Starting phenix.real_space_refine on Thu Aug 6 15:10:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz9_45057/08_2026/9bz9_45057_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz9_45057/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9bz9_45057/08_2026/9bz9_45057_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz9_45057/08_2026/9bz9_45057_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bz9_45057/08_2026/9bz9_45057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz9_45057/08_2026/9bz9_45057.map" } 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-2.2rc3-6140/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, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.41, per 1000 atoms: 0.21 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: 1.29 Conformation dependent library (CDL) restraints added in 682.5 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: 0.46 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: 2.76 Time building geometry restraints manager: 1.74 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 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.964 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 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: 1.450 Set stop_for_unknowns flag: 0.010 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: 0.260 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.880 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.290 ------------------------------------------------------------------------------- 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 : 0.609 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: 0.8413 (t) REVERT: A 51 LEU cc_start: 0.8122 (tp) cc_final: 0.7512 (tp) REVERT: A 81 PHE cc_start: 0.7597 (m-80) cc_final: 0.7374 (m-80) REVERT: A 125 VAL cc_start: 0.9045 (t) cc_final: 0.7560 (t) REVERT: A 143 LEU cc_start: 0.9043 (tp) cc_final: 0.8605 (tp) REVERT: A 166 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8068 (mm-30) REVERT: A 181 ASP cc_start: 0.8496 (m-30) cc_final: 0.8084 (m-30) REVERT: A 193 SER cc_start: 0.8717 (m) cc_final: 0.8516 (p) REVERT: A 213 ILE cc_start: 0.8120 (mt) cc_final: 0.7579 (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: 0.7262 (t) REVERT: A 288 PHE cc_start: 0.7249 (t80) cc_final: 0.6806 (t80) REVERT: A 300 VAL cc_start: 0.7424 (m) cc_final: 0.7063 (m) REVERT: A 322 MET cc_start: 0.7645 (mmp) cc_final: 0.6462 (mmm) REVERT: A 342 LEU cc_start: 0.9170 (tp) cc_final: 0.8674 (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: 0.7291 (m-10) REVERT: A 362 ASP cc_start: 0.6185 (m-30) cc_final: 0.4947 (m-30) REVERT: A 367 VAL cc_start: 0.8092 (m) cc_final: 0.7839 (m) REVERT: A 370 ASN cc_start: 0.7524 (m-40) cc_final: 0.6771 (m-40) REVERT: A 416 ILE cc_start: 0.8779 (mt) cc_final: 0.8557 (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: 0.8889 (mt) REVERT: A 500 ILE cc_start: 0.9201 (mt) cc_final: 0.8592 (mt) REVERT: A 550 MET cc_start: 0.6900 (mtm) cc_final: 0.6699 (mtp) REVERT: A 634 MET cc_start: 0.8337 (mmp) cc_final: 0.7983 (mpp) REVERT: A 641 ILE cc_start: 0.9277 (mm) cc_final: 0.9032 (mm) REVERT: A 652 ILE cc_start: 0.8789 (mt) cc_final: 0.8488 (mt) REVERT: A 653 SER cc_start: 0.9052 (OUTLIER) cc_final: 0.8696 (p) REVERT: A 682 ILE cc_start: 0.8321 (mt) cc_final: 0.8051 (mt) REVERT: B 41 ILE cc_start: 0.8853 (mm) cc_final: 0.8164 (mt) REVERT: B 51 LEU cc_start: 0.8561 (tp) cc_final: 0.8184 (tp) REVERT: B 95 MET cc_start: 0.7883 (tpp) cc_final: 0.7676 (tpp) REVERT: B 98 PHE cc_start: 0.7798 (t80) cc_final: 0.7462 (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: 0.7618 (t80) REVERT: B 101 TYR cc_start: 0.7554 (m-80) cc_final: 0.7058 (m-80) REVERT: B 143 LEU cc_start: 0.9038 (tp) cc_final: 0.8824 (tp) REVERT: B 149 TYR cc_start: 0.8345 (t80) cc_final: 0.7635 (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: 0.8184 (mm-40) REVERT: B 213 ILE cc_start: 0.8783 (mt) cc_final: 0.8575 (tp) REVERT: B 232 ASN cc_start: 0.8293 (OUTLIER) cc_final: 0.8039 (m-40) REVERT: B 240 MET cc_start: 0.6884 (mpt) cc_final: 0.6323 (mpt) REVERT: B 288 PHE cc_start: 0.7313 (t80) cc_final: 0.6324 (t80) REVERT: B 322 MET cc_start: 0.7357 (mmm) cc_final: 0.5743 (tpp) REVERT: B 337 ILE cc_start: 0.8308 (pt) cc_final: 0.8011 (pt) REVERT: B 361 GLN cc_start: 0.6689 (tt0) cc_final: 0.6384 (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: 0.8323 (mt) REVERT: B 415 ASN cc_start: 0.8552 (t0) cc_final: 0.7838 (t0) REVERT: B 418 ASN cc_start: 0.7652 (m-40) cc_final: 0.6533 (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: 0.9098 (mt) REVERT: B 493 MET cc_start: 0.7437 (tmm) cc_final: 0.7146 (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: 0.5335 (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: 0.6952 (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: 0.7235 (mt) REVERT: B 613 TYR cc_start: 0.7838 (t80) cc_final: 0.7529 (t80) REVERT: B 641 ILE cc_start: 0.9444 (mm) cc_final: 0.9122 (mm) REVERT: B 645 GLN cc_start: 0.8410 (tp-100) cc_final: 0.8210 (tp-100) 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: 0.4883 (tt0) REVERT: C 90 LEU cc_start: 0.5509 (mt) cc_final: 0.4979 (mt) REVERT: C 137 MET cc_start: 0.4147 (mtp) cc_final: 0.3341 (mtt) REVERT: C 194 ILE cc_start: 0.7431 (mt) cc_final: 0.7188 (mp) REVERT: C 205 VAL cc_start: 0.7608 (t) cc_final: 0.7334 (t) REVERT: C 275 PRO cc_start: 0.5456 (Cg_endo) cc_final: 0.4941 (Cg_exo) REVERT: D 31 LEU cc_start: 0.8392 (mt) cc_final: 0.8044 (mt) REVERT: D 100 VAL cc_start: 0.3534 (t) cc_final: 0.2881 (t) REVERT: D 205 VAL cc_start: 0.7168 (t) cc_final: 0.6775 (t) REVERT: D 317 ASP cc_start: 0.6461 (t0) cc_final: 0.5769 (t70) outliers start: 24 outliers final: 5 residues processed: 915 average time/residue: 0.1430 time to fit residues: 189.6214 Evaluate side-chains 632 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 625 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN C 28 GLN C 84 HIS C 119 ASN C 132 GLN D 71 ASN D 80 HIS D 186 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.110143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.077008 restraints weight = 51666.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.079741 restraints weight = 31456.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.081737 restraints weight = 22174.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.083053 restraints weight = 17123.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.083969 restraints weight = 14094.615| |-----------------------------------------------------------------------------| r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3127 r_free = 0.3127 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 13 (19 function evaluations) r_final: 0.3127 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 16386 Z= 0.254 Angle : 0.697 7.875 22134 Z= 0.378 Chirality : 0.044 0.294 2360 Planarity : 0.004 0.040 2818 Dihedral : 9.788 127.230 2290 Min Nonbonded Distance : 1.720 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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: 1.12 (0.18), residues: 1932 helix: 1.17 (0.15), residues: 1104 sheet: 0.01 (0.40), residues: 126 loop : 0.39 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 293 TYR 0.029 0.002 TYR C 247 PHE 0.042 0.003 PHE D 178 TRP 0.014 0.002 TRP A 558 HIS 0.007 0.002 HIS B 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.25 (16386) covalent geometry : angle 0.69742 / 0.38 (22134) hydrogen bonds : bond 0.04714 / 2.99 ( 869) hydrogen bonds : angle 5.24834 / 3.75 ( 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 704 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 699 time to evaluate : 0.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ILE cc_start: 0.9725 (mm) cc_final: 0.9235 (mt) REVERT: A 65 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8151 (mm-30) REVERT: A 87 LYS cc_start: 0.9181 (tptm) cc_final: 0.8833 (tptm) REVERT: A 107 LYS cc_start: 0.9403 (mttm) cc_final: 0.9165 (mmmt) REVERT: A 136 LYS cc_start: 0.9760 (mmpt) cc_final: 0.9495 (ttpp) REVERT: A 143 LEU cc_start: 0.9263 (tp) cc_final: 0.9007 (tp) REVERT: A 144 MET cc_start: 0.9296 (mtm) cc_final: 0.8812 (mtm) REVERT: A 145 ILE cc_start: 0.9410 (tp) cc_final: 0.9166 (tp) REVERT: A 194 LYS cc_start: 0.9458 (ttpt) cc_final: 0.9111 (ttpp) REVERT: A 195 LEU cc_start: 0.9563 (mt) cc_final: 0.9273 (mt) REVERT: A 252 ASN cc_start: 0.8599 (t0) cc_final: 0.8150 (t0) REVERT: A 279 SER cc_start: 0.7705 (m) cc_final: 0.7492 (p) REVERT: A 286 ASP cc_start: 0.9058 (m-30) cc_final: 0.8655 (m-30) REVERT: A 362 ASP cc_start: 0.8521 (m-30) cc_final: 0.7990 (m-30) REVERT: A 385 VAL cc_start: 0.9612 (t) cc_final: 0.9406 (t) REVERT: A 387 GLN cc_start: 0.8674 (mt0) cc_final: 0.8273 (mt0) REVERT: A 418 ASN cc_start: 0.8965 (m110) cc_final: 0.8566 (m110) REVERT: A 421 GLU cc_start: 0.9445 (tm-30) cc_final: 0.9237 (tm-30) REVERT: A 436 LEU cc_start: 0.9628 (mt) cc_final: 0.9402 (mt) REVERT: A 502 ARG cc_start: 0.9487 (tpt170) cc_final: 0.9202 (tpt90) REVERT: A 510 LYS cc_start: 0.9685 (mmmt) cc_final: 0.9013 (mmtm) REVERT: A 550 MET cc_start: 0.6657 (mtm) cc_final: 0.5609 (ptp) REVERT: A 571 TYR cc_start: 0.8915 (t80) cc_final: 0.8500 (t80) REVERT: A 572 HIS cc_start: 0.9491 (m90) cc_final: 0.8909 (m90) REVERT: A 598 MET cc_start: 0.8401 (ttt) cc_final: 0.7232 (ttm) REVERT: A 615 MET cc_start: 0.8897 (mmp) cc_final: 0.8524 (mmp) REVERT: A 626 TYR cc_start: 0.9133 (m-80) cc_final: 0.8745 (m-10) REVERT: A 634 MET cc_start: 0.9354 (mmp) cc_final: 0.9081 (mpp) REVERT: A 655 THR cc_start: 0.9447 (t) cc_final: 0.9053 (t) REVERT: A 667 LEU cc_start: 0.9450 (tt) cc_final: 0.9208 (tt) REVERT: A 683 TYR cc_start: 0.8475 (t80) cc_final: 0.7739 (t80) REVERT: B 19 GLN cc_start: 0.9349 (mt0) cc_final: 0.8872 (pp30) REVERT: B 51 LEU cc_start: 0.9467 (tp) cc_final: 0.9082 (tp) REVERT: B 77 ILE cc_start: 0.9756 (mt) cc_final: 0.9451 (mt) REVERT: B 87 LYS cc_start: 0.9311 (tptp) cc_final: 0.9002 (tptp) REVERT: B 89 PHE cc_start: 0.9275 (t80) cc_final: 0.9027 (t80) REVERT: B 95 MET cc_start: 0.9503 (tpp) cc_final: 0.8561 (tpp) REVERT: B 99 LYS cc_start: 0.9476 (mmmt) cc_final: 0.8757 (mmmt) REVERT: B 115 LEU cc_start: 0.9042 (mp) cc_final: 0.8813 (mp) REVERT: B 144 MET cc_start: 0.9624 (mtm) cc_final: 0.8968 (mtm) REVERT: B 149 TYR cc_start: 0.8992 (t80) cc_final: 0.8646 (t80) REVERT: B 150 GLN cc_start: 0.9047 (tp40) cc_final: 0.8713 (tp40) REVERT: B 161 ARG cc_start: 0.8827 (ttm110) cc_final: 0.8614 (mtt-85) REVERT: B 162 LYS cc_start: 0.9330 (tppt) cc_final: 0.8900 (mttm) REVERT: B 168 VAL cc_start: 0.9156 (t) cc_final: 0.8794 (p) REVERT: B 191 GLN cc_start: 0.9128 (mm-40) cc_final: 0.8836 (mm-40) REVERT: B 211 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8065 (mt-10) REVERT: B 220 THR cc_start: 0.8216 (p) cc_final: 0.7556 (p) REVERT: B 236 TYR cc_start: 0.8837 (t80) cc_final: 0.8631 (t80) REVERT: B 259 ASN cc_start: 0.8919 (m-40) cc_final: 0.8706 (m-40) REVERT: B 267 ILE cc_start: 0.8834 (pt) cc_final: 0.8531 (pt) REVERT: B 286 ASP cc_start: 0.8995 (m-30) cc_final: 0.8318 (m-30) REVERT: B 317 MET cc_start: 0.8649 (pmm) cc_final: 0.8282 (pmm) REVERT: B 319 MET cc_start: 0.9192 (tpp) cc_final: 0.8868 (tpp) REVERT: B 321 GLU cc_start: 0.8668 (tm-30) cc_final: 0.8366 (tm-30) REVERT: B 322 MET cc_start: 0.8674 (mmm) cc_final: 0.7720 (mmm) REVERT: B 355 TYR cc_start: 0.9335 (m-10) cc_final: 0.8958 (m-10) REVERT: B 362 ASP cc_start: 0.8602 (m-30) cc_final: 0.7799 (m-30) REVERT: B 373 ILE cc_start: 0.9722 (mt) cc_final: 0.9512 (mt) REVERT: B 396 ASP cc_start: 0.7854 (p0) cc_final: 0.7172 (p0) REVERT: B 399 GLU cc_start: 0.9466 (mm-30) cc_final: 0.9198 (mp0) REVERT: B 415 ASN cc_start: 0.9026 (t0) cc_final: 0.7670 (t0) REVERT: B 418 ASN cc_start: 0.9327 (m-40) cc_final: 0.8682 (m-40) REVERT: B 425 ILE cc_start: 0.9074 (mt) cc_final: 0.8872 (mt) REVERT: B 458 MET cc_start: 0.9448 (mmm) cc_final: 0.9002 (mmm) REVERT: B 466 MET cc_start: 0.9337 (ptp) cc_final: 0.8911 (ptp) REVERT: B 467 ASN cc_start: 0.9212 (m-40) cc_final: 0.8846 (m110) REVERT: B 492 PHE cc_start: 0.9743 (m-80) cc_final: 0.9517 (m-80) REVERT: B 494 MET cc_start: 0.9426 (mtp) cc_final: 0.8624 (mtp) REVERT: B 496 ASN cc_start: 0.9708 (t0) cc_final: 0.9229 (t0) REVERT: B 501 GLN cc_start: 0.9069 (tp-100) cc_final: 0.8535 (tp-100) REVERT: B 515 ASP cc_start: 0.9075 (m-30) cc_final: 0.8764 (m-30) REVERT: B 570 MET cc_start: 0.9234 (tpp) cc_final: 0.8688 (tpp) REVERT: B 574 TYR cc_start: 0.8313 (m-80) cc_final: 0.7974 (m-80) REVERT: B 575 ARG cc_start: 0.8832 (mtm110) cc_final: 0.8334 (mtm-85) REVERT: B 588 GLN cc_start: 0.9390 (mm-40) cc_final: 0.8779 (mm-40) REVERT: B 601 ILE cc_start: 0.9277 (mt) cc_final: 0.8975 (mp) REVERT: B 613 TYR cc_start: 0.9348 (t80) cc_final: 0.8880 (t80) REVERT: B 615 MET cc_start: 0.9062 (mmp) cc_final: 0.8267 (mmp) REVERT: B 618 LEU cc_start: 0.8887 (mt) cc_final: 0.8614 (mt) REVERT: B 645 GLN cc_start: 0.9259 (tp-100) cc_final: 0.9008 (tp-100) REVERT: C 21 PHE cc_start: 0.8763 (m-80) cc_final: 0.8143 (m-80) REVERT: C 46 TYR cc_start: 0.7839 (m-80) cc_final: 0.7577 (m-80) REVERT: C 89 VAL cc_start: 0.7586 (t) cc_final: 0.7330 (t) REVERT: C 96 MET cc_start: 0.6738 (mmt) cc_final: 0.6156 (mmt) REVERT: C 139 VAL cc_start: 0.8841 (p) cc_final: 0.8538 (t) REVERT: C 204 TYR cc_start: 0.9562 (t80) cc_final: 0.9088 (t80) REVERT: C 315 LEU cc_start: 0.8410 (mt) cc_final: 0.7949 (mt) REVERT: D 33 GLU cc_start: 0.9363 (mp0) cc_final: 0.9139 (mp0) REVERT: D 46 TYR cc_start: 0.8832 (m-80) cc_final: 0.8408 (m-80) REVERT: D 96 MET cc_start: 0.8468 (mmt) cc_final: 0.7893 (mmm) REVERT: D 109 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.7017 (m-80) REVERT: D 185 MET cc_start: 0.6622 (mmm) cc_final: 0.5446 (mmp) REVERT: D 189 GLU cc_start: 0.8955 (tp30) cc_final: 0.8554 (mp0) REVERT: D 259 PHE cc_start: 0.7810 (t80) cc_final: 0.7288 (t80) REVERT: D 317 ASP cc_start: 0.9290 (t0) cc_final: 0.8166 (t0) outliers start: 5 outliers final: 2 residues processed: 702 average time/residue: 0.1379 time to fit residues: 142.3547 Evaluate side-chains 560 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 557 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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: 0.8980 chunk 28 optimal weight: 0.8980 chunk 182 optimal weight: 9.9990 chunk 159 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 158 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- 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 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 645 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 475 ASN B 676 HIS C 84 HIS D 25 ASN D 80 HIS D 238 ASN D 263 ASN 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 = 0.112095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.079513 restraints weight = 50394.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.082378 restraints weight = 30059.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.084265 restraints weight = 21185.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.085625 restraints weight = 16171.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.086560 restraints weight = 13225.896| |-----------------------------------------------------------------------------| r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (19 function evaluations) r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.5660 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= 0.156 Angle : 0.602 8.690 22134 Z= 0.322 Chirality : 0.042 0.219 2360 Planarity : 0.004 0.051 2818 Dihedral : 9.268 126.774 2290 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.06 % Allowed : 2.39 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.19), residues: 1932 helix: 1.14 (0.15), residues: 1138 sheet: -0.27 (0.41), residues: 132 loop : 0.32 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 243 TYR 0.027 0.002 TYR A 606 PHE 0.031 0.002 PHE D 109 TRP 0.008 0.001 TRP C 30 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 (16386) covalent geometry : angle 0.60180 / 0.32 (22134) hydrogen bonds : bond 0.04146 / 2.61 ( 869) hydrogen bonds : angle 4.91840 / 3.49 ( 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 679 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 678 time to evaluate : 0.659 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: A 87 LYS cc_start: 0.9272 (tptm) cc_final: 0.8958 (tptm) REVERT: A 95 MET cc_start: 0.9748 (tpt) cc_final: 0.9442 (mmm) REVERT: A 117 ARG cc_start: 0.9246 (mtp85) cc_final: 0.8854 (mmt180) REVERT: A 129 PHE cc_start: 0.9405 (m-80) cc_final: 0.9143 (m-80) REVERT: A 136 LYS cc_start: 0.9766 (mmpt) cc_final: 0.9467 (ttpt) REVERT: A 143 LEU cc_start: 0.9179 (tp) cc_final: 0.8941 (tp) REVERT: A 144 MET cc_start: 0.9115 (mtm) cc_final: 0.8632 (mtm) REVERT: A 168 VAL cc_start: 0.9135 (m) cc_final: 0.8851 (p) REVERT: A 191 GLN cc_start: 0.8770 (mm110) cc_final: 0.8424 (mm110) REVERT: A 194 LYS cc_start: 0.9421 (ttpt) cc_final: 0.9170 (ttpp) REVERT: A 204 SER cc_start: 0.8680 (p) cc_final: 0.8327 (p) REVERT: A 227 MET cc_start: 0.9347 (mtp) cc_final: 0.8850 (mtp) REVERT: A 252 ASN cc_start: 0.8531 (t0) cc_final: 0.7890 (t0) REVERT: A 254 PHE cc_start: 0.8243 (m-10) cc_final: 0.7851 (m-10) REVERT: A 286 ASP cc_start: 0.9128 (m-30) cc_final: 0.8608 (m-30) REVERT: A 362 ASP cc_start: 0.8915 (m-30) cc_final: 0.8506 (m-30) REVERT: A 370 ASN cc_start: 0.9376 (m-40) cc_final: 0.9035 (m110) REVERT: A 396 ASP cc_start: 0.9014 (p0) cc_final: 0.8798 (p0) REVERT: A 421 GLU cc_start: 0.9414 (tm-30) cc_final: 0.9211 (tm-30) REVERT: A 500 ILE cc_start: 0.9746 (mt) cc_final: 0.9383 (mt) REVERT: A 601 ILE cc_start: 0.9218 (tt) cc_final: 0.8841 (tt) REVERT: A 615 MET cc_start: 0.8861 (mmp) cc_final: 0.8620 (mmp) REVERT: A 626 TYR cc_start: 0.9210 (m-80) cc_final: 0.8770 (m-10) REVERT: A 634 MET cc_start: 0.9349 (mmp) cc_final: 0.9148 (mpp) REVERT: A 637 VAL cc_start: 0.9777 (t) cc_final: 0.9447 (t) REVERT: A 645 GLN cc_start: 0.8498 (tp-100) cc_final: 0.7305 (tp-100) REVERT: A 650 GLN cc_start: 0.7477 (mm110) cc_final: 0.7210 (mm110) REVERT: A 653 SER cc_start: 0.9059 (p) cc_final: 0.8805 (p) REVERT: A 680 LYS cc_start: 0.8444 (mttt) cc_final: 0.7864 (mttt) REVERT: B 41 ILE cc_start: 0.9651 (mm) cc_final: 0.9279 (mt) REVERT: B 51 LEU cc_start: 0.9475 (tp) cc_final: 0.9061 (tp) REVERT: B 77 ILE cc_start: 0.9717 (mt) cc_final: 0.9339 (mt) REVERT: B 87 LYS cc_start: 0.9324 (tptp) cc_final: 0.9027 (tptp) REVERT: B 89 PHE cc_start: 0.9171 (t80) cc_final: 0.8738 (t80) REVERT: B 95 MET cc_start: 0.9454 (tpp) cc_final: 0.8513 (tpp) REVERT: B 99 LYS cc_start: 0.9469 (mmmt) cc_final: 0.8726 (mmmt) REVERT: B 144 MET cc_start: 0.9528 (mtm) cc_final: 0.8832 (mtm) REVERT: B 149 TYR cc_start: 0.9080 (t80) cc_final: 0.8588 (t80) REVERT: B 161 ARG cc_start: 0.8755 (ttm110) cc_final: 0.8419 (mtt-85) REVERT: B 162 LYS cc_start: 0.9340 (tppt) cc_final: 0.9063 (mttt) REVERT: B 211 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8092 (mt-10) REVERT: B 235 ARG cc_start: 0.8758 (mtm110) cc_final: 0.8470 (mtm110) REVERT: B 257 ASP cc_start: 0.8348 (m-30) cc_final: 0.8080 (m-30) REVERT: B 286 ASP cc_start: 0.8983 (m-30) cc_final: 0.8315 (m-30) REVERT: B 317 MET cc_start: 0.8647 (pmm) cc_final: 0.8368 (pmm) REVERT: B 333 LYS cc_start: 0.9233 (tptm) cc_final: 0.8901 (tptm) REVERT: B 350 ARG cc_start: 0.9007 (tpp80) cc_final: 0.8413 (tpp80) REVERT: B 355 TYR cc_start: 0.9241 (m-10) cc_final: 0.8924 (m-10) REVERT: B 362 ASP cc_start: 0.8711 (m-30) cc_final: 0.7901 (m-30) REVERT: B 390 GLN cc_start: 0.9124 (mm-40) cc_final: 0.8854 (mm-40) REVERT: B 396 ASP cc_start: 0.7782 (p0) cc_final: 0.7134 (p0) REVERT: B 399 GLU cc_start: 0.9452 (mm-30) cc_final: 0.9214 (mm-30) REVERT: B 415 ASN cc_start: 0.9118 (t0) cc_final: 0.7834 (t0) REVERT: B 418 ASN cc_start: 0.9193 (m-40) cc_final: 0.8636 (m-40) REVERT: B 459 LYS cc_start: 0.8938 (mttm) cc_final: 0.8654 (mmmt) REVERT: B 467 ASN cc_start: 0.9343 (m-40) cc_final: 0.9017 (m110) REVERT: B 493 MET cc_start: 0.9466 (tmm) cc_final: 0.9203 (tmm) REVERT: B 496 ASN cc_start: 0.9567 (t0) cc_final: 0.9226 (t0) REVERT: B 501 GLN cc_start: 0.9023 (tp-100) cc_final: 0.8444 (tp-100) REVERT: B 515 ASP cc_start: 0.9082 (m-30) cc_final: 0.8738 (m-30) REVERT: B 543 ILE cc_start: 0.9334 (mp) cc_final: 0.9052 (mt) REVERT: B 575 ARG cc_start: 0.8709 (mtm110) cc_final: 0.8377 (mtm-85) REVERT: B 588 GLN cc_start: 0.9409 (mm-40) cc_final: 0.8990 (mm-40) REVERT: B 601 ILE cc_start: 0.9116 (mt) cc_final: 0.8857 (mp) REVERT: B 618 LEU cc_start: 0.9064 (mt) cc_final: 0.8600 (mt) REVERT: B 650 GLN cc_start: 0.8296 (mm-40) cc_final: 0.8003 (mm-40) REVERT: B 667 LEU cc_start: 0.9456 (tt) cc_final: 0.9044 (tt) REVERT: C 21 PHE cc_start: 0.9092 (m-80) cc_final: 0.8498 (m-80) REVERT: C 46 TYR cc_start: 0.7652 (m-80) cc_final: 0.7117 (m-80) REVERT: C 157 MET cc_start: 0.5627 (ptm) cc_final: 0.5406 (ptt) REVERT: C 179 TYR cc_start: 0.9335 (t80) cc_final: 0.9080 (t80) REVERT: C 204 TYR cc_start: 0.9563 (t80) cc_final: 0.9200 (t80) REVERT: D 46 TYR cc_start: 0.8900 (m-80) cc_final: 0.8573 (m-80) REVERT: D 96 MET cc_start: 0.8237 (mmt) cc_final: 0.7670 (mmm) REVERT: D 185 MET cc_start: 0.7207 (mmm) cc_final: 0.6412 (mmm) REVERT: D 189 GLU cc_start: 0.8887 (tp30) cc_final: 0.8649 (pt0) REVERT: D 239 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7134 (pm20) REVERT: D 259 PHE cc_start: 0.7497 (t80) cc_final: 0.7098 (t80) REVERT: D 317 ASP cc_start: 0.9293 (t0) cc_final: 0.8590 (t0) outliers start: 1 outliers final: 0 residues processed: 679 average time/residue: 0.1335 time to fit residues: 135.0713 Evaluate side-chains 568 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 567 time to evaluate : 0.619 ------------------------------------------------------------------------------- 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: 20.0000 chunk 168 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 185 optimal weight: 20.0000 chunk 191 optimal weight: 0.0060 chunk 159 optimal weight: 2.9990 chunk 182 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 overall best weight: 2.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN A 232 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 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 19 GLN ** 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 91 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.107589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.075670 restraints weight = 52646.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.078421 restraints weight = 31463.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.080227 restraints weight = 22350.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.081181 restraints weight = 17176.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.082319 restraints weight = 14455.182| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.6339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16386 Z= 0.193 Angle : 0.619 8.434 22134 Z= 0.331 Chirality : 0.042 0.156 2360 Planarity : 0.004 0.050 2818 Dihedral : 9.156 133.354 2290 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.19), residues: 1932 helix: 1.04 (0.15), residues: 1127 sheet: -0.70 (0.41), residues: 132 loop : 0.22 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 446 TYR 0.031 0.002 TYR D 174 PHE 0.021 0.002 PHE A 129 TRP 0.009 0.002 TRP A 623 HIS 0.010 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 (16386) covalent geometry : angle 0.61904 / 0.33 (22134) hydrogen bonds : bond 0.03972 / 2.50 ( 869) hydrogen bonds : angle 4.96985 / 3.54 ( 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 638 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 638 time to evaluate : 0.622 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: A 8 LYS cc_start: 0.9523 (tptp) cc_final: 0.9296 (tppt) REVERT: A 18 ILE cc_start: 0.9755 (mm) cc_final: 0.9262 (mt) REVERT: A 95 MET cc_start: 0.9599 (tpt) cc_final: 0.9395 (mmm) REVERT: A 103 ASP cc_start: 0.9273 (m-30) cc_final: 0.8954 (m-30) REVERT: A 104 TYR cc_start: 0.8892 (m-80) cc_final: 0.8044 (m-80) REVERT: A 107 LYS cc_start: 0.9432 (mttm) cc_final: 0.9173 (mmmt) REVERT: A 117 ARG cc_start: 0.9276 (mtp85) cc_final: 0.8753 (mmt180) REVERT: A 129 PHE cc_start: 0.9516 (m-80) cc_final: 0.9204 (m-80) REVERT: A 136 LYS cc_start: 0.9768 (mmpt) cc_final: 0.9465 (ttpt) REVERT: A 144 MET cc_start: 0.9054 (mtm) cc_final: 0.8601 (mtm) REVERT: A 168 VAL cc_start: 0.9092 (m) cc_final: 0.8798 (p) REVERT: A 194 LYS cc_start: 0.9384 (ttpt) cc_final: 0.9113 (ttpp) REVERT: A 205 LYS cc_start: 0.8748 (mmmt) cc_final: 0.8263 (mmtt) REVERT: A 214 LYS cc_start: 0.9597 (tppt) cc_final: 0.9391 (mmtt) REVERT: A 227 MET cc_start: 0.9287 (mtp) cc_final: 0.8931 (mtp) REVERT: A 252 ASN cc_start: 0.8695 (t0) cc_final: 0.8278 (t0) REVERT: A 254 PHE cc_start: 0.8486 (m-10) cc_final: 0.8201 (m-10) REVERT: A 286 ASP cc_start: 0.9135 (m-30) cc_final: 0.8551 (m-30) REVERT: A 362 ASP cc_start: 0.9168 (m-30) cc_final: 0.8656 (m-30) REVERT: A 366 LYS cc_start: 0.9514 (ptpp) cc_final: 0.9083 (pttm) REVERT: A 370 ASN cc_start: 0.9404 (m-40) cc_final: 0.9030 (m110) REVERT: A 375 LYS cc_start: 0.9505 (mttt) cc_final: 0.9136 (mttt) REVERT: A 390 GLN cc_start: 0.8374 (mm-40) cc_final: 0.8020 (mm-40) REVERT: A 396 ASP cc_start: 0.9102 (p0) cc_final: 0.8826 (p0) REVERT: A 402 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8778 (tm-30) REVERT: A 468 LEU cc_start: 0.9580 (tp) cc_final: 0.9266 (tp) REVERT: A 515 ASP cc_start: 0.9498 (m-30) cc_final: 0.9245 (m-30) REVERT: A 571 TYR cc_start: 0.9067 (t80) cc_final: 0.8480 (t80) REVERT: A 583 SER cc_start: 0.9442 (t) cc_final: 0.9065 (t) REVERT: A 599 GLU cc_start: 0.8487 (mp0) cc_final: 0.8283 (mp0) REVERT: A 602 GLU cc_start: 0.9105 (pt0) cc_final: 0.7909 (pt0) REVERT: A 615 MET cc_start: 0.8672 (mmp) cc_final: 0.8463 (mmp) REVERT: A 626 TYR cc_start: 0.9301 (m-80) cc_final: 0.8992 (m-10) REVERT: A 645 GLN cc_start: 0.8711 (tp-100) cc_final: 0.8432 (tp-100) REVERT: A 667 LEU cc_start: 0.9599 (tt) cc_final: 0.9333 (tt) REVERT: B 51 LEU cc_start: 0.9554 (tp) cc_final: 0.9177 (tp) REVERT: B 77 ILE cc_start: 0.9718 (mt) cc_final: 0.9388 (mt) REVERT: B 81 PHE cc_start: 0.9530 (m-80) cc_final: 0.9296 (m-80) REVERT: B 87 LYS cc_start: 0.9363 (tptp) cc_final: 0.9082 (tptp) REVERT: B 95 MET cc_start: 0.9527 (tpp) cc_final: 0.8467 (tpp) REVERT: B 99 LYS cc_start: 0.9533 (mmmt) cc_final: 0.8783 (mmmt) REVERT: B 114 ILE cc_start: 0.9615 (mt) cc_final: 0.9350 (pt) REVERT: B 144 MET cc_start: 0.9527 (mtm) cc_final: 0.8986 (mtm) REVERT: B 149 TYR cc_start: 0.9168 (t80) cc_final: 0.8596 (t80) REVERT: B 150 GLN cc_start: 0.9135 (tp40) cc_final: 0.8909 (tp40) REVERT: B 161 ARG cc_start: 0.8826 (ttm110) cc_final: 0.8472 (mtt-85) REVERT: B 162 LYS cc_start: 0.9403 (tppt) cc_final: 0.9129 (mttt) REVERT: B 191 GLN cc_start: 0.9203 (mm-40) cc_final: 0.8902 (mm-40) REVERT: B 211 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8564 (mm-30) REVERT: B 250 TYR cc_start: 0.8816 (m-80) cc_final: 0.8413 (m-80) REVERT: B 257 ASP cc_start: 0.8267 (m-30) cc_final: 0.8050 (m-30) REVERT: B 263 ASP cc_start: 0.9440 (m-30) cc_final: 0.9216 (m-30) REVERT: B 286 ASP cc_start: 0.9084 (m-30) cc_final: 0.8406 (m-30) REVERT: B 317 MET cc_start: 0.8669 (pmm) cc_final: 0.8425 (pmm) REVERT: B 333 LYS cc_start: 0.9273 (tptm) cc_final: 0.9018 (tptp) REVERT: B 355 TYR cc_start: 0.9191 (m-10) cc_final: 0.8939 (m-10) REVERT: B 362 ASP cc_start: 0.8845 (m-30) cc_final: 0.7996 (m-30) REVERT: B 373 ILE cc_start: 0.9808 (mt) cc_final: 0.9413 (mt) REVERT: B 375 LYS cc_start: 0.9250 (mmmm) cc_final: 0.8982 (mmtt) REVERT: B 390 GLN cc_start: 0.9216 (mm-40) cc_final: 0.8895 (mm-40) REVERT: B 396 ASP cc_start: 0.8090 (p0) cc_final: 0.7408 (p0) REVERT: B 399 GLU cc_start: 0.9476 (mm-30) cc_final: 0.9196 (mm-30) REVERT: B 415 ASN cc_start: 0.9072 (t0) cc_final: 0.7763 (t0) REVERT: B 418 ASN cc_start: 0.9170 (m-40) cc_final: 0.8654 (m-40) REVERT: B 426 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8743 (tm-30) REVERT: B 459 LYS cc_start: 0.9050 (mttm) cc_final: 0.8781 (mmmt) REVERT: B 472 LEU cc_start: 0.9768 (mt) cc_final: 0.9556 (mt) REVERT: B 496 ASN cc_start: 0.9565 (t0) cc_final: 0.9227 (t0) REVERT: B 500 ILE cc_start: 0.9776 (mt) cc_final: 0.9235 (mt) REVERT: B 501 GLN cc_start: 0.8954 (tp-100) cc_final: 0.8399 (tp-100) REVERT: B 515 ASP cc_start: 0.9193 (m-30) cc_final: 0.8810 (m-30) REVERT: B 570 MET cc_start: 0.9162 (tpp) cc_final: 0.8121 (tpt) REVERT: B 588 GLN cc_start: 0.9400 (mm-40) cc_final: 0.8804 (mm-40) REVERT: B 602 GLU cc_start: 0.8432 (mp0) cc_final: 0.7907 (mp0) REVERT: B 615 MET cc_start: 0.9091 (mmp) cc_final: 0.8815 (mmp) REVERT: B 618 LEU cc_start: 0.9051 (mt) cc_final: 0.8656 (mt) REVERT: B 650 GLN cc_start: 0.8276 (mm-40) cc_final: 0.8055 (mm-40) REVERT: B 654 PHE cc_start: 0.9426 (t80) cc_final: 0.9212 (t80) REVERT: B 667 LEU cc_start: 0.9505 (tt) cc_final: 0.9215 (tt) REVERT: C 204 TYR cc_start: 0.9628 (t80) cc_final: 0.9318 (t80) REVERT: C 278 GLU cc_start: 0.9213 (pm20) cc_final: 0.8951 (pm20) REVERT: D 179 TYR cc_start: 0.9202 (t80) cc_final: 0.8956 (t80) REVERT: D 185 MET cc_start: 0.7683 (mmm) cc_final: 0.7058 (mmm) REVERT: D 259 PHE cc_start: 0.7487 (t80) cc_final: 0.7278 (t80) outliers start: 0 outliers final: 0 residues processed: 638 average time/residue: 0.1273 time to fit residues: 120.7243 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 : 0.639 ------------------------------------------------------------------------------- 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: 9.9990 chunk 46 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 168 optimal weight: 8.9990 chunk 157 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN ** 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 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 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** B 645 GLN D 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.106041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.075399 restraints weight = 54225.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.078051 restraints weight = 32464.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.079772 restraints weight = 22923.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.081069 restraints weight = 17486.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.081895 restraints weight = 14331.419| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 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 = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (13 function evaluations) r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.6984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16386 Z= 0.220 Angle : 0.643 8.310 22134 Z= 0.344 Chirality : 0.042 0.234 2360 Planarity : 0.004 0.058 2818 Dihedral : 9.145 134.218 2290 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.06 % Allowed : 2.16 % Favored : 97.79 % 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: 0.64 (0.18), residues: 1932 helix: 0.81 (0.15), residues: 1137 sheet: 0.19 (0.49), residues: 106 loop : 0.01 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 452 TYR 0.032 0.002 TYR D 142 PHE 0.021 0.002 PHE B 378 TRP 0.011 0.001 TRP A 558 HIS 0.008 0.001 HIS B 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.22 (16386) covalent geometry : angle 0.64283 / 0.34 (22134) hydrogen bonds : bond 0.03944 / 2.51 ( 869) hydrogen bonds : angle 5.02001 / 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 629 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 628 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9511 (tptp) cc_final: 0.9249 (tppt) REVERT: A 65 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8381 (mm-30) REVERT: A 95 MET cc_start: 0.9719 (tpt) cc_final: 0.8484 (mmm) REVERT: A 99 LYS cc_start: 0.9564 (mmtp) cc_final: 0.9047 (mmtp) REVERT: A 104 TYR cc_start: 0.8889 (m-80) cc_final: 0.8221 (m-80) REVERT: A 107 LYS cc_start: 0.9418 (mttm) cc_final: 0.8927 (tptt) REVERT: A 115 LEU cc_start: 0.9409 (mt) cc_final: 0.9188 (mt) REVERT: A 117 ARG cc_start: 0.9274 (mtp85) cc_final: 0.8812 (mmt180) REVERT: A 129 PHE cc_start: 0.9537 (m-80) cc_final: 0.9210 (m-80) REVERT: A 136 LYS cc_start: 0.9766 (mmpt) cc_final: 0.9470 (ttpt) REVERT: A 144 MET cc_start: 0.9014 (mtm) cc_final: 0.8580 (mtm) REVERT: A 150 GLN cc_start: 0.9174 (tp40) cc_final: 0.8934 (tp40) REVERT: A 151 PRO cc_start: 0.9671 (Cg_exo) cc_final: 0.9328 (Cg_endo) REVERT: A 168 VAL cc_start: 0.9157 (m) cc_final: 0.8953 (p) REVERT: A 194 LYS cc_start: 0.9410 (ttpt) cc_final: 0.9116 (ttpp) REVERT: A 205 LYS cc_start: 0.8649 (mmmt) cc_final: 0.8102 (mmtt) REVERT: A 227 MET cc_start: 0.9319 (mtp) cc_final: 0.8813 (mtp) REVERT: A 252 ASN cc_start: 0.8935 (t0) cc_final: 0.8681 (t0) REVERT: A 286 ASP cc_start: 0.9159 (m-30) cc_final: 0.8601 (m-30) REVERT: A 362 ASP cc_start: 0.9165 (m-30) cc_final: 0.8739 (m-30) REVERT: A 366 LYS cc_start: 0.9497 (ptpp) cc_final: 0.9098 (pttp) REVERT: A 370 ASN cc_start: 0.9485 (m-40) cc_final: 0.9269 (m-40) REVERT: A 375 LYS cc_start: 0.9508 (mttt) cc_final: 0.9088 (mttt) REVERT: A 387 GLN cc_start: 0.8363 (mt0) cc_final: 0.8133 (mt0) REVERT: A 396 ASP cc_start: 0.9118 (p0) cc_final: 0.8883 (p0) REVERT: A 402 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8806 (tm-30) REVERT: A 405 LEU cc_start: 0.9084 (mt) cc_final: 0.8531 (mt) REVERT: A 414 LEU cc_start: 0.9570 (mt) cc_final: 0.9337 (mt) REVERT: A 468 LEU cc_start: 0.9534 (tp) cc_final: 0.9241 (tp) REVERT: A 506 ILE cc_start: 0.9785 (mm) cc_final: 0.9466 (mm) REVERT: A 515 ASP cc_start: 0.9458 (m-30) cc_final: 0.9182 (m-30) REVERT: A 583 SER cc_start: 0.9395 (t) cc_final: 0.9105 (t) REVERT: A 586 TYR cc_start: 0.9208 (m-80) cc_final: 0.8612 (m-80) REVERT: A 591 THR cc_start: 0.9255 (p) cc_final: 0.8961 (p) REVERT: A 602 GLU cc_start: 0.8959 (pt0) cc_final: 0.8044 (pt0) REVERT: A 626 TYR cc_start: 0.9389 (m-80) cc_final: 0.9158 (m-10) REVERT: A 627 LYS cc_start: 0.9573 (tttt) cc_final: 0.9266 (tttm) REVERT: A 653 SER cc_start: 0.9201 (p) cc_final: 0.8983 (p) REVERT: B 51 LEU cc_start: 0.9506 (tp) cc_final: 0.9139 (tp) REVERT: B 77 ILE cc_start: 0.9657 (mt) cc_final: 0.9280 (mt) REVERT: B 81 PHE cc_start: 0.9515 (m-80) cc_final: 0.9230 (m-80) REVERT: B 87 LYS cc_start: 0.9383 (tptp) cc_final: 0.9097 (tptp) REVERT: B 95 MET cc_start: 0.9535 (tpp) cc_final: 0.8487 (tpp) REVERT: B 99 LYS cc_start: 0.9575 (mmmt) cc_final: 0.8759 (mmmt) REVERT: B 114 ILE cc_start: 0.9620 (mt) cc_final: 0.9275 (pt) REVERT: B 144 MET cc_start: 0.9447 (mtm) cc_final: 0.8980 (mtm) REVERT: B 149 TYR cc_start: 0.9235 (t80) cc_final: 0.8617 (t80) REVERT: B 161 ARG cc_start: 0.8899 (ttm110) cc_final: 0.8210 (mtt180) REVERT: B 162 LYS cc_start: 0.9404 (tppt) cc_final: 0.9159 (mttt) REVERT: B 211 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8612 (mm-30) REVERT: B 240 MET cc_start: 0.8190 (mpp) cc_final: 0.7737 (mpp) REVERT: B 252 ASN cc_start: 0.8955 (t0) cc_final: 0.8719 (t0) REVERT: B 263 ASP cc_start: 0.9431 (m-30) cc_final: 0.9207 (m-30) REVERT: B 286 ASP cc_start: 0.9049 (m-30) cc_final: 0.8409 (m-30) REVERT: B 333 LYS cc_start: 0.9269 (tptm) cc_final: 0.9017 (tptp) REVERT: B 350 ARG cc_start: 0.9104 (tpp80) cc_final: 0.8286 (tpp80) REVERT: B 362 ASP cc_start: 0.8848 (m-30) cc_final: 0.8191 (m-30) REVERT: B 396 ASP cc_start: 0.8209 (p0) cc_final: 0.7654 (p0) REVERT: B 399 GLU cc_start: 0.9478 (mm-30) cc_final: 0.9171 (mp0) REVERT: B 415 ASN cc_start: 0.9068 (t0) cc_final: 0.8234 (t0) REVERT: B 416 ILE cc_start: 0.9810 (mt) cc_final: 0.9489 (mt) REVERT: B 418 ASN cc_start: 0.9268 (m-40) cc_final: 0.8916 (m-40) REVERT: B 420 MET cc_start: 0.9106 (mmm) cc_final: 0.8687 (mmm) REVERT: B 427 LYS cc_start: 0.9719 (ptpp) cc_final: 0.9280 (ptpp) REVERT: B 459 LYS cc_start: 0.9022 (mptt) cc_final: 0.8602 (mmmt) REVERT: B 467 ASN cc_start: 0.9308 (m-40) cc_final: 0.9009 (m110) REVERT: B 468 LEU cc_start: 0.9484 (tp) cc_final: 0.9262 (tp) REVERT: B 496 ASN cc_start: 0.9510 (t0) cc_final: 0.9047 (t0) REVERT: B 500 ILE cc_start: 0.9790 (mt) cc_final: 0.9319 (mt) REVERT: B 505 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8744 (mt-10) REVERT: B 515 ASP cc_start: 0.9030 (m-30) cc_final: 0.8567 (m-30) REVERT: B 588 GLN cc_start: 0.9387 (mm-40) cc_final: 0.9162 (mm-40) REVERT: B 601 ILE cc_start: 0.9408 (mp) cc_final: 0.8727 (mp) REVERT: B 602 GLU cc_start: 0.8487 (mp0) cc_final: 0.7996 (mm-30) REVERT: B 618 LEU cc_start: 0.9051 (mt) cc_final: 0.8766 (mt) REVERT: B 632 MET cc_start: 0.9306 (mmm) cc_final: 0.8874 (mmm) REVERT: B 654 PHE cc_start: 0.9473 (t80) cc_final: 0.8988 (t80) REVERT: B 667 LEU cc_start: 0.9576 (tt) cc_final: 0.9308 (tt) REVERT: C 46 TYR cc_start: 0.8695 (m-80) cc_final: 0.8449 (m-80) REVERT: C 108 ILE cc_start: 0.9222 (mt) cc_final: 0.8992 (mt) REVERT: C 157 MET cc_start: 0.4710 (ptt) cc_final: 0.3923 (ptt) REVERT: C 185 MET cc_start: 0.8813 (mpp) cc_final: 0.8569 (mpp) REVERT: C 204 TYR cc_start: 0.9654 (t80) cc_final: 0.9334 (t80) REVERT: C 278 GLU cc_start: 0.9175 (pm20) cc_final: 0.8916 (pm20) REVERT: D 46 TYR cc_start: 0.9028 (m-80) cc_final: 0.8788 (m-10) REVERT: D 179 TYR cc_start: 0.9226 (t80) cc_final: 0.8897 (t80) REVERT: D 185 MET cc_start: 0.7774 (mmm) cc_final: 0.6748 (mmm) REVERT: D 189 GLU cc_start: 0.9018 (tp30) cc_final: 0.8725 (pt0) outliers start: 1 outliers final: 0 residues processed: 629 average time/residue: 0.1340 time to fit residues: 125.2857 Evaluate side-chains 541 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 541 time to evaluate : 0.542 ------------------------------------------------------------------------------- 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: 10.0000 chunk 72 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 136 optimal weight: 0.2980 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** ** B 158 ASN ** 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 390 GLN B 645 GLN C 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.109962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.078186 restraints weight = 51608.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.080937 restraints weight = 30727.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.082730 restraints weight = 21531.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.084129 restraints weight = 16381.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.085063 restraints weight = 13251.528| |-----------------------------------------------------------------------------| r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3149 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3149 r_free = 0.3149 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (12 function evaluations) r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.7200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16386 Z= 0.139 Angle : 0.595 7.941 22134 Z= 0.318 Chirality : 0.042 0.225 2360 Planarity : 0.004 0.083 2818 Dihedral : 8.941 134.921 2290 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.06 % Allowed : 1.40 % 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: 0.71 (0.19), residues: 1932 helix: 0.86 (0.15), residues: 1160 sheet: -0.65 (0.45), residues: 136 loop : 0.28 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 665 TYR 0.049 0.002 TYR C 142 PHE 0.039 0.002 PHE D 109 TRP 0.006 0.001 TRP A 623 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (16386) covalent geometry : angle 0.59513 / 0.32 (22134) hydrogen bonds : bond 0.03800 / 2.40 ( 869) hydrogen bonds : angle 4.92246 / 3.51 ( 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 622 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 621 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9523 (tptp) cc_final: 0.9228 (tppt) REVERT: A 65 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8374 (mm-30) REVERT: A 87 LYS cc_start: 0.9616 (tptp) cc_final: 0.9395 (tptp) REVERT: A 95 MET cc_start: 0.9594 (tpt) cc_final: 0.9385 (mmm) REVERT: A 104 TYR cc_start: 0.8675 (m-80) cc_final: 0.8226 (m-80) REVERT: A 117 ARG cc_start: 0.9249 (mtp85) cc_final: 0.8828 (mmt180) REVERT: A 120 ASP cc_start: 0.9386 (m-30) cc_final: 0.9178 (m-30) REVERT: A 129 PHE cc_start: 0.9576 (m-80) cc_final: 0.9167 (m-80) REVERT: A 136 LYS cc_start: 0.9767 (mmpt) cc_final: 0.9467 (ttpt) REVERT: A 144 MET cc_start: 0.8968 (mtm) cc_final: 0.8472 (mtm) REVERT: A 191 GLN cc_start: 0.8693 (mm110) cc_final: 0.8293 (mm-40) REVERT: A 194 LYS cc_start: 0.9351 (ttpt) cc_final: 0.9106 (ttpp) REVERT: A 205 LYS cc_start: 0.8637 (mmmt) cc_final: 0.8158 (mmtt) REVERT: A 227 MET cc_start: 0.9145 (mtp) cc_final: 0.8824 (mtp) REVERT: A 252 ASN cc_start: 0.8955 (t0) cc_final: 0.8678 (t0) REVERT: A 266 LYS cc_start: 0.9383 (ptmm) cc_final: 0.9106 (pttp) REVERT: A 286 ASP cc_start: 0.9125 (m-30) cc_final: 0.8644 (m-30) REVERT: A 350 ARG cc_start: 0.8545 (mtp85) cc_final: 0.7887 (mtp85) REVERT: A 362 ASP cc_start: 0.9100 (m-30) cc_final: 0.8565 (m-30) REVERT: A 370 ASN cc_start: 0.9398 (m-40) cc_final: 0.9035 (m-40) REVERT: A 375 LYS cc_start: 0.9513 (mttt) cc_final: 0.9084 (mttt) REVERT: A 385 VAL cc_start: 0.9671 (t) cc_final: 0.9341 (m) REVERT: A 402 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8875 (tm-30) REVERT: A 414 LEU cc_start: 0.9579 (mt) cc_final: 0.9308 (mt) REVERT: A 468 LEU cc_start: 0.9534 (tp) cc_final: 0.9250 (tp) REVERT: A 515 ASP cc_start: 0.9467 (m-30) cc_final: 0.9188 (m-30) REVERT: A 601 ILE cc_start: 0.9466 (tt) cc_final: 0.9185 (tt) REVERT: A 615 MET cc_start: 0.8675 (mmp) cc_final: 0.8108 (mmp) REVERT: A 626 TYR cc_start: 0.9266 (m-80) cc_final: 0.9028 (m-10) REVERT: A 653 SER cc_start: 0.8958 (p) cc_final: 0.8654 (p) REVERT: B 51 LEU cc_start: 0.9474 (tp) cc_final: 0.9087 (tp) REVERT: B 77 ILE cc_start: 0.9648 (mt) cc_final: 0.9230 (mt) REVERT: B 87 LYS cc_start: 0.9385 (tptp) cc_final: 0.9086 (tptp) REVERT: B 95 MET cc_start: 0.9499 (tpp) cc_final: 0.8451 (tpp) REVERT: B 99 LYS cc_start: 0.9589 (mmmt) cc_final: 0.8781 (mmmt) REVERT: B 114 ILE cc_start: 0.9610 (mt) cc_final: 0.9296 (pt) REVERT: B 144 MET cc_start: 0.9352 (mtm) cc_final: 0.8925 (mtm) REVERT: B 149 TYR cc_start: 0.9258 (t80) cc_final: 0.8534 (t80) REVERT: B 161 ARG cc_start: 0.8866 (ttm110) cc_final: 0.8542 (mtt-85) REVERT: B 162 LYS cc_start: 0.9403 (tppt) cc_final: 0.9157 (mttt) REVERT: B 211 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8489 (mm-30) REVERT: B 240 MET cc_start: 0.8229 (mpp) cc_final: 0.7778 (mpp) REVERT: B 257 ASP cc_start: 0.8388 (m-30) cc_final: 0.8047 (m-30) REVERT: B 263 ASP cc_start: 0.9410 (m-30) cc_final: 0.9185 (m-30) REVERT: B 286 ASP cc_start: 0.9065 (m-30) cc_final: 0.8427 (m-30) REVERT: B 317 MET cc_start: 0.8432 (pmm) cc_final: 0.8183 (pmm) REVERT: B 333 LYS cc_start: 0.9274 (tptm) cc_final: 0.9029 (tptp) REVERT: B 335 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8198 (mt-10) REVERT: B 350 ARG cc_start: 0.9190 (tpp80) cc_final: 0.8267 (tpp80) REVERT: B 362 ASP cc_start: 0.8822 (m-30) cc_final: 0.8138 (m-30) REVERT: B 390 GLN cc_start: 0.9215 (mm110) cc_final: 0.8944 (mm-40) REVERT: B 396 ASP cc_start: 0.8031 (p0) cc_final: 0.7476 (p0) REVERT: B 399 GLU cc_start: 0.9481 (mm-30) cc_final: 0.9124 (mp0) REVERT: B 415 ASN cc_start: 0.8951 (t0) cc_final: 0.7918 (t0) REVERT: B 416 ILE cc_start: 0.9820 (mt) cc_final: 0.9527 (mt) REVERT: B 418 ASN cc_start: 0.9295 (m-40) cc_final: 0.8948 (m-40) REVERT: B 420 MET cc_start: 0.9076 (mmm) cc_final: 0.8659 (mmm) REVERT: B 426 GLU cc_start: 0.9236 (pm20) cc_final: 0.8849 (pm20) REVERT: B 427 LYS cc_start: 0.9683 (ptpp) cc_final: 0.9203 (ptpp) REVERT: B 459 LYS cc_start: 0.9061 (mptt) cc_final: 0.8617 (mmmt) REVERT: B 467 ASN cc_start: 0.9265 (m-40) cc_final: 0.8363 (m110) REVERT: B 515 ASP cc_start: 0.9099 (m-30) cc_final: 0.8615 (m-30) REVERT: B 570 MET cc_start: 0.9180 (tpp) cc_final: 0.8454 (tpt) REVERT: B 601 ILE cc_start: 0.9335 (mp) cc_final: 0.9112 (mp) REVERT: B 615 MET cc_start: 0.8807 (mmp) cc_final: 0.8598 (mmp) REVERT: B 618 LEU cc_start: 0.9064 (mt) cc_final: 0.8703 (mt) REVERT: B 667 LEU cc_start: 0.9588 (tt) cc_final: 0.9302 (tt) REVERT: C 21 PHE cc_start: 0.9386 (m-80) cc_final: 0.8647 (m-80) REVERT: C 74 MET cc_start: 0.7732 (ttm) cc_final: 0.7394 (mtm) REVERT: C 107 ASN cc_start: 0.9266 (t0) cc_final: 0.8966 (p0) REVERT: C 108 ILE cc_start: 0.9083 (mt) cc_final: 0.8854 (mt) REVERT: C 157 MET cc_start: 0.4028 (ptt) cc_final: 0.3725 (ptt) REVERT: C 179 TYR cc_start: 0.9514 (t80) cc_final: 0.9243 (t80) REVERT: C 185 MET cc_start: 0.8734 (mpp) cc_final: 0.8493 (mpp) REVERT: C 204 TYR cc_start: 0.9638 (t80) cc_final: 0.9277 (t80) REVERT: C 278 GLU cc_start: 0.9131 (pm20) cc_final: 0.8901 (pm20) REVERT: D 46 TYR cc_start: 0.8995 (m-80) cc_final: 0.8736 (m-10) REVERT: D 179 TYR cc_start: 0.9182 (t80) cc_final: 0.8938 (t80) REVERT: D 185 MET cc_start: 0.7928 (mmm) cc_final: 0.7100 (mmm) REVERT: D 189 GLU cc_start: 0.9024 (tp30) cc_final: 0.8784 (pt0) REVERT: D 259 PHE cc_start: 0.7716 (t80) cc_final: 0.7126 (t80) outliers start: 1 outliers final: 1 residues processed: 622 average time/residue: 0.1267 time to fit residues: 117.3038 Evaluate side-chains 554 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 553 time to evaluate : 0.594 ------------------------------------------------------------------------------- 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: 0.9990 chunk 51 optimal weight: 6.9990 chunk 74 optimal weight: 9.9990 chunk 105 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 186 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 115 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 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 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** A 647 HIS ** 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.110094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.078911 restraints weight = 51264.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.081704 restraints weight = 30533.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.083443 restraints weight = 21530.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.084693 restraints weight = 16597.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.085548 restraints weight = 13629.712| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3156 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3156 r_free = 0.3156 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.7486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16386 Z= 0.158 Angle : 0.620 7.509 22134 Z= 0.331 Chirality : 0.042 0.230 2360 Planarity : 0.004 0.053 2818 Dihedral : 8.968 137.784 2290 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: 0.62 (0.19), residues: 1932 helix: 0.78 (0.15), residues: 1161 sheet: -0.63 (0.46), residues: 136 loop : 0.22 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 161 TYR 0.035 0.002 TYR C 142 PHE 0.029 0.002 PHE D 109 TRP 0.010 0.001 TRP A 623 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (16386) covalent geometry : angle 0.61964 / 0.33 (22134) hydrogen bonds : bond 0.03823 / 2.42 ( 869) hydrogen bonds : angle 4.93521 / 3.51 ( 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 624 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 624 time to evaluate : 0.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8842 (mm-30) cc_final: 0.7978 (mm-30) REVERT: A 95 MET cc_start: 0.9670 (tpt) cc_final: 0.9336 (mmm) REVERT: A 104 TYR cc_start: 0.8721 (m-80) cc_final: 0.8295 (m-80) REVERT: A 106 LEU cc_start: 0.9285 (tp) cc_final: 0.9015 (tp) REVERT: A 107 LYS cc_start: 0.9450 (mttm) cc_final: 0.9144 (mmmt) REVERT: A 114 ILE cc_start: 0.9490 (mp) cc_final: 0.8944 (mp) REVERT: A 129 PHE cc_start: 0.9524 (m-80) cc_final: 0.9088 (m-80) REVERT: A 136 LYS cc_start: 0.9760 (mmpt) cc_final: 0.9450 (ttpt) REVERT: A 144 MET cc_start: 0.8883 (mtm) cc_final: 0.8468 (mtm) REVERT: A 158 ASN cc_start: 0.9541 (m110) cc_final: 0.9235 (m-40) REVERT: A 161 ARG cc_start: 0.9124 (ttm110) cc_final: 0.8320 (ttm110) REVERT: A 168 VAL cc_start: 0.9276 (m) cc_final: 0.9020 (p) REVERT: A 194 LYS cc_start: 0.9408 (ttpt) cc_final: 0.9112 (ttpp) REVERT: A 227 MET cc_start: 0.9270 (mtp) cc_final: 0.8749 (mtp) REVERT: A 235 ARG cc_start: 0.8810 (ttp-110) cc_final: 0.7871 (mtm180) REVERT: A 239 GLN cc_start: 0.8476 (tt0) cc_final: 0.8230 (tp40) REVERT: A 252 ASN cc_start: 0.8999 (t0) cc_final: 0.8661 (t0) REVERT: A 286 ASP cc_start: 0.9137 (m-30) cc_final: 0.8607 (m-30) REVERT: A 307 TYR cc_start: 0.9405 (t80) cc_final: 0.9188 (t80) REVERT: A 349 LEU cc_start: 0.9465 (mt) cc_final: 0.8927 (mt) REVERT: A 350 ARG cc_start: 0.8540 (mtp85) cc_final: 0.7919 (mtp85) REVERT: A 359 MET cc_start: 0.9121 (ttp) cc_final: 0.8902 (ttp) REVERT: A 362 ASP cc_start: 0.8954 (m-30) cc_final: 0.8673 (m-30) REVERT: A 370 ASN cc_start: 0.9444 (m-40) cc_final: 0.9180 (m-40) REVERT: A 375 LYS cc_start: 0.9485 (mttt) cc_final: 0.9156 (mttt) REVERT: A 414 LEU cc_start: 0.9577 (mt) cc_final: 0.9305 (mt) REVERT: A 455 ASN cc_start: 0.9501 (t0) cc_final: 0.9281 (t0) REVERT: A 456 LYS cc_start: 0.9662 (mmpt) cc_final: 0.9345 (mmmt) REVERT: A 468 LEU cc_start: 0.9547 (tp) cc_final: 0.9275 (tp) REVERT: A 515 ASP cc_start: 0.9455 (m-30) cc_final: 0.9160 (m-30) REVERT: A 585 SER cc_start: 0.9684 (p) cc_final: 0.9451 (t) REVERT: A 591 THR cc_start: 0.9274 (p) cc_final: 0.8896 (p) REVERT: A 653 SER cc_start: 0.9040 (p) cc_final: 0.8773 (p) REVERT: B 51 LEU cc_start: 0.9511 (tp) cc_final: 0.8927 (tp) REVERT: B 77 ILE cc_start: 0.9520 (mt) cc_final: 0.9167 (mt) REVERT: B 81 PHE cc_start: 0.9497 (m-10) cc_final: 0.9120 (m-80) REVERT: B 87 LYS cc_start: 0.9418 (tptp) cc_final: 0.9151 (tptp) REVERT: B 89 PHE cc_start: 0.9133 (t80) cc_final: 0.8703 (t80) REVERT: B 95 MET cc_start: 0.9499 (tpp) cc_final: 0.8424 (tpp) REVERT: B 99 LYS cc_start: 0.9607 (mmmt) cc_final: 0.8762 (mmmt) REVERT: B 114 ILE cc_start: 0.9615 (mt) cc_final: 0.9285 (pt) REVERT: B 144 MET cc_start: 0.9327 (mtm) cc_final: 0.8889 (mtm) REVERT: B 149 TYR cc_start: 0.9301 (t80) cc_final: 0.8681 (t80) REVERT: B 161 ARG cc_start: 0.8822 (ttm110) cc_final: 0.8499 (mtt-85) REVERT: B 162 LYS cc_start: 0.9411 (tppt) cc_final: 0.9151 (mttt) REVERT: B 191 GLN cc_start: 0.9145 (mm-40) cc_final: 0.8835 (mm-40) REVERT: B 211 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8538 (mm-30) REVERT: B 236 TYR cc_start: 0.8803 (t80) cc_final: 0.8385 (t80) REVERT: B 240 MET cc_start: 0.8241 (mpp) cc_final: 0.7775 (mpp) REVERT: B 257 ASP cc_start: 0.8401 (m-30) cc_final: 0.8092 (m-30) REVERT: B 286 ASP cc_start: 0.8963 (m-30) cc_final: 0.8298 (m-30) REVERT: B 319 MET cc_start: 0.8985 (tpt) cc_final: 0.8742 (tpp) REVERT: B 322 MET cc_start: 0.8404 (ttt) cc_final: 0.7870 (ttt) REVERT: B 326 PHE cc_start: 0.9399 (m-10) cc_final: 0.8561 (m-80) REVERT: B 333 LYS cc_start: 0.9299 (tptm) cc_final: 0.9042 (tptp) REVERT: B 335 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8135 (mt-10) REVERT: B 362 ASP cc_start: 0.8700 (m-30) cc_final: 0.8021 (m-30) REVERT: B 373 ILE cc_start: 0.9682 (mt) cc_final: 0.9444 (mt) REVERT: B 390 GLN cc_start: 0.9237 (mm110) cc_final: 0.8955 (mm-40) REVERT: B 396 ASP cc_start: 0.8075 (p0) cc_final: 0.7523 (p0) REVERT: B 399 GLU cc_start: 0.9466 (mm-30) cc_final: 0.9119 (mp0) REVERT: B 415 ASN cc_start: 0.9348 (t0) cc_final: 0.8681 (t0) REVERT: B 416 ILE cc_start: 0.9817 (mt) cc_final: 0.9565 (mt) REVERT: B 418 ASN cc_start: 0.9342 (m-40) cc_final: 0.9039 (m-40) REVERT: B 420 MET cc_start: 0.9150 (mmm) cc_final: 0.8747 (mmm) REVERT: B 426 GLU cc_start: 0.9199 (pm20) cc_final: 0.8788 (pm20) REVERT: B 427 LYS cc_start: 0.9686 (ptpp) cc_final: 0.9162 (ptpp) REVERT: B 501 GLN cc_start: 0.8966 (tp-100) cc_final: 0.8489 (tp-100) REVERT: B 505 GLU cc_start: 0.9018 (mt-10) cc_final: 0.7774 (mt-10) REVERT: B 515 ASP cc_start: 0.9070 (m-30) cc_final: 0.8535 (m-30) REVERT: B 570 MET cc_start: 0.9268 (tpp) cc_final: 0.8571 (tpt) REVERT: B 601 ILE cc_start: 0.9508 (mp) cc_final: 0.9092 (mp) REVERT: B 613 TYR cc_start: 0.9327 (t80) cc_final: 0.9122 (t80) REVERT: B 618 LEU cc_start: 0.9025 (mt) cc_final: 0.8748 (mt) REVERT: B 631 ASP cc_start: 0.9578 (t70) cc_final: 0.9302 (t0) REVERT: B 654 PHE cc_start: 0.9323 (t80) cc_final: 0.8869 (t80) REVERT: B 656 LEU cc_start: 0.9448 (mt) cc_final: 0.9202 (mt) REVERT: B 667 LEU cc_start: 0.9580 (tt) cc_final: 0.9307 (tt) REVERT: C 21 PHE cc_start: 0.9389 (m-80) cc_final: 0.8661 (m-80) REVERT: C 179 TYR cc_start: 0.9497 (t80) cc_final: 0.9193 (t80) REVERT: C 185 MET cc_start: 0.8712 (mpp) cc_final: 0.8459 (mpp) REVERT: C 204 TYR cc_start: 0.9661 (t80) cc_final: 0.9200 (t80) REVERT: C 278 GLU cc_start: 0.9074 (pm20) cc_final: 0.8866 (pm20) REVERT: D 46 TYR cc_start: 0.9024 (m-80) cc_final: 0.8769 (m-10) REVERT: D 179 TYR cc_start: 0.9138 (t80) cc_final: 0.8777 (t80) REVERT: D 185 MET cc_start: 0.7919 (mmm) cc_final: 0.6889 (mmm) REVERT: D 189 GLU cc_start: 0.9007 (tp30) cc_final: 0.8806 (pt0) outliers start: 0 outliers final: 0 residues processed: 624 average time/residue: 0.1150 time to fit residues: 107.5740 Evaluate side-chains 551 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 551 time to evaluate : 0.539 ------------------------------------------------------------------------------- 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: 7.9990 chunk 99 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 158 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 151 optimal weight: 30.0000 chunk 81 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** 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 158 ASN ** 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 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 HIS ** 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 = 0.3533 r_free = 0.3533 target = 0.108269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.077645 restraints weight = 52517.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.080233 restraints weight = 31512.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.082131 restraints weight = 21864.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.083322 restraints weight = 16870.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.084193 restraints weight = 13819.353| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.7747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16386 Z= 0.195 Angle : 0.658 7.014 22134 Z= 0.353 Chirality : 0.043 0.200 2360 Planarity : 0.004 0.053 2818 Dihedral : 9.213 138.680 2290 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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: 0.54 (0.19), residues: 1932 helix: 0.74 (0.15), residues: 1156 sheet: -0.78 (0.45), residues: 136 loop : 0.19 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 196 TYR 0.033 0.002 TYR C 142 PHE 0.023 0.002 PHE D 109 TRP 0.020 0.002 TRP A 558 HIS 0.007 0.001 HIS A 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 (16386) covalent geometry : angle 0.65813 / 0.35 (22134) hydrogen bonds : bond 0.03938 / 2.47 ( 869) hydrogen bonds : angle 5.05088 / 3.59 ( 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 623 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 623 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8596 (mm-30) cc_final: 0.7731 (mm-30) REVERT: A 87 LYS cc_start: 0.9625 (tptp) cc_final: 0.9360 (tptp) REVERT: A 95 MET cc_start: 0.9701 (tpt) cc_final: 0.9136 (mmm) REVERT: A 104 TYR cc_start: 0.8815 (m-80) cc_final: 0.8355 (m-80) REVERT: A 107 LYS cc_start: 0.9472 (mttm) cc_final: 0.8998 (tptt) REVERT: A 129 PHE cc_start: 0.9543 (m-80) cc_final: 0.9124 (m-80) REVERT: A 136 LYS cc_start: 0.9769 (mmpt) cc_final: 0.9467 (ttpt) REVERT: A 144 MET cc_start: 0.8904 (mtm) cc_final: 0.8515 (mtm) REVERT: A 161 ARG cc_start: 0.9040 (ttm110) cc_final: 0.8689 (ttm110) REVERT: A 164 ARG cc_start: 0.8883 (ptt-90) cc_final: 0.8200 (ptt-90) REVERT: A 191 GLN cc_start: 0.8890 (mm110) cc_final: 0.8603 (mp10) REVERT: A 194 LYS cc_start: 0.9369 (ttpt) cc_final: 0.9026 (ttpp) REVERT: A 227 MET cc_start: 0.9104 (mtp) cc_final: 0.8687 (mtp) REVERT: A 235 ARG cc_start: 0.8760 (ttp-110) cc_final: 0.8466 (ttp-110) REVERT: A 239 GLN cc_start: 0.8475 (tt0) cc_final: 0.8187 (tp40) REVERT: A 252 ASN cc_start: 0.8984 (t0) cc_final: 0.8701 (t0) REVERT: A 255 HIS cc_start: 0.8326 (t-90) cc_final: 0.7897 (t-90) REVERT: A 286 ASP cc_start: 0.9101 (m-30) cc_final: 0.8589 (m-30) REVERT: A 349 LEU cc_start: 0.9470 (mt) cc_final: 0.8925 (mt) REVERT: A 350 ARG cc_start: 0.8511 (mtp85) cc_final: 0.7930 (mtp85) REVERT: A 359 MET cc_start: 0.9114 (ttp) cc_final: 0.8902 (ttp) REVERT: A 362 ASP cc_start: 0.9154 (m-30) cc_final: 0.8569 (m-30) REVERT: A 370 ASN cc_start: 0.9470 (m-40) cc_final: 0.9224 (m-40) REVERT: A 375 LYS cc_start: 0.9466 (mttt) cc_final: 0.9108 (mttt) REVERT: A 396 ASP cc_start: 0.9074 (p0) cc_final: 0.8870 (p0) REVERT: A 414 LEU cc_start: 0.9511 (mt) cc_final: 0.9086 (mt) REVERT: A 426 GLU cc_start: 0.9202 (tm-30) cc_final: 0.8582 (tm-30) REVERT: A 456 LYS cc_start: 0.9652 (mmpt) cc_final: 0.9309 (mmmt) REVERT: A 468 LEU cc_start: 0.9513 (tp) cc_final: 0.9259 (tp) REVERT: A 515 ASP cc_start: 0.9445 (m-30) cc_final: 0.9151 (m-30) REVERT: A 562 LYS cc_start: 0.9784 (ttmt) cc_final: 0.9553 (tppt) REVERT: A 585 SER cc_start: 0.9670 (p) cc_final: 0.9423 (t) REVERT: A 586 TYR cc_start: 0.9044 (m-80) cc_final: 0.8781 (m-80) REVERT: A 591 THR cc_start: 0.9208 (p) cc_final: 0.8988 (p) REVERT: A 601 ILE cc_start: 0.9408 (tt) cc_final: 0.9207 (tt) REVERT: A 602 GLU cc_start: 0.8950 (pt0) cc_final: 0.7915 (pm20) REVERT: A 615 MET cc_start: 0.8727 (mmp) cc_final: 0.8339 (mmm) REVERT: A 618 LEU cc_start: 0.9302 (tt) cc_final: 0.9100 (tt) REVERT: A 632 MET cc_start: 0.8829 (mmp) cc_final: 0.8411 (mmp) REVERT: A 653 SER cc_start: 0.9029 (p) cc_final: 0.8752 (p) REVERT: B 51 LEU cc_start: 0.9488 (tp) cc_final: 0.9004 (tp) REVERT: B 77 ILE cc_start: 0.9540 (mt) cc_final: 0.9259 (mt) REVERT: B 81 PHE cc_start: 0.9515 (m-10) cc_final: 0.9171 (m-10) REVERT: B 87 LYS cc_start: 0.9401 (tptp) cc_final: 0.9102 (tptp) REVERT: B 95 MET cc_start: 0.9567 (tpp) cc_final: 0.8561 (tpp) REVERT: B 99 LYS cc_start: 0.9658 (mmmt) cc_final: 0.8821 (mmmt) REVERT: B 114 ILE cc_start: 0.9612 (mt) cc_final: 0.9257 (pt) REVERT: B 144 MET cc_start: 0.9318 (mtm) cc_final: 0.8752 (mtm) REVERT: B 145 ILE cc_start: 0.9654 (tp) cc_final: 0.9423 (tp) REVERT: B 147 GLN cc_start: 0.9293 (mm110) cc_final: 0.8678 (mm110) REVERT: B 149 TYR cc_start: 0.9364 (t80) cc_final: 0.8859 (t80) REVERT: B 161 ARG cc_start: 0.8855 (ttm110) cc_final: 0.8110 (mtt180) REVERT: B 162 LYS cc_start: 0.9396 (tppt) cc_final: 0.9087 (tppt) REVERT: B 173 LEU cc_start: 0.9468 (mt) cc_final: 0.9190 (mt) REVERT: B 211 GLU cc_start: 0.8896 (mm-30) cc_final: 0.8540 (mm-30) REVERT: B 240 MET cc_start: 0.8348 (mpp) cc_final: 0.7892 (mpp) REVERT: B 252 ASN cc_start: 0.8991 (t0) cc_final: 0.8715 (t0) REVERT: B 257 ASP cc_start: 0.8381 (m-30) cc_final: 0.8052 (m-30) REVERT: B 263 ASP cc_start: 0.9309 (m-30) cc_final: 0.9022 (m-30) REVERT: B 286 ASP cc_start: 0.8987 (m-30) cc_final: 0.8366 (m-30) REVERT: B 319 MET cc_start: 0.9043 (tpt) cc_final: 0.8820 (tpp) REVERT: B 326 PHE cc_start: 0.9301 (m-10) cc_final: 0.9069 (m-80) REVERT: B 335 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8291 (mt-10) REVERT: B 359 MET cc_start: 0.7996 (ptp) cc_final: 0.7774 (ptp) REVERT: B 362 ASP cc_start: 0.8692 (m-30) cc_final: 0.7982 (m-30) REVERT: B 390 GLN cc_start: 0.9219 (mm110) cc_final: 0.8908 (mm-40) REVERT: B 396 ASP cc_start: 0.8084 (p0) cc_final: 0.7588 (p0) REVERT: B 399 GLU cc_start: 0.9462 (mm-30) cc_final: 0.9124 (mp0) REVERT: B 415 ASN cc_start: 0.9316 (t0) cc_final: 0.8624 (t0) REVERT: B 416 ILE cc_start: 0.9784 (mt) cc_final: 0.9524 (mt) REVERT: B 418 ASN cc_start: 0.9353 (m-40) cc_final: 0.9024 (m-40) REVERT: B 420 MET cc_start: 0.9209 (mmm) cc_final: 0.8851 (mmm) REVERT: B 426 GLU cc_start: 0.9188 (pm20) cc_final: 0.8812 (pm20) REVERT: B 427 LYS cc_start: 0.9708 (ptpp) cc_final: 0.9230 (ptpp) REVERT: B 501 GLN cc_start: 0.8999 (tp-100) cc_final: 0.8551 (tp-100) REVERT: B 505 GLU cc_start: 0.9011 (mt-10) cc_final: 0.7801 (mt-10) REVERT: B 515 ASP cc_start: 0.8994 (m-30) cc_final: 0.8513 (m-30) REVERT: B 570 MET cc_start: 0.9218 (tpp) cc_final: 0.8595 (tpt) REVERT: B 588 GLN cc_start: 0.9415 (mm-40) cc_final: 0.9189 (mm-40) REVERT: B 631 ASP cc_start: 0.9522 (t70) cc_final: 0.9176 (t0) REVERT: C 21 PHE cc_start: 0.9441 (m-80) cc_final: 0.8849 (m-80) REVERT: C 46 TYR cc_start: 0.8808 (m-80) cc_final: 0.8570 (m-80) REVERT: C 108 ILE cc_start: 0.9110 (mt) cc_final: 0.8903 (mt) REVERT: C 179 TYR cc_start: 0.9492 (t80) cc_final: 0.9193 (t80) REVERT: C 185 MET cc_start: 0.8723 (mpp) cc_final: 0.8424 (mpp) REVERT: C 196 ARG cc_start: 0.9275 (mtm110) cc_final: 0.9069 (mtm110) REVERT: C 204 TYR cc_start: 0.9677 (t80) cc_final: 0.9234 (t80) REVERT: D 46 TYR cc_start: 0.9050 (m-80) cc_final: 0.8819 (m-10) REVERT: D 179 TYR cc_start: 0.9066 (t80) cc_final: 0.8771 (t80) REVERT: D 185 MET cc_start: 0.7895 (mmm) cc_final: 0.6844 (mmm) REVERT: D 189 GLU cc_start: 0.9054 (tp30) cc_final: 0.8788 (pt0) REVERT: D 193 LEU cc_start: 0.8590 (mt) cc_final: 0.8364 (mt) outliers start: 0 outliers final: 0 residues processed: 623 average time/residue: 0.1083 time to fit residues: 101.0503 Evaluate side-chains 550 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 550 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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: 2.9990 chunk 133 optimal weight: 9.9990 chunk 149 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 77 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 GLN ** 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 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 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 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.112883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.081842 restraints weight = 52580.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.084575 restraints weight = 31526.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.086481 restraints weight = 21936.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.087847 restraints weight = 16523.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.088855 restraints weight = 13297.700| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.7922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16386 Z= 0.164 Angle : 0.645 6.880 22134 Z= 0.346 Chirality : 0.043 0.218 2360 Planarity : 0.004 0.104 2818 Dihedral : 9.165 138.440 2290 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.19), residues: 1932 helix: 0.67 (0.15), residues: 1166 sheet: -0.86 (0.45), residues: 130 loop : 0.13 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG D 261 TYR 0.026 0.002 TYR C 142 PHE 0.019 0.002 PHE D 109 TRP 0.012 0.001 TRP A 558 HIS 0.006 0.001 HIS B 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (16386) covalent geometry : angle 0.64528 / 0.35 (22134) hydrogen bonds : bond 0.03866 / 2.43 ( 869) hydrogen bonds : angle 5.04101 / 3.60 ( 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 612 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 612 time to evaluate : 0.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9453 (tptp) cc_final: 0.9127 (tptp) REVERT: A 87 LYS cc_start: 0.9592 (tptp) cc_final: 0.9366 (tptp) REVERT: A 95 MET cc_start: 0.9730 (tpt) cc_final: 0.9490 (mmm) REVERT: A 104 TYR cc_start: 0.8842 (m-80) cc_final: 0.8430 (m-80) REVERT: A 129 PHE cc_start: 0.9552 (m-80) cc_final: 0.9111 (m-80) REVERT: A 136 LYS cc_start: 0.9768 (mmpt) cc_final: 0.9519 (ttpt) REVERT: A 144 MET cc_start: 0.8906 (mtm) cc_final: 0.8454 (mtm) REVERT: A 158 ASN cc_start: 0.9558 (m110) cc_final: 0.8998 (p0) REVERT: A 186 ILE cc_start: 0.9552 (mt) cc_final: 0.9175 (mt) REVERT: A 190 MET cc_start: 0.9496 (mmm) cc_final: 0.8813 (mmm) REVERT: A 194 LYS cc_start: 0.9349 (ttpt) cc_final: 0.9063 (ttpp) REVERT: A 205 LYS cc_start: 0.8796 (mmmm) cc_final: 0.8264 (mmmm) REVERT: A 227 MET cc_start: 0.9199 (mtp) cc_final: 0.8626 (mtp) REVERT: A 235 ARG cc_start: 0.8761 (ttp-110) cc_final: 0.8460 (ttm110) REVERT: A 239 GLN cc_start: 0.8423 (tt0) cc_final: 0.8111 (tp40) REVERT: A 252 ASN cc_start: 0.8944 (t0) cc_final: 0.8605 (t0) REVERT: A 255 HIS cc_start: 0.8265 (t-90) cc_final: 0.7792 (t-90) REVERT: A 286 ASP cc_start: 0.9147 (m-30) cc_final: 0.8606 (m-30) REVERT: A 349 LEU cc_start: 0.9452 (mt) cc_final: 0.8938 (mt) REVERT: A 350 ARG cc_start: 0.8512 (mtp85) cc_final: 0.7957 (mtp85) REVERT: A 359 MET cc_start: 0.9160 (ttp) cc_final: 0.8939 (ttp) REVERT: A 362 ASP cc_start: 0.9178 (m-30) cc_final: 0.8673 (m-30) REVERT: A 370 ASN cc_start: 0.9454 (m-40) cc_final: 0.9226 (m-40) REVERT: A 375 LYS cc_start: 0.9472 (mttt) cc_final: 0.9096 (mttt) REVERT: A 390 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8743 (mm110) REVERT: A 414 LEU cc_start: 0.9398 (mt) cc_final: 0.9047 (mt) REVERT: A 426 GLU cc_start: 0.9256 (tm-30) cc_final: 0.8712 (tm-30) REVERT: A 456 LYS cc_start: 0.9653 (mmpt) cc_final: 0.9323 (mmmt) REVERT: A 468 LEU cc_start: 0.9531 (tp) cc_final: 0.9294 (tp) REVERT: A 494 MET cc_start: 0.9567 (mtt) cc_final: 0.9246 (mtp) REVERT: A 515 ASP cc_start: 0.9448 (m-30) cc_final: 0.9190 (m-30) REVERT: A 562 LYS cc_start: 0.9792 (ttmt) cc_final: 0.9574 (tppt) REVERT: A 591 THR cc_start: 0.9139 (p) cc_final: 0.8931 (p) REVERT: A 602 GLU cc_start: 0.8977 (pt0) cc_final: 0.8415 (pm20) REVERT: A 615 MET cc_start: 0.8792 (mmp) cc_final: 0.8481 (mmm) REVERT: A 618 LEU cc_start: 0.9299 (tt) cc_final: 0.9075 (tt) REVERT: A 653 SER cc_start: 0.8974 (p) cc_final: 0.8315 (t) REVERT: B 51 LEU cc_start: 0.9489 (tp) cc_final: 0.9022 (tp) REVERT: B 77 ILE cc_start: 0.9533 (mt) cc_final: 0.9245 (mt) REVERT: B 81 PHE cc_start: 0.9517 (m-10) cc_final: 0.9174 (m-10) REVERT: B 87 LYS cc_start: 0.9385 (tptp) cc_final: 0.9078 (tptp) REVERT: B 95 MET cc_start: 0.9553 (tpp) cc_final: 0.8495 (tpp) REVERT: B 99 LYS cc_start: 0.9644 (mmmt) cc_final: 0.8794 (mmmt) REVERT: B 114 ILE cc_start: 0.9573 (mt) cc_final: 0.9246 (pt) REVERT: B 144 MET cc_start: 0.9289 (mtm) cc_final: 0.8755 (mtm) REVERT: B 147 GLN cc_start: 0.9229 (mm110) cc_final: 0.8706 (mm110) REVERT: B 149 TYR cc_start: 0.9369 (t80) cc_final: 0.8881 (t80) REVERT: B 161 ARG cc_start: 0.8839 (ttm110) cc_final: 0.8208 (mtt180) REVERT: B 162 LYS cc_start: 0.9386 (tppt) cc_final: 0.9074 (tppt) REVERT: B 211 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8495 (mm-30) REVERT: B 240 MET cc_start: 0.8314 (mpp) cc_final: 0.7824 (mpp) REVERT: B 252 ASN cc_start: 0.8996 (t0) cc_final: 0.8722 (t0) REVERT: B 257 ASP cc_start: 0.8361 (m-30) cc_final: 0.8084 (m-30) REVERT: B 286 ASP cc_start: 0.9081 (m-30) cc_final: 0.8456 (m-30) REVERT: B 322 MET cc_start: 0.8619 (ttt) cc_final: 0.8173 (ttt) REVERT: B 333 LYS cc_start: 0.9448 (tptm) cc_final: 0.9226 (tptp) REVERT: B 335 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8151 (mt-10) REVERT: B 350 ARG cc_start: 0.9230 (tpp80) cc_final: 0.8865 (tpp80) REVERT: B 359 MET cc_start: 0.7963 (ptp) cc_final: 0.7673 (ptp) REVERT: B 362 ASP cc_start: 0.8752 (m-30) cc_final: 0.8030 (m-30) REVERT: B 396 ASP cc_start: 0.8119 (p0) cc_final: 0.7575 (p0) REVERT: B 399 GLU cc_start: 0.9468 (mm-30) cc_final: 0.9106 (mp0) REVERT: B 415 ASN cc_start: 0.9352 (t0) cc_final: 0.8672 (t0) REVERT: B 416 ILE cc_start: 0.9795 (mt) cc_final: 0.9546 (mt) REVERT: B 418 ASN cc_start: 0.9407 (m-40) cc_final: 0.9064 (m-40) REVERT: B 420 MET cc_start: 0.9203 (mmm) cc_final: 0.8842 (mmm) REVERT: B 426 GLU cc_start: 0.9228 (pm20) cc_final: 0.8914 (pm20) REVERT: B 427 LYS cc_start: 0.9716 (ptpp) cc_final: 0.9261 (ptpp) REVERT: B 501 GLN cc_start: 0.9040 (tp-100) cc_final: 0.8583 (tp-100) REVERT: B 505 GLU cc_start: 0.9031 (mt-10) cc_final: 0.7811 (mt-10) REVERT: B 515 ASP cc_start: 0.8800 (m-30) cc_final: 0.8342 (m-30) REVERT: B 531 TYR cc_start: 0.8648 (m-80) cc_final: 0.8311 (m-80) REVERT: B 570 MET cc_start: 0.9241 (tpp) cc_final: 0.8621 (tpt) REVERT: B 595 MET cc_start: 0.9558 (mmm) cc_final: 0.9295 (mpp) REVERT: B 654 PHE cc_start: 0.9453 (t80) cc_final: 0.8895 (t80) REVERT: C 17 PHE cc_start: 0.8570 (p90) cc_final: 0.7655 (p90) REVERT: C 21 PHE cc_start: 0.9405 (m-80) cc_final: 0.8794 (m-80) REVERT: C 46 TYR cc_start: 0.8822 (m-80) cc_final: 0.8604 (m-80) REVERT: C 179 TYR cc_start: 0.9499 (t80) cc_final: 0.9195 (t80) REVERT: C 185 MET cc_start: 0.8679 (mpp) cc_final: 0.8387 (mpp) REVERT: C 204 TYR cc_start: 0.9660 (t80) cc_final: 0.9025 (t80) REVERT: D 46 TYR cc_start: 0.9047 (m-80) cc_final: 0.8811 (m-10) REVERT: D 185 MET cc_start: 0.7866 (mmm) cc_final: 0.7534 (mmm) REVERT: D 193 LEU cc_start: 0.8573 (mt) cc_final: 0.8360 (mt) outliers start: 0 outliers final: 0 residues processed: 612 average time/residue: 0.1105 time to fit residues: 100.7826 Evaluate side-chains 545 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 545 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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: 0.4980 chunk 62 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 189 optimal weight: 0.9980 chunk 181 optimal weight: 9.9990 chunk 165 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 132 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 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 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 568 HIS ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.112999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.081175 restraints weight = 53282.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.084081 restraints weight = 31707.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.085942 restraints weight = 21969.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.087325 restraints weight = 16804.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.088279 restraints weight = 13606.985| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3167 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.8125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16386 Z= 0.152 Angle : 0.657 8.348 22134 Z= 0.351 Chirality : 0.043 0.193 2360 Planarity : 0.004 0.063 2818 Dihedral : 9.081 138.711 2290 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % 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: 0.40 (0.19), residues: 1932 helix: 0.66 (0.15), residues: 1164 sheet: -0.96 (0.44), residues: 130 loop : 0.07 (0.24), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 196 TYR 0.023 0.002 TYR C 142 PHE 0.019 0.002 PHE B 81 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 0.00334 / 0.15 (16386) covalent geometry : angle 0.65728 / 0.35 (22134) hydrogen bonds : bond 0.03813 / 2.42 ( 869) hydrogen bonds : angle 5.07591 / 3.63 ( 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 606 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 606 time to evaluate : 0.581 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: 0.9454 (tptp) cc_final: 0.9123 (tptp) REVERT: A 64 TYR cc_start: 0.9327 (m-10) cc_final: 0.9086 (m-80) REVERT: A 65 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8472 (mp0) REVERT: A 87 LYS cc_start: 0.9668 (tptp) cc_final: 0.9370 (tptp) REVERT: A 104 TYR cc_start: 0.8800 (m-80) cc_final: 0.8452 (m-80) REVERT: A 119 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8628 (pm20) REVERT: A 129 PHE cc_start: 0.9562 (m-80) cc_final: 0.9139 (m-80) REVERT: A 136 LYS cc_start: 0.9739 (mmpt) cc_final: 0.9522 (ttpt) REVERT: A 144 MET cc_start: 0.8935 (mtm) cc_final: 0.8473 (mtm) REVERT: A 158 ASN cc_start: 0.9563 (m110) cc_final: 0.9070 (p0) REVERT: A 186 ILE cc_start: 0.9537 (mt) cc_final: 0.9117 (mt) REVERT: A 190 MET cc_start: 0.9487 (mmm) cc_final: 0.8876 (mmm) REVERT: A 205 LYS cc_start: 0.8814 (mmmm) cc_final: 0.8236 (mmmm) REVERT: A 227 MET cc_start: 0.9045 (mtp) cc_final: 0.8631 (mtp) REVERT: A 235 ARG cc_start: 0.8822 (ttp-110) cc_final: 0.8501 (ttm110) REVERT: A 252 ASN cc_start: 0.9043 (t0) cc_final: 0.8743 (t0) REVERT: A 255 HIS cc_start: 0.8201 (t-90) cc_final: 0.7595 (t-90) REVERT: A 263 ASP cc_start: 0.9145 (m-30) cc_final: 0.8942 (m-30) REVERT: A 286 ASP cc_start: 0.9148 (m-30) cc_final: 0.8637 (m-30) REVERT: A 314 MET cc_start: 0.8677 (ppp) cc_final: 0.8205 (ppp) REVERT: A 319 MET cc_start: 0.9053 (mmp) cc_final: 0.8831 (mmm) REVERT: A 349 LEU cc_start: 0.9462 (mt) cc_final: 0.8927 (mt) REVERT: A 350 ARG cc_start: 0.8468 (mtp85) cc_final: 0.7909 (mtp85) REVERT: A 362 ASP cc_start: 0.9170 (m-30) cc_final: 0.8585 (m-30) REVERT: A 370 ASN cc_start: 0.9456 (m-40) cc_final: 0.9200 (m-40) REVERT: A 375 LYS cc_start: 0.9477 (mttt) cc_final: 0.9089 (mttt) REVERT: A 390 GLN cc_start: 0.9088 (mm-40) cc_final: 0.8724 (mm110) REVERT: A 396 ASP cc_start: 0.9096 (p0) cc_final: 0.8873 (p0) REVERT: A 402 GLU cc_start: 0.9048 (tm-30) cc_final: 0.8806 (tm-30) REVERT: A 414 LEU cc_start: 0.9442 (mt) cc_final: 0.9131 (mt) REVERT: A 426 GLU cc_start: 0.9273 (tm-30) cc_final: 0.8763 (tm-30) REVERT: A 456 LYS cc_start: 0.9658 (mmpt) cc_final: 0.9343 (mmmt) REVERT: A 468 LEU cc_start: 0.9545 (tp) cc_final: 0.9268 (tp) REVERT: A 479 TYR cc_start: 0.9089 (t80) cc_final: 0.8480 (t80) REVERT: A 494 MET cc_start: 0.9538 (mtt) cc_final: 0.9229 (mtp) REVERT: A 515 ASP cc_start: 0.9441 (m-30) cc_final: 0.9158 (m-30) REVERT: A 562 LYS cc_start: 0.9775 (ttmt) cc_final: 0.9549 (tppt) REVERT: A 602 GLU cc_start: 0.8951 (pt0) cc_final: 0.8393 (pm20) REVERT: A 615 MET cc_start: 0.8778 (mmp) cc_final: 0.8490 (mmm) REVERT: A 618 LEU cc_start: 0.9277 (tt) cc_final: 0.9051 (tt) REVERT: A 647 HIS cc_start: 0.8643 (m-70) cc_final: 0.8442 (m-70) REVERT: A 653 SER cc_start: 0.8961 (p) cc_final: 0.8677 (p) REVERT: A 677 ARG cc_start: 0.9444 (mmm-85) cc_final: 0.8285 (mmm-85) REVERT: B 51 LEU cc_start: 0.9476 (tp) cc_final: 0.9021 (tp) REVERT: B 75 GLU cc_start: 0.9573 (mp0) cc_final: 0.9352 (pm20) REVERT: B 77 ILE cc_start: 0.9535 (mt) cc_final: 0.9248 (mt) REVERT: B 81 PHE cc_start: 0.9509 (m-10) cc_final: 0.9175 (m-10) REVERT: B 87 LYS cc_start: 0.9385 (tptp) cc_final: 0.9119 (tptp) REVERT: B 95 MET cc_start: 0.9558 (tpp) cc_final: 0.8511 (tpp) REVERT: B 99 LYS cc_start: 0.9625 (mmmt) cc_final: 0.8794 (mmmt) REVERT: B 114 ILE cc_start: 0.9568 (mt) cc_final: 0.9220 (pt) REVERT: B 144 MET cc_start: 0.9310 (mtm) cc_final: 0.8854 (mtm) REVERT: B 147 GLN cc_start: 0.9361 (mm110) cc_final: 0.9013 (mm110) REVERT: B 149 TYR cc_start: 0.9408 (t80) cc_final: 0.8935 (t80) REVERT: B 161 ARG cc_start: 0.8857 (ttm110) cc_final: 0.8308 (mtt180) REVERT: B 162 LYS cc_start: 0.9365 (tppt) cc_final: 0.9097 (ttmt) REVERT: B 211 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8461 (mm-30) REVERT: B 257 ASP cc_start: 0.8339 (m-30) cc_final: 0.8045 (m-30) REVERT: B 263 ASP cc_start: 0.9345 (m-30) cc_final: 0.9005 (m-30) REVERT: B 286 ASP cc_start: 0.9095 (m-30) cc_final: 0.7759 (m-30) REVERT: B 307 TYR cc_start: 0.9301 (t80) cc_final: 0.9030 (t80) REVERT: B 322 MET cc_start: 0.8639 (ttt) cc_final: 0.8210 (ttt) REVERT: B 333 LYS cc_start: 0.9477 (tptm) cc_final: 0.9246 (tptp) REVERT: B 335 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8115 (mt-10) REVERT: B 350 ARG cc_start: 0.9270 (tpp80) cc_final: 0.9005 (tpp80) REVERT: B 359 MET cc_start: 0.7987 (ptp) cc_final: 0.7666 (ptp) REVERT: B 361 GLN cc_start: 0.9490 (tt0) cc_final: 0.9159 (pp30) REVERT: B 362 ASP cc_start: 0.8747 (m-30) cc_final: 0.6418 (m-30) REVERT: B 396 ASP cc_start: 0.8072 (p0) cc_final: 0.7560 (p0) REVERT: B 399 GLU cc_start: 0.9493 (mm-30) cc_final: 0.9167 (mp0) REVERT: B 415 ASN cc_start: 0.9355 (t0) cc_final: 0.8931 (t0) REVERT: B 416 ILE cc_start: 0.9797 (mt) cc_final: 0.9540 (mt) REVERT: B 418 ASN cc_start: 0.9440 (m-40) cc_final: 0.9151 (m-40) REVERT: B 420 MET cc_start: 0.9233 (mmm) cc_final: 0.8870 (mmm) REVERT: B 426 GLU cc_start: 0.9221 (pm20) cc_final: 0.8917 (pm20) REVERT: B 427 LYS cc_start: 0.9725 (ptpp) cc_final: 0.9233 (ptpp) REVERT: B 459 LYS cc_start: 0.8890 (mppt) cc_final: 0.8514 (mmmt) REVERT: B 501 GLN cc_start: 0.9016 (tp-100) cc_final: 0.8542 (tp-100) REVERT: B 505 GLU cc_start: 0.9054 (mt-10) cc_final: 0.7782 (mt-10) REVERT: B 515 ASP cc_start: 0.8733 (m-30) cc_final: 0.8393 (m-30) REVERT: B 570 MET cc_start: 0.9261 (tpp) cc_final: 0.8764 (tpp) REVERT: B 588 GLN cc_start: 0.9431 (mm-40) cc_final: 0.8663 (mm-40) REVERT: B 595 MET cc_start: 0.9545 (mmm) cc_final: 0.9137 (mpp) REVERT: B 654 PHE cc_start: 0.9398 (t80) cc_final: 0.8780 (t80) REVERT: C 17 PHE cc_start: 0.8420 (p90) cc_final: 0.7546 (p90) REVERT: C 21 PHE cc_start: 0.9378 (m-80) cc_final: 0.8875 (m-80) REVERT: C 46 TYR cc_start: 0.8850 (m-80) cc_final: 0.8634 (m-80) REVERT: C 108 ILE cc_start: 0.9180 (mt) cc_final: 0.8970 (mt) REVERT: C 179 TYR cc_start: 0.9476 (t80) cc_final: 0.9145 (t80) REVERT: C 185 MET cc_start: 0.8637 (mpp) cc_final: 0.8346 (mpp) REVERT: C 204 TYR cc_start: 0.9694 (t80) cc_final: 0.9014 (t80) REVERT: C 276 TYR cc_start: 0.9163 (t80) cc_final: 0.8898 (t80) REVERT: D 46 TYR cc_start: 0.9072 (m-80) cc_final: 0.8810 (m-10) REVERT: D 179 TYR cc_start: 0.9153 (t80) cc_final: 0.8944 (t80) REVERT: D 185 MET cc_start: 0.7664 (mmm) cc_final: 0.7435 (mmm) REVERT: D 201 HIS cc_start: 0.8715 (m170) cc_final: 0.8502 (m170) outliers start: 0 outliers final: 0 residues processed: 606 average time/residue: 0.1075 time to fit residues: 97.4491 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 : 0.377 ------------------------------------------------------------------------------- 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: 8.9990 chunk 1 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 148 optimal weight: 20.0000 chunk 125 optimal weight: 0.1980 chunk 28 optimal weight: 0.2980 chunk 34 optimal weight: 0.4980 chunk 13 optimal weight: 8.9990 chunk 29 optimal weight: 5.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- 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 365 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 147 GLN B 150 GLN ** B 191 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 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN C 23 ASN C 25 ASN C 233 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.113769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.081964 restraints weight = 52355.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.084716 restraints weight = 31016.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.086789 restraints weight = 21319.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.088037 restraints weight = 16345.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.088994 restraints weight = 13433.302| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.8294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16386 Z= 0.147 Angle : 0.659 7.255 22134 Z= 0.354 Chirality : 0.043 0.184 2360 Planarity : 0.004 0.063 2818 Dihedral : 9.034 139.885 2290 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % 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: 0.33 (0.19), residues: 1932 helix: 0.61 (0.15), residues: 1164 sheet: -1.12 (0.43), residues: 142 loop : 0.07 (0.25), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 196 TYR 0.041 0.002 TYR B 574 PHE 0.020 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 0.00324 / 0.15 (16386) covalent geometry : angle 0.65904 / 0.35 (22134) hydrogen bonds : bond 0.03861 / 2.45 ( 869) hydrogen bonds : angle 5.11525 / 3.66 ( 2568) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3036.96 seconds wall clock time: 53 minutes 33.13 seconds (3213.13 seconds total)