start: 0.9556 (mt) cc_final: 0.9152 (mt) REVERT: A 426 GLU cc_start: 0.9380 (tm-30) cc_final: 0.8673 (tm-30) REVERT: A 468 LEU cc_start: 0.9568 (tp) cc_final: 0.9320 (tp) REVERT: A 493 MET cc_start: 0.9163 (tmm) cc_final: 0.8816 (tmm) REVERT: A 494 MET cc_start: 0.9483 (mtt) cc_final: 0.9100 (mtp) REVERT: A 515 ASP cc_start: 0.9488 (m-30) cc_final: 0.9210 (m-30) REVERT: A 570 MET cc_start: 0.9124 (ptp) cc_final: 0.8592 (pmm) REVERT: A 583 SER cc_start: 0.9425 (t) cc_final: 0.9124 (t) REVERT: A 585 SER cc_start: 0.9673 (p) cc_final: 0.9277 (t) REVERT: A 586 TYR cc_start: 0.9100 (m-10) cc_final: 0.8799 (m-80) REVERT: A 595 MET cc_start: 0.9216 (tpp) cc_final: 0.8854 (tpp) REVERT: A 598 MET cc_start: 0.8304 (tpt) cc_final: 0.8070 (tpp) REVERT: A 653 SER cc_start: 0.9152 (p) cc_final: 0.8720 (p) REVERT: B 51 LEU cc_start: 0.9525 (tp) cc_final: 0.9180 (tp) REVERT: B 81 PHE cc_start: 0.9550 (m-10) cc_final: 0.9239 (m-10) REVERT: B 87 LYS cc_start: 0.9353 (tptp) cc_final: 0.9011 (tptp) REVERT: B 95 MET cc_start: 0.9604 (tpp) cc_final: 0.9394 (tpp) REVERT: B 99 LYS cc_start: 0.9631 (mmmt) cc_final: 0.9210 (ttmt) REVERT: B 114 ILE cc_start: 0.9550 (mt) cc_final: 0.9229 (pt) REVERT: B 144 MET cc_start: 0.9108 (mtm) cc_final: 0.8640 (mtm) REVERT: B 147 GLN cc_start: 0.9071 (tt0) cc_final: 0.8715 (tt0) REVERT: B 168 VAL cc_start: 0.9090 (t) cc_final: 0.8706 (p) REVERT: B 190 MET cc_start: 0.9611 (mtm) cc_final: 0.9270 (tpp) REVERT: B 211 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8496 (mm-30) REVERT: B 240 MET cc_start: 0.8241 (mpp) cc_final: 0.7766 (mpp) REVERT: B 257 ASP cc_start: 0.8376 (m-30) cc_final: 0.8001 (m-30) REVERT: B 286 ASP cc_start: 0.9211 (m-30) cc_final: 0.8610 (m-30) REVERT: B 290 GLU cc_start: 0.9460 (pt0) cc_final: 0.9218 (pp20) REVERT: B 322 MET cc_start: 0.8647 (ttt) cc_final: 0.8125 (ttt) REVERT: B 335 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8208 (mt-10) REVERT: B 350 ARG cc_start: 0.9095 (tpp80) cc_final: 0.8760 (tpp80) REVERT: B 362 ASP cc_start: 0.8789 (m-30) cc_final: 0.8035 (m-30) REVERT: B 396 ASP cc_start: 0.8205 (p0) cc_final: 0.7625 (p0) REVERT: B 399 GLU cc_start: 0.9492 (mm-30) cc_final: 0.9148 (mp0) REVERT: B 415 ASN cc_start: 0.9095 (t0) cc_final: 0.7983 (t0) REVERT: B 416 ILE cc_start: 0.9808 (mt) cc_final: 0.9515 (mt) REVERT: B 418 ASN cc_start: 0.9178 (m-40) cc_final: 0.8577 (m-40) REVERT: B 420 MET cc_start: 0.9239 (mmm) cc_final: 0.8813 (mmm) REVERT: B 426 GLU cc_start: 0.9214 (pm20) cc_final: 0.8919 (pm20) REVERT: B 427 LYS cc_start: 0.9711 (ptpp) cc_final: 0.9256 (ptpp) REVERT: B 466 MET cc_start: 0.9262 (ptp) cc_final: 0.8466 (ptp) REVERT: B 467 ASN cc_start: 0.9159 (m-40) cc_final: 0.8358 (m-40) REVERT: B 480 GLU cc_start: 0.9282 (pm20) cc_final: 0.9023 (pm20) REVERT: B 496 ASN cc_start: 0.9574 (t0) cc_final: 0.9018 (t0) REVERT: B 500 ILE cc_start: 0.9800 (mt) cc_final: 0.9406 (mt) REVERT: B 505 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8786 (mt-10) REVERT: B 515 ASP cc_start: 0.9137 (m-30) cc_final: 0.8722 (m-30) REVERT: B 531 TYR cc_start: 0.8542 (m-80) cc_final: 0.8143 (m-80) REVERT: B 570 MET cc_start: 0.9071 (tpp) cc_final: 0.8803 (tpp) REVERT: B 632 MET cc_start: 0.9230 (mmp) cc_final: 0.8871 (mmm) REVERT: C 17 PHE cc_start: 0.8591 (p90) cc_final: 0.7466 (p90) REVERT: C 21 PHE cc_start: 0.9422 (m-80) cc_final: 0.8672 (m-80) REVERT: C 46 TYR cc_start: 0.8744 (m-80) cc_final: 0.8483 (m-80) REVERT: C 179 TYR cc_start: 0.9526 (t80) cc_final: 0.9237 (t80) REVERT: C 185 MET cc_start: 0.8767 (mpp) cc_final: 0.8448 (mpp) REVERT: C 204 TYR cc_start: 0.9698 (t80) cc_final: 0.9029 (t80) REVERT: C 276 TYR cc_start: 0.9133 (t80) cc_final: 0.8906 (t80) REVERT: D 46 TYR cc_start: 0.9054 (m-80) cc_final: 0.8785 (m-10) REVERT: D 185 MET cc_start: 0.7906 (mmm) cc_final: 0.7596 (mmm) REVERT: D 201 HIS cc_start: 0.9310 (m170) cc_final: 0.9107 (m170) REVERT: D 317 ASP cc_start: 0.9233 (t0) cc_final: 0.8639 (t70) REVERT: D 318 ASP cc_start: 0.9404 (m-30) cc_final: 0.9153 (m-30) outliers start: 0 outliers final: 0 residues processed: 616 average time/residue: 0.1208 time to fit residues: 110.4057 Evaluate side-chains 530 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 530 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 4.9990 chunk 133 optimal weight: 0.0670 chunk 149 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 88 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 GLN A 34 HIS ** A 131 ASN ** 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 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 489 ASN ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 HIS ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.114172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.082127 restraints weight = 53428.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.085006 restraints weight = 32218.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.087135 restraints weight = 21922.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.088442 restraints weight = 16622.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.089474 restraints weight = 13503.540| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.8174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16386 Z= 0.149 Angle : 0.642 8.821 22134 Z= 0.343 Chirality : 0.043 0.181 2360 Planarity : 0.004 0.089 2818 Dihedral : 9.252 137.908 2290 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.12 % Allowed : 0.58 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.19), residues: 1932 helix: 0.65 (0.15), residues: 1147 sheet: -1.30 (0.42), residues: 136 loop : 0.10 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 261 TYR 0.022 0.002 TYR A 571 PHE 0.025 0.002 PHE B 254 TRP 0.009 0.001 TRP A 558 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (16386) covalent geometry : angle 0.64200 / 0.34 (22134) hydrogen bonds : bond 0.03875 / 2.42 ( 869) hydrogen bonds : angle 5.12007 / 3.65 ( 2568) *********************** 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 611 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 609 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.9200 (m-80) cc_final: 0.8917 (m-80) REVERT: A 65 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8446 (mp0) REVERT: A 95 MET cc_start: 0.9618 (tpt) cc_final: 0.8660 (mmm) REVERT: A 99 LYS cc_start: 0.9612 (mmtp) cc_final: 0.9308 (mmtp) REVERT: A 104 TYR cc_start: 0.8891 (m-80) cc_final: 0.8578 (m-80) REVERT: A 107 LYS cc_start: 0.9479 (mttm) cc_final: 0.9173 (mmmt) REVERT: A 119 GLU cc_start: 0.8982 (pm20) cc_final: 0.8715 (pm20) REVERT: A 120 ASP cc_start: 0.9224 (m-30) cc_final: 0.8353 (m-30) REVERT: A 129 PHE cc_start: 0.9544 (m-80) cc_final: 0.9124 (m-80) REVERT: A 136 LYS cc_start: 0.9821 (mmtt) cc_final: 0.9509 (ttpt) REVERT: A 144 MET cc_start: 0.8895 (mtm) cc_final: 0.8436 (mtm) REVERT: A 168 VAL cc_start: 0.9297 (m) cc_final: 0.9011 (p) REVERT: A 227 MET cc_start: 0.9185 (mtp) cc_final: 0.8674 (mtp) REVERT: A 235 ARG cc_start: 0.8796 (ttp-110) cc_final: 0.8212 (mtm-85) REVERT: A 252 ASN cc_start: 0.8839 (t0) cc_final: 0.8577 (t0) REVERT: A 266 LYS cc_start: 0.9407 (ptmm) cc_final: 0.9132 (pptt) REVERT: A 286 ASP cc_start: 0.9108 (m-30) cc_final: 0.8615 (m-30) REVERT: A 317 MET cc_start: 0.8783 (mtm) cc_final: 0.8531 (mtm) REVERT: A 322 MET cc_start: 0.8886 (mmm) cc_final: 0.8619 (mmm) REVERT: A 357 TYR cc_start: 0.7747 (m-80) cc_final: 0.7238 (m-80) REVERT: A 359 MET cc_start: 0.9302 (ptt) cc_final: 0.8637 (ppp) REVERT: A 362 ASP cc_start: 0.9255 (m-30) cc_final: 0.8891 (m-30) REVERT: A 366 LYS cc_start: 0.9428 (ptpp) cc_final: 0.9004 (pttp) REVERT: A 370 ASN cc_start: 0.9519 (m-40) cc_final: 0.9157 (m-40) REVERT: A 375 LYS cc_start: 0.9500 (mttt) cc_final: 0.9139 (mttt) REVERT: A 414 LEU cc_start: 0.9588 (mt) cc_final: 0.9236 (mt) REVERT: A 431 LEU cc_start: 0.9052 (mm) cc_final: 0.8691 (tp) REVERT: A 456 LYS cc_start: 0.9660 (mmpt) cc_final: 0.9334 (mmmt) REVERT: A 468 LEU cc_start: 0.9562 (tp) cc_final: 0.9299 (tp) REVERT: A 479 TYR cc_start: 0.8830 (t80) cc_final: 0.8134 (t80) REVERT: A 493 MET cc_start: 0.9187 (tmm) cc_final: 0.8864 (tmm) REVERT: A 494 MET cc_start: 0.9470 (mtt) cc_final: 0.9080 (mtp) REVERT: A 515 ASP cc_start: 0.9470 (m-30) cc_final: 0.9187 (m-30) REVERT: A 522 TYR cc_start: 0.9238 (m-80) cc_final: 0.8840 (m-80) REVERT: A 570 MET cc_start: 0.9002 (ptp) cc_final: 0.8526 (pmm) REVERT: A 586 TYR cc_start: 0.9056 (m-10) cc_final: 0.8714 (m-80) REVERT: A 595 MET cc_start: 0.9176 (tpp) cc_final: 0.8757 (tpp) REVERT: A 615 MET cc_start: 0.8813 (mmp) cc_final: 0.8479 (mmp) REVERT: A 618 LEU cc_start: 0.9305 (tt) cc_final: 0.9075 (tt) REVERT: A 627 LYS cc_start: 0.9522 (tttt) cc_final: 0.9240 (tttm) REVERT: A 632 MET cc_start: 0.8679 (mmp) cc_final: 0.8345 (mmm) REVERT: A 653 SER cc_start: 0.9025 (p) cc_final: 0.8527 (p) REVERT: A 654 PHE cc_start: 0.8957 (t80) cc_final: 0.8693 (t80) REVERT: A 667 LEU cc_start: 0.9684 (tt) cc_final: 0.9461 (tt) REVERT: A 677 ARG cc_start: 0.9416 (mmm-85) cc_final: 0.8192 (mmm-85) REVERT: B 51 LEU cc_start: 0.9462 (tp) cc_final: 0.9074 (tp) REVERT: B 81 PHE cc_start: 0.9527 (m-10) cc_final: 0.9210 (m-10) REVERT: B 87 LYS cc_start: 0.9340 (tptp) cc_final: 0.9021 (tptp) REVERT: B 95 MET cc_start: 0.9552 (tpp) cc_final: 0.8576 (tpp) REVERT: B 99 LYS cc_start: 0.9637 (mmmt) cc_final: 0.8872 (mmmt) REVERT: B 114 ILE cc_start: 0.9487 (mt) cc_final: 0.9193 (pt) REVERT: B 143 LEU cc_start: 0.9686 (tp) cc_final: 0.9471 (tp) REVERT: B 144 MET cc_start: 0.8990 (mtm) cc_final: 0.8520 (mtm) REVERT: B 147 GLN cc_start: 0.9088 (tt0) cc_final: 0.8778 (tt0) REVERT: B 148 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8447 (mm-30) REVERT: B 149 TYR cc_start: 0.9485 (t80) cc_final: 0.8807 (t80) REVERT: B 164 ARG cc_start: 0.9194 (ptt90) cc_final: 0.8826 (ttp80) REVERT: B 168 VAL cc_start: 0.9182 (t) cc_final: 0.8844 (p) REVERT: B 190 MET cc_start: 0.9600 (mtm) cc_final: 0.9229 (mmp) REVERT: B 211 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8456 (mm-30) REVERT: B 240 MET cc_start: 0.8296 (mpp) cc_final: 0.7824 (mpp) REVERT: B 257 ASP cc_start: 0.8399 (m-30) cc_final: 0.8035 (m-30) REVERT: B 263 ASP cc_start: 0.9337 (m-30) cc_final: 0.9038 (m-30) REVERT: B 290 GLU cc_start: 0.9453 (pt0) cc_final: 0.9216 (pp20) REVERT: B 314 MET cc_start: 0.8724 (ppp) cc_final: 0.8449 (ppp) REVERT: B 335 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8185 (mt-10) REVERT: B 357 TYR cc_start: 0.9126 (m-10) cc_final: 0.8581 (m-80) REVERT: B 359 MET cc_start: 0.8410 (ttm) cc_final: 0.8192 (ttm) REVERT: B 362 ASP cc_start: 0.8725 (m-30) cc_final: 0.8288 (m-30) REVERT: B 375 LYS cc_start: 0.9202 (mmmm) cc_final: 0.8973 (mmmt) REVERT: B 396 ASP cc_start: 0.8092 (p0) cc_final: 0.7557 (p0) REVERT: B 399 GLU cc_start: 0.9497 (mm-30) cc_final: 0.9165 (mp0) REVERT: B 415 ASN cc_start: 0.9212 (t0) cc_final: 0.8092 (t0) REVERT: B 416 ILE cc_start: 0.9819 (mt) cc_final: 0.9520 (mt) REVERT: B 418 ASN cc_start: 0.9169 (m-40) cc_final: 0.8775 (m-40) REVERT: B 420 MET cc_start: 0.9253 (mmm) cc_final: 0.8817 (mmm) REVERT: B 426 GLU cc_start: 0.9202 (pm20) cc_final: 0.8895 (pm20) REVERT: B 427 LYS cc_start: 0.9720 (ptpp) cc_final: 0.9219 (ptpp) REVERT: B 466 MET cc_start: 0.9280 (ptp) cc_final: 0.8478 (ptp) REVERT: B 467 ASN cc_start: 0.9320 (m-40) cc_final: 0.8475 (m110) REVERT: B 472 LEU cc_start: 0.9709 (mm) cc_final: 0.9500 (mm) REVERT: B 480 GLU cc_start: 0.9306 (pm20) cc_final: 0.9042 (pm20) REVERT: B 501 GLN cc_start: 0.8973 (tp-100) cc_final: 0.8549 (tp-100) REVERT: B 505 GLU cc_start: 0.9035 (mt-10) cc_final: 0.7842 (mt-10) REVERT: B 515 ASP cc_start: 0.9084 (m-30) cc_final: 0.8650 (m-30) REVERT: B 570 MET cc_start: 0.9313 (tpp) cc_final: 0.8670 (tpt) REVERT: B 585 SER cc_start: 0.9237 (p) cc_final: 0.8811 (t) REVERT: B 631 ASP cc_start: 0.9579 (m-30) cc_final: 0.9282 (m-30) REVERT: B 632 MET cc_start: 0.9216 (mmp) cc_final: 0.8794 (mmm) REVERT: B 671 ASP cc_start: 0.9570 (m-30) cc_final: 0.9361 (m-30) REVERT: C 17 PHE cc_start: 0.8119 (p90) cc_final: 0.7153 (p90) REVERT: C 21 PHE cc_start: 0.9435 (m-80) cc_final: 0.8718 (m-80) REVERT: C 46 TYR cc_start: 0.8783 (m-80) cc_final: 0.8523 (m-80) REVERT: C 176 LEU cc_start: 0.9448 (tt) cc_final: 0.9223 (pp) REVERT: C 179 TYR cc_start: 0.9461 (t80) cc_final: 0.9129 (t80) REVERT: C 185 MET cc_start: 0.8644 (mpp) cc_final: 0.8332 (mpp) REVERT: C 204 TYR cc_start: 0.9697 (t80) cc_final: 0.8932 (t80) REVERT: C 276 TYR cc_start: 0.9168 (t80) cc_final: 0.8930 (t80) REVERT: D 46 TYR cc_start: 0.9080 (m-80) cc_final: 0.8831 (m-10) REVERT: D 201 HIS cc_start: 0.9460 (m170) cc_final: 0.9207 (m170) REVERT: D 317 ASP cc_start: 0.9198 (t0) cc_final: 0.8891 (t0) outliers start: 2 outliers final: 0 residues processed: 611 average time/residue: 0.1213 time to fit residues: 109.7551 Evaluate side-chains 535 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 535 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 189 optimal weight: 9.9990 chunk 181 optimal weight: 10.0000 chunk 165 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 54 optimal weight: 7.9990 chunk 132 optimal weight: 4.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 ASN ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.115995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.084776 restraints weight = 53003.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.087540 restraints weight = 32046.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.089500 restraints weight = 22179.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.090865 restraints weight = 16776.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.091880 restraints weight = 13602.695| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.8336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16386 Z= 0.143 Angle : 0.656 10.728 22134 Z= 0.350 Chirality : 0.043 0.178 2360 Planarity : 0.004 0.058 2818 Dihedral : 9.209 139.217 2290 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.06 % Allowed : 0.23 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.26 (0.19), residues: 1932 helix: 0.57 (0.15), residues: 1148 sheet: -1.25 (0.43), residues: 138 loop : 0.06 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 261 TYR 0.020 0.001 TYR C 177 PHE 0.045 0.002 PHE D 227 TRP 0.008 0.001 TRP A 623 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (16386) covalent geometry : angle 0.65605 / 0.35 (22134) hydrogen bonds : bond 0.03943 / 2.49 ( 869) hydrogen bonds : angle 5.18000 / 3.70 ( 2568) ********************** 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 618 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 617 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.9550 (mp0) cc_final: 0.9337 (mp0) REVERT: A 95 MET cc_start: 0.9596 (tpt) cc_final: 0.8624 (mmm) REVERT: A 99 LYS cc_start: 0.9619 (mmtp) cc_final: 0.9287 (mmtp) REVERT: A 104 TYR cc_start: 0.8932 (m-80) cc_final: 0.8564 (m-80) REVERT: A 107 LYS cc_start: 0.9511 (mttm) cc_final: 0.9205 (mmmt) REVERT: A 119 GLU cc_start: 0.8975 (pm20) cc_final: 0.8762 (pm20) REVERT: A 120 ASP cc_start: 0.9211 (m-30) cc_final: 0.8284 (m-30) REVERT: A 129 PHE cc_start: 0.9536 (m-80) cc_final: 0.9089 (m-80) REVERT: A 136 LYS cc_start: 0.9831 (mmtt) cc_final: 0.9596 (mmmm) REVERT: A 144 MET cc_start: 0.8885 (mtm) cc_final: 0.8392 (mtm) REVERT: A 158 ASN cc_start: 0.9373 (m-40) cc_final: 0.9115 (m-40) REVERT: A 188 ILE cc_start: 0.9474 (mt) cc_final: 0.9254 (mt) REVERT: A 205 LYS cc_start: 0.8077 (mmmt) cc_final: 0.7665 (mmmt) REVERT: A 227 MET cc_start: 0.9168 (mtp) cc_final: 0.8733 (mtp) REVERT: A 235 ARG cc_start: 0.8920 (ttp-110) cc_final: 0.8331 (mtm-85) REVERT: A 252 ASN cc_start: 0.8908 (t0) cc_final: 0.8596 (t0) REVERT: A 266 LYS cc_start: 0.9398 (ptmm) cc_final: 0.9136 (pptt) REVERT: A 277 THR cc_start: 0.9441 (p) cc_final: 0.9128 (p) REVERT: A 286 ASP cc_start: 0.9076 (m-30) cc_final: 0.8623 (m-30) REVERT: A 317 MET cc_start: 0.9004 (mtm) cc_final: 0.8724 (mtm) REVERT: A 357 TYR cc_start: 0.7764 (m-80) cc_final: 0.7132 (m-80) REVERT: A 359 MET cc_start: 0.9349 (ptt) cc_final: 0.8645 (ppp) REVERT: A 362 ASP cc_start: 0.9191 (m-30) cc_final: 0.8759 (m-30) REVERT: A 366 LYS cc_start: 0.9390 (ptpp) cc_final: 0.9060 (pttp) REVERT: A 370 ASN cc_start: 0.9514 (m-40) cc_final: 0.9111 (m-40) REVERT: A 375 LYS cc_start: 0.9482 (mttt) cc_final: 0.9091 (mttt) REVERT: A 396 ASP cc_start: 0.8875 (p0) cc_final: 0.8645 (p0) REVERT: A 414 LEU cc_start: 0.9470 (mt) cc_final: 0.9217 (mt) REVERT: A 431 LEU cc_start: 0.9031 (mm) cc_final: 0.8689 (tp) REVERT: A 456 LYS cc_start: 0.9657 (mmpt) cc_final: 0.9355 (mmmt) REVERT: A 468 LEU cc_start: 0.9567 (tp) cc_final: 0.9288 (tp) REVERT: A 479 TYR cc_start: 0.8801 (t80) cc_final: 0.8092 (t80) REVERT: A 493 MET cc_start: 0.9180 (tmm) cc_final: 0.8807 (tmm) REVERT: A 494 MET cc_start: 0.9403 (mtt) cc_final: 0.8988 (mtp) REVERT: A 515 ASP cc_start: 0.9478 (m-30) cc_final: 0.9185 (m-30) REVERT: A 522 TYR cc_start: 0.9177 (m-80) cc_final: 0.8715 (m-80) REVERT: A 562 LYS cc_start: 0.9761 (ttmt) cc_final: 0.9431 (tttt) REVERT: A 570 MET cc_start: 0.8931 (ptp) cc_final: 0.8367 (pmm) REVERT: A 586 TYR cc_start: 0.9043 (m-10) cc_final: 0.8744 (m-80) REVERT: A 595 MET cc_start: 0.9091 (tpp) cc_final: 0.8677 (tpp) REVERT: A 601 ILE cc_start: 0.9510 (tt) cc_final: 0.9250 (tt) REVERT: A 602 GLU cc_start: 0.8877 (pt0) cc_final: 0.7832 (pt0) REVERT: A 618 LEU cc_start: 0.9271 (tt) cc_final: 0.9051 (tt) REVERT: A 627 LYS cc_start: 0.9504 (tttt) cc_final: 0.9173 (tttm) REVERT: A 632 MET cc_start: 0.8807 (mmp) cc_final: 0.8346 (mmm) REVERT: A 647 HIS cc_start: 0.8709 (m-70) cc_final: 0.8458 (m-70) REVERT: A 653 SER cc_start: 0.9098 (p) cc_final: 0.8196 (t) REVERT: A 654 PHE cc_start: 0.8959 (t80) cc_final: 0.8758 (t80) REVERT: A 667 LEU cc_start: 0.9664 (tt) cc_final: 0.9433 (tt) REVERT: A 677 ARG cc_start: 0.9421 (mmm-85) cc_final: 0.8224 (mmm-85) REVERT: B 25 GLN cc_start: 0.9236 (mt0) cc_final: 0.8944 (mt0) REVERT: B 51 LEU cc_start: 0.9427 (tp) cc_final: 0.9032 (tp) REVERT: B 77 ILE cc_start: 0.9565 (mt) cc_final: 0.9361 (mt) REVERT: B 81 PHE cc_start: 0.9520 (m-10) cc_final: 0.9215 (m-10) REVERT: B 87 LYS cc_start: 0.9345 (tptp) cc_final: 0.9030 (tptp) REVERT: B 95 MET cc_start: 0.9503 (tpp) cc_final: 0.9014 (tpp) REVERT: B 114 ILE cc_start: 0.9460 (mt) cc_final: 0.9229 (pt) REVERT: B 144 MET cc_start: 0.9048 (mtm) cc_final: 0.8740 (mtm) REVERT: B 147 GLN cc_start: 0.9106 (tt0) cc_final: 0.8866 (tp40) REVERT: B 149 TYR cc_start: 0.9469 (t80) cc_final: 0.8775 (t80) REVERT: B 164 ARG cc_start: 0.9180 (ptt90) cc_final: 0.8717 (ptm-80) REVERT: B 168 VAL cc_start: 0.9174 (t) cc_final: 0.8780 (p) REVERT: B 190 MET cc_start: 0.9607 (mtm) cc_final: 0.9243 (tpp) REVERT: B 191 GLN cc_start: 0.9410 (mm-40) cc_final: 0.9129 (mm-40) REVERT: B 211 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8466 (mm-30) REVERT: B 236 TYR cc_start: 0.8891 (t80) cc_final: 0.8651 (t80) REVERT: B 240 MET cc_start: 0.8278 (mpp) cc_final: 0.7852 (mpp) REVERT: B 257 ASP cc_start: 0.8378 (m-30) cc_final: 0.8057 (m-30) REVERT: B 263 ASP cc_start: 0.9355 (m-30) cc_final: 0.9079 (m-30) REVERT: B 290 GLU cc_start: 0.9445 (pt0) cc_final: 0.9226 (pp20) REVERT: B 322 MET cc_start: 0.8891 (tpt) cc_final: 0.8355 (tpp) REVERT: B 326 PHE cc_start: 0.9514 (m-10) cc_final: 0.8650 (m-80) REVERT: B 335 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8126 (mt-10) REVERT: B 359 MET cc_start: 0.8461 (ttm) cc_final: 0.8248 (ttm) REVERT: B 362 ASP cc_start: 0.8694 (m-30) cc_final: 0.8267 (m-30) REVERT: B 373 ILE cc_start: 0.9650 (mt) cc_final: 0.9086 (mt) REVERT: B 375 LYS cc_start: 0.9194 (mmmm) cc_final: 0.8946 (mmmm) REVERT: B 390 GLN cc_start: 0.9250 (mm110) cc_final: 0.8949 (mm-40) REVERT: B 396 ASP cc_start: 0.7989 (p0) cc_final: 0.7483 (p0) REVERT: B 399 GLU cc_start: 0.9476 (mm-30) cc_final: 0.9159 (mp0) REVERT: B 415 ASN cc_start: 0.9271 (t0) cc_final: 0.8177 (t0) REVERT: B 416 ILE cc_start: 0.9793 (mt) cc_final: 0.9435 (mt) REVERT: B 418 ASN cc_start: 0.9231 (m-40) cc_final: 0.8908 (m-40) REVERT: B 420 MET cc_start: 0.9201 (mmm) cc_final: 0.8727 (mmm) REVERT: B 426 GLU cc_start: 0.9201 (pm20) cc_final: 0.8924 (pm20) REVERT: B 427 LYS cc_start: 0.9723 (ptpp) cc_final: 0.9180 (ptpp) REVERT: B 466 MET cc_start: 0.9202 (ptp) cc_final: 0.8412 (ptp) REVERT: B 467 ASN cc_start: 0.9298 (m-40) cc_final: 0.8424 (m110) REVERT: B 480 GLU cc_start: 0.9269 (pm20) cc_final: 0.9008 (pm20) REVERT: B 501 GLN cc_start: 0.9005 (tp-100) cc_final: 0.8565 (tp-100) REVERT: B 505 GLU cc_start: 0.9051 (mt-10) cc_final: 0.7825 (mt-10) REVERT: B 515 ASP cc_start: 0.9083 (m-30) cc_final: 0.8684 (m-30) REVERT: B 516 GLN cc_start: 0.9063 (tt0) cc_final: 0.8752 (tt0) REVERT: B 527 TYR cc_start: 0.8971 (t80) cc_final: 0.8720 (t80) REVERT: B 570 MET cc_start: 0.9176 (tpp) cc_final: 0.8684 (tpp) REVERT: B 585 SER cc_start: 0.9194 (p) cc_final: 0.8847 (t) REVERT: B 597 ILE cc_start: 0.9330 (pt) cc_final: 0.8782 (pt) REVERT: B 631 ASP cc_start: 0.9570 (m-30) cc_final: 0.9277 (m-30) REVERT: B 632 MET cc_start: 0.9237 (mmp) cc_final: 0.8728 (mmm) REVERT: C 17 PHE cc_start: 0.8310 (p90) cc_final: 0.7304 (p90) REVERT: C 21 PHE cc_start: 0.9489 (m-80) cc_final: 0.8753 (m-80) REVERT: C 46 TYR cc_start: 0.8804 (m-80) cc_final: 0.8546 (m-80) REVERT: C 176 LEU cc_start: 0.9430 (tt) cc_final: 0.9195 (pp) REVERT: C 179 TYR cc_start: 0.9455 (t80) cc_final: 0.9086 (t80) REVERT: C 185 MET cc_start: 0.8595 (mpp) cc_final: 0.8265 (mpp) REVERT: C 204 TYR cc_start: 0.9680 (t80) cc_final: 0.8926 (t80) REVERT: C 276 TYR cc_start: 0.9137 (t80) cc_final: 0.8876 (t80) REVERT: D 46 TYR cc_start: 0.9058 (m-80) cc_final: 0.8814 (m-10) REVERT: D 185 MET cc_start: 0.7433 (mmm) cc_final: 0.6939 (mmp) REVERT: D 201 HIS cc_start: 0.9489 (m170) cc_final: 0.9155 (m170) REVERT: D 317 ASP cc_start: 0.9235 (t0) cc_final: 0.8961 (t0) outliers start: 1 outliers final: 0 residues processed: 618 average time/residue: 0.1268 time to fit residues: 116.9531 Evaluate side-chains 539 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 539 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 148 optimal weight: 7.9990 chunk 125 optimal weight: 2.9990 chunk 28 optimal weight: 0.2980 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.111584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.081234 restraints weight = 53371.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.084012 restraints weight = 32525.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.085823 restraints weight = 22871.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.087195 restraints weight = 17638.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.088114 restraints weight = 14348.679| |-----------------------------------------------------------------------------| r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.8513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16386 Z= 0.142 Angle : 0.650 7.259 22134 Z= 0.349 Chirality : 0.043 0.183 2360 Planarity : 0.004 0.053 2818 Dihedral : 9.131 140.476 2290 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.06 % Allowed : 0.17 % Favored : 99.77 % 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: 0.28 (0.19), residues: 1932 helix: 0.62 (0.15), residues: 1140 sheet: -1.17 (0.43), residues: 138 loop : -0.04 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 261 TYR 0.021 0.001 TYR A 571 PHE 0.041 0.002 PHE D 227 TRP 0.009 0.001 TRP A 623 HIS 0.005 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (16386) covalent geometry : angle 0.65009 / 0.35 (22134) hydrogen bonds : bond 0.03998 / 2.50 ( 869) hydrogen bonds : angle 5.16146 / 3.69 ( 2568) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3052.05 seconds wall clock time: 53 minutes 45.47 seconds (3225.47 seconds total)