Starting phenix.real_space_refine on Thu Aug 6 15:16:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byw_45046/08_2026/9byw_45046_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byw_45046/08_2026/9byw_45046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9byw_45046/08_2026/9byw_45046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byw_45046/08_2026/9byw_45046.map" model { file = "/net/cci-nas-00/data/ceres_data/9byw_45046/08_2026/9byw_45046_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byw_45046/08_2026/9byw_45046_neut.cif" } resolution = 4.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 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: 3.55, per 1000 atoms: 0.22 Number of scatterers: 16038 At special positions: 0 Unit cell: (96.615, 125.091, 132.21, 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: 1.28 Conformation dependent library (CDL) restraints added in 680.3 milliseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 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: 3.516A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.985A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A 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: 3.948A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.694A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A 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: 3.628A 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: 3.580A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.676A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A 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: 3.730A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.027A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.067A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.669A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.360A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.198A 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: 7.901A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.478A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.185A 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: 4.049A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.48 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: 4896 1.34 - 1.46: 2984 1.46 - 1.58: 8324 1.58 - 1.70: 26 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 4.81e+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 2.31e+01 bond pdb=" O3A TTP A 803 " pdb=" PB TTP A 803 " ideal model delta sigma weight residual 1.675 1.605 0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.15e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21525 2.09 - 4.19: 528 4.19 - 6.28: 64 6.28 - 8.37: 8 8.37 - 10.47: 9 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.65 -6.11 1.36e+00 5.41e-01 2.02e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.11 -4.40 1.15e+00 7.56e-01 1.46e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.83 -4.33 1.23e+00 6.61e-01 1.24e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.70 -3.99 1.15e+00 7.56e-01 1.21e+01 angle pdb=" O1A TTP B 801 " pdb=" PA TTP B 801 " pdb=" O2A TTP B 801 " ideal model delta sigma weight residual 121.23 110.96 10.27 3.00e+00 1.11e-01 1.17e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.04: 9087 25.04 - 50.08: 656 50.08 - 75.13: 127 75.13 - 100.17: 26 100.17 - 125.21: 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 -98.19 125.21 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 -95.60 122.62 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 -134.40 12.40 0 2.50e+00 1.60e-01 2.46e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2139 0.093 - 0.186: 187 0.186 - 0.279: 29 0.279 - 0.372: 3 0.372 - 0.465: 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 2.05 0.46 2.00e-01 2.50e+01 5.40e+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 4.61e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO D 75 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " 0.017 2.00e-02 2.50e+03 1.12e-02 2.20e+00 pdb=" CG PHE D 92 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 169 " 0.017 2.00e-02 2.50e+03 9.90e-03 1.96e+00 pdb=" CG TYR C 169 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 169 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 169 " 0.008 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 129 2.51 - 3.11: 11553 3.11 - 3.70: 27038 3.70 - 4.30: 41546 4.30 - 4.90: 65401 Nonbonded interactions: 145667 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 145662 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.890 Find NCS groups from input model: 0.310 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5626 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= 0.334 Angle : 0.788 10.466 22134 Z= 0.472 Chirality : 0.058 0.465 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.681 125.209 6202 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.34 % Allowed : 15.38 % Favored : 83.28 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.18), residues: 1932 helix: 0.58 (0.14), residues: 1151 sheet: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE D 92 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 0.00596 / 0.33 (16386) covalent geometry : angle 0.78770 / 0.47 (22134) hydrogen bonds : bond 0.15421 / 9.51 ( 871) hydrogen bonds : angle 6.51765 / 4.65 ( 2571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 802 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 779 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.9137 (mt) cc_final: 0.6542 (mt) REVERT: A 95 MET cc_start: 0.8221 (tpp) cc_final: 0.7892 (mmm) REVERT: A 136 LYS cc_start: 0.8133 (tptt) cc_final: 0.7433 (tttt) REVERT: A 143 LEU cc_start: 0.9004 (tp) cc_final: 0.8638 (tp) REVERT: A 147 GLN cc_start: 0.8416 (mt0) cc_final: 0.7913 (mt0) REVERT: A 155 THR cc_start: 0.9063 (m) cc_final: 0.8749 (m) REVERT: A 166 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8431 (mm-30) REVERT: A 172 LEU cc_start: 0.8583 (mp) cc_final: 0.8353 (mp) REVERT: A 173 LEU cc_start: 0.7045 (mt) cc_final: 0.6673 (mt) REVERT: A 181 ASP cc_start: 0.7470 (m-30) cc_final: 0.6966 (m-30) REVERT: A 190 MET cc_start: 0.7882 (mtt) cc_final: 0.7606 (mtt) REVERT: A 205 LYS cc_start: 0.7012 (mttp) cc_final: 0.6718 (mttt) REVERT: A 288 PHE cc_start: 0.7716 (t80) cc_final: 0.7511 (t80) REVERT: A 367 VAL cc_start: 0.8760 (m) cc_final: 0.8356 (m) REVERT: A 550 MET cc_start: 0.6875 (mtm) cc_final: 0.6163 (mtp) REVERT: A 597 ILE cc_start: 0.8618 (pt) cc_final: 0.8411 (pt) REVERT: A 634 MET cc_start: 0.8480 (mmp) cc_final: 0.8021 (mmm) REVERT: A 637 VAL cc_start: 0.8973 (t) cc_final: 0.8597 (p) REVERT: A 645 GLN cc_start: 0.7000 (tp40) cc_final: 0.6708 (tp-100) REVERT: A 650 GLN cc_start: 0.6815 (mt0) cc_final: 0.6450 (mt0) REVERT: A 655 THR cc_start: 0.7159 (m) cc_final: 0.6489 (m) REVERT: A 658 LEU cc_start: 0.8182 (mt) cc_final: 0.7626 (mt) REVERT: A 667 LEU cc_start: 0.8626 (tt) cc_final: 0.8219 (tp) REVERT: B 62 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8324 (mp10) REVERT: B 89 PHE cc_start: 0.7137 (t80) cc_final: 0.6792 (t80) REVERT: B 96 SER cc_start: 0.9285 (m) cc_final: 0.8885 (p) REVERT: B 125 VAL cc_start: 0.9205 (t) cc_final: 0.8977 (t) REVERT: B 143 LEU cc_start: 0.9058 (tp) cc_final: 0.8853 (tp) REVERT: B 179 LEU cc_start: 0.8385 (tp) cc_final: 0.8122 (tp) REVERT: B 191 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8216 (mm-40) REVERT: B 193 SER cc_start: 0.8165 (m) cc_final: 0.7935 (p) REVERT: B 200 SER cc_start: 0.8143 (t) cc_final: 0.7857 (m) REVERT: B 213 ILE cc_start: 0.8628 (mt) cc_final: 0.8239 (mp) REVERT: B 216 VAL cc_start: 0.8357 (OUTLIER) cc_final: 0.7796 (m) REVERT: B 232 ASN cc_start: 0.7483 (OUTLIER) cc_final: 0.7131 (t0) REVERT: B 265 LYS cc_start: 0.7847 (mmtt) cc_final: 0.7548 (mmmm) REVERT: B 282 VAL cc_start: 0.8805 (t) cc_final: 0.8491 (m) REVERT: B 288 PHE cc_start: 0.7211 (t80) cc_final: 0.6414 (t80) REVERT: B 319 MET cc_start: 0.7581 (tpp) cc_final: 0.6762 (tpp) REVERT: B 358 ILE cc_start: 0.8730 (mm) cc_final: 0.8282 (mm) REVERT: B 362 ASP cc_start: 0.5783 (m-30) cc_final: 0.4558 (m-30) REVERT: B 373 ILE cc_start: 0.9091 (mt) cc_final: 0.8001 (mt) REVERT: B 384 GLU cc_start: 0.6657 (pm20) cc_final: 0.6285 (pm20) REVERT: B 391 VAL cc_start: 0.9072 (p) cc_final: 0.8869 (p) REVERT: B 410 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8107 (m-40) REVERT: B 411 LEU cc_start: 0.7569 (mp) cc_final: 0.7154 (mp) REVERT: B 417 LEU cc_start: 0.8670 (tp) cc_final: 0.7411 (tt) REVERT: B 445 ILE cc_start: 0.8671 (mt) cc_final: 0.8447 (mm) REVERT: B 471 TYR cc_start: 0.6004 (t80) cc_final: 0.5307 (t80) REVERT: B 474 GLN cc_start: 0.8332 (mt0) cc_final: 0.8121 (mt0) REVERT: B 565 VAL cc_start: 0.9399 (t) cc_final: 0.9122 (p) REVERT: B 585 SER cc_start: 0.9134 (p) cc_final: 0.8444 (t) REVERT: B 589 SER cc_start: 0.8091 (m) cc_final: 0.7538 (t) REVERT: B 613 TYR cc_start: 0.7322 (t80) cc_final: 0.6637 (t80) REVERT: B 634 MET cc_start: 0.8149 (mmp) cc_final: 0.7804 (mmm) REVERT: B 656 LEU cc_start: 0.8616 (mt) cc_final: 0.8200 (mt) REVERT: C 90 LEU cc_start: 0.5686 (mt) cc_final: 0.4387 (mt) REVERT: C 151 ILE cc_start: 0.6601 (mm) cc_final: 0.6134 (mm) REVERT: C 208 LEU cc_start: 0.6294 (mt) cc_final: 0.5703 (mt) REVERT: D 126 LYS cc_start: 0.2376 (OUTLIER) cc_final: 0.2032 (tptp) REVERT: D 174 TYR cc_start: 0.1481 (t80) cc_final: 0.0317 (t80) REVERT: D 195 LEU cc_start: 0.8036 (tt) cc_final: 0.7760 (tt) REVERT: D 229 ILE cc_start: 0.5863 (mm) cc_final: 0.5618 (mm) REVERT: D 282 ILE cc_start: -0.1245 (OUTLIER) cc_final: -0.1508 (tp) outliers start: 23 outliers final: 5 residues processed: 799 average time/residue: 0.1394 time to fit residues: 162.8283 Evaluate side-chains 523 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 513 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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: 5.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 43 GLN ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN A 239 GLN A 320 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 304 HIS ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 ASN B 645 GLN C 24 GLN C 28 GLN C 38 ASN C 119 ASN D 80 HIS D 136 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.134341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.092373 restraints weight = 48169.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.095879 restraints weight = 30330.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.098358 restraints weight = 20949.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.099995 restraints weight = 16216.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.101169 restraints weight = 13108.533| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3429 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3429 r_free = 0.3429 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6792 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16386 Z= 0.202 Angle : 0.636 7.162 22134 Z= 0.343 Chirality : 0.044 0.229 2360 Planarity : 0.004 0.063 2818 Dihedral : 9.536 128.697 2290 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.29 % Allowed : 3.79 % Favored : 95.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.19), residues: 1932 helix: 1.38 (0.15), residues: 1116 sheet: -0.16 (0.40), residues: 152 loop : 0.68 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 207 TYR 0.026 0.002 TYR A 140 PHE 0.034 0.002 PHE D 178 TRP 0.027 0.002 TRP B 558 HIS 0.007 0.001 HIS B 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.20 (16386) covalent geometry : angle 0.63647 / 0.34 (22134) hydrogen bonds : bond 0.04833 / 3.02 ( 871) hydrogen bonds : angle 5.16502 / 3.67 ( 2571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 583 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 PHE cc_start: 0.9134 (t80) cc_final: 0.8659 (t80) REVERT: A 143 LEU cc_start: 0.9110 (tp) cc_final: 0.8901 (tp) REVERT: A 147 GLN cc_start: 0.9084 (mt0) cc_final: 0.8587 (mt0) REVERT: A 168 VAL cc_start: 0.8602 (t) cc_final: 0.8329 (t) REVERT: A 172 LEU cc_start: 0.8896 (mp) cc_final: 0.8378 (mp) REVERT: A 173 LEU cc_start: 0.9084 (mt) cc_final: 0.8788 (mt) REVERT: A 214 LYS cc_start: 0.9148 (mmmt) cc_final: 0.8749 (mmtt) REVERT: A 259 ASN cc_start: 0.8180 (p0) cc_final: 0.7950 (p0) REVERT: A 270 ASP cc_start: 0.8754 (m-30) cc_final: 0.8079 (t70) REVERT: A 286 ASP cc_start: 0.8725 (m-30) cc_final: 0.8433 (m-30) REVERT: A 291 LEU cc_start: 0.8759 (mt) cc_final: 0.8417 (mt) REVERT: A 319 MET cc_start: 0.8993 (tpp) cc_final: 0.8727 (tpp) REVERT: A 322 MET cc_start: 0.8712 (mmm) cc_final: 0.7873 (mmm) REVERT: A 325 LYS cc_start: 0.9230 (mttt) cc_final: 0.8939 (mtmm) REVERT: A 348 MET cc_start: 0.9428 (ttp) cc_final: 0.9117 (ptp) REVERT: A 349 LEU cc_start: 0.8471 (tp) cc_final: 0.8229 (tp) REVERT: A 375 LYS cc_start: 0.9110 (mmtm) cc_final: 0.8610 (mmtm) REVERT: A 406 ASP cc_start: 0.8194 (m-30) cc_final: 0.7912 (m-30) REVERT: A 407 ILE cc_start: 0.8878 (mt) cc_final: 0.8579 (mt) REVERT: A 425 ILE cc_start: 0.9428 (mt) cc_final: 0.9196 (mt) REVERT: A 427 LYS cc_start: 0.9364 (mmpt) cc_final: 0.9127 (mttp) REVERT: A 444 ASP cc_start: 0.7893 (t0) cc_final: 0.7165 (t0) REVERT: A 498 TYR cc_start: 0.8741 (m-80) cc_final: 0.8342 (m-80) REVERT: A 500 ILE cc_start: 0.9353 (OUTLIER) cc_final: 0.9139 (mp) REVERT: A 512 GLU cc_start: 0.8443 (pm20) cc_final: 0.7967 (pm20) REVERT: A 546 LEU cc_start: 0.9370 (mt) cc_final: 0.9152 (mt) REVERT: A 550 MET cc_start: 0.7306 (mtm) cc_final: 0.6260 (mtp) REVERT: A 598 MET cc_start: 0.8910 (mtm) cc_final: 0.8537 (mtt) REVERT: A 599 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7152 (mm-30) REVERT: A 601 ILE cc_start: 0.8868 (tt) cc_final: 0.8592 (tt) REVERT: A 602 GLU cc_start: 0.8339 (pm20) cc_final: 0.6587 (mp0) REVERT: A 645 GLN cc_start: 0.8387 (tp40) cc_final: 0.7987 (tp-100) REVERT: A 650 GLN cc_start: 0.7718 (mt0) cc_final: 0.7065 (mt0) REVERT: A 655 THR cc_start: 0.7728 (m) cc_final: 0.6873 (m) REVERT: A 659 LYS cc_start: 0.8693 (mttt) cc_final: 0.8459 (mmmt) REVERT: A 672 LEU cc_start: 0.8876 (mt) cc_final: 0.8635 (mt) REVERT: B 8 LYS cc_start: 0.9432 (tttm) cc_final: 0.9190 (tppt) REVERT: B 12 LEU cc_start: 0.9557 (mt) cc_final: 0.9286 (mt) REVERT: B 95 MET cc_start: 0.8947 (tpp) cc_final: 0.7683 (tpp) REVERT: B 98 PHE cc_start: 0.9457 (t80) cc_final: 0.9245 (t80) REVERT: B 99 LYS cc_start: 0.9579 (mmmt) cc_final: 0.8791 (mmmt) REVERT: B 115 LEU cc_start: 0.8584 (mp) cc_final: 0.8298 (mp) REVERT: B 162 LYS cc_start: 0.9004 (tppt) cc_final: 0.8775 (ttmt) REVERT: B 229 LEU cc_start: 0.8039 (mp) cc_final: 0.7815 (mp) REVERT: B 260 ASP cc_start: 0.9206 (m-30) cc_final: 0.8794 (m-30) REVERT: B 288 PHE cc_start: 0.9338 (t80) cc_final: 0.8836 (t80) REVERT: B 322 MET cc_start: 0.8448 (mmm) cc_final: 0.8209 (mmt) REVERT: B 326 PHE cc_start: 0.9288 (m-80) cc_final: 0.8548 (m-80) REVERT: B 350 ARG cc_start: 0.7825 (mtm-85) cc_final: 0.7584 (mtm110) REVERT: B 358 ILE cc_start: 0.8542 (mm) cc_final: 0.8247 (mm) REVERT: B 394 TYR cc_start: 0.8777 (m-80) cc_final: 0.7977 (m-80) REVERT: B 413 SER cc_start: 0.9181 (m) cc_final: 0.8438 (t) REVERT: B 417 LEU cc_start: 0.9372 (tt) cc_final: 0.8935 (tt) REVERT: B 425 ILE cc_start: 0.9048 (mt) cc_final: 0.8668 (mt) REVERT: B 453 ARG cc_start: 0.9004 (ttt-90) cc_final: 0.8597 (ttt-90) REVERT: B 458 MET cc_start: 0.9257 (mmm) cc_final: 0.8904 (mmm) REVERT: B 479 TYR cc_start: 0.8296 (t80) cc_final: 0.7865 (t80) REVERT: B 493 MET cc_start: 0.9172 (tmm) cc_final: 0.8965 (tmm) REVERT: B 494 MET cc_start: 0.9447 (mtp) cc_final: 0.9054 (mtp) REVERT: B 512 GLU cc_start: 0.8571 (pm20) cc_final: 0.8331 (pm20) REVERT: B 586 TYR cc_start: 0.9412 (m-80) cc_final: 0.9005 (m-80) REVERT: B 602 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8260 (pp20) REVERT: B 645 GLN cc_start: 0.8955 (tp40) cc_final: 0.8679 (tp-100) REVERT: C 38 ASN cc_start: 0.7087 (m-40) cc_final: 0.6195 (p0) REVERT: C 93 MET cc_start: 0.8821 (mtm) cc_final: 0.8592 (mmt) REVERT: C 95 MET cc_start: 0.8222 (tmm) cc_final: 0.7827 (tmm) REVERT: C 96 MET cc_start: 0.8528 (mmm) cc_final: 0.8008 (mmm) REVERT: C 151 ILE cc_start: 0.8237 (mm) cc_final: 0.7975 (mm) REVERT: C 227 PHE cc_start: 0.7906 (t80) cc_final: 0.7582 (t80) REVERT: C 259 PHE cc_start: 0.6593 (t80) cc_final: 0.5823 (t80) REVERT: D 154 PHE cc_start: 0.8100 (t80) cc_final: 0.7798 (t80) REVERT: D 169 TYR cc_start: 0.7651 (m-80) cc_final: 0.6855 (m-80) REVERT: D 174 TYR cc_start: 0.1808 (t80) cc_final: 0.1241 (t80) REVERT: D 178 PHE cc_start: 0.7973 (m-80) cc_final: 0.7751 (m-80) outliers start: 5 outliers final: 0 residues processed: 585 average time/residue: 0.1338 time to fit residues: 117.2679 Evaluate side-chains 464 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 462 time to evaluate : 0.549 ------------------------------------------------------------------------------- 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: 7.9990 chunk 131 optimal weight: 0.9990 chunk 164 optimal weight: 9.9990 chunk 28 optimal weight: 0.6980 chunk 182 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 150 optimal weight: 10.0000 chunk 63 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 158 optimal weight: 20.0000 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN A 365 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN A 475 ASN B 11 GLN B 44 ASN B 218 ASN B 232 ASN B 475 ASN ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 HIS C 132 GLN C 201 HIS D 71 ASN D 265 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.127916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.087269 restraints weight = 50397.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.090728 restraints weight = 30931.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.092851 restraints weight = 21537.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.094441 restraints weight = 16430.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.095519 restraints weight = 13343.657| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 16386 Z= 0.201 Angle : 0.600 6.410 22134 Z= 0.325 Chirality : 0.043 0.168 2360 Planarity : 0.004 0.042 2818 Dihedral : 9.343 130.659 2290 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.23 % Allowed : 3.26 % Favored : 96.50 % 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: 1.24 (0.19), residues: 1932 helix: 1.27 (0.15), residues: 1128 sheet: -0.48 (0.39), residues: 160 loop : 0.62 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 164 TYR 0.019 0.002 TYR B 626 PHE 0.034 0.002 PHE D 166 TRP 0.033 0.002 TRP B 558 HIS 0.007 0.001 HIS B 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.20 (16386) covalent geometry : angle 0.59958 / 0.32 (22134) hydrogen bonds : bond 0.04327 / 2.68 ( 871) hydrogen bonds : angle 4.98862 / 3.53 ( 2571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 535 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.9265 (tp30) cc_final: 0.8768 (tp30) REVERT: A 71 LEU cc_start: 0.9451 (mt) cc_final: 0.9096 (mt) REVERT: A 99 LYS cc_start: 0.9260 (mmtp) cc_final: 0.8679 (mttt) REVERT: A 108 THR cc_start: 0.9251 (OUTLIER) cc_final: 0.8867 (p) REVERT: A 117 ARG cc_start: 0.9080 (mmt90) cc_final: 0.8725 (mtp85) REVERT: A 128 PHE cc_start: 0.9212 (t80) cc_final: 0.8828 (t80) REVERT: A 143 LEU cc_start: 0.9041 (tp) cc_final: 0.8544 (tp) REVERT: A 147 GLN cc_start: 0.9076 (mt0) cc_final: 0.8665 (mt0) REVERT: A 148 GLU cc_start: 0.8154 (mp0) cc_final: 0.7559 (mp0) REVERT: A 158 ASN cc_start: 0.8841 (m110) cc_final: 0.8596 (m110) REVERT: A 168 VAL cc_start: 0.8334 (t) cc_final: 0.8014 (p) REVERT: A 172 LEU cc_start: 0.8831 (mp) cc_final: 0.8244 (mp) REVERT: A 173 LEU cc_start: 0.9100 (mt) cc_final: 0.8848 (mt) REVERT: A 205 LYS cc_start: 0.7436 (mttt) cc_final: 0.7127 (mttt) REVERT: A 259 ASN cc_start: 0.8205 (p0) cc_final: 0.7925 (p0) REVERT: A 270 ASP cc_start: 0.8759 (m-30) cc_final: 0.8105 (t70) REVERT: A 349 LEU cc_start: 0.8554 (tp) cc_final: 0.8275 (tp) REVERT: A 375 LYS cc_start: 0.9103 (mmtm) cc_final: 0.8639 (mmtm) REVERT: A 385 VAL cc_start: 0.8733 (t) cc_final: 0.8455 (p) REVERT: A 386 LEU cc_start: 0.9336 (mt) cc_final: 0.9129 (mt) REVERT: A 402 GLU cc_start: 0.8802 (mp0) cc_final: 0.8535 (mp0) REVERT: A 406 ASP cc_start: 0.8250 (m-30) cc_final: 0.7999 (m-30) REVERT: A 407 ILE cc_start: 0.8871 (mt) cc_final: 0.8491 (mt) REVERT: A 425 ILE cc_start: 0.9424 (mt) cc_final: 0.9140 (mm) REVERT: A 458 MET cc_start: 0.9129 (mmp) cc_final: 0.8781 (mmp) REVERT: A 466 MET cc_start: 0.9272 (ptt) cc_final: 0.9007 (ptp) REVERT: A 479 TYR cc_start: 0.8700 (t80) cc_final: 0.8481 (t80) REVERT: A 498 TYR cc_start: 0.8874 (m-80) cc_final: 0.8462 (m-80) REVERT: A 546 LEU cc_start: 0.9425 (mt) cc_final: 0.9177 (mt) REVERT: A 550 MET cc_start: 0.7454 (mtm) cc_final: 0.6539 (mtp) REVERT: A 598 MET cc_start: 0.8876 (mtm) cc_final: 0.8474 (mtm) REVERT: A 599 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7416 (mm-30) REVERT: A 602 GLU cc_start: 0.8993 (pm20) cc_final: 0.8142 (pm20) REVERT: A 615 MET cc_start: 0.8313 (mmp) cc_final: 0.7965 (mmp) REVERT: A 650 GLN cc_start: 0.7925 (mt0) cc_final: 0.7567 (mt0) REVERT: A 659 LYS cc_start: 0.8571 (mttt) cc_final: 0.8367 (mmmt) REVERT: B 8 LYS cc_start: 0.9476 (tttm) cc_final: 0.9190 (tppt) REVERT: B 12 LEU cc_start: 0.9607 (mt) cc_final: 0.9363 (mt) REVERT: B 24 PHE cc_start: 0.8693 (m-80) cc_final: 0.8271 (m-80) REVERT: B 67 GLU cc_start: 0.8696 (mp0) cc_final: 0.8424 (mp0) REVERT: B 95 MET cc_start: 0.9084 (tpp) cc_final: 0.7861 (tpp) REVERT: B 99 LYS cc_start: 0.9596 (mmmt) cc_final: 0.8826 (mmmt) REVERT: B 107 LYS cc_start: 0.8842 (mppt) cc_final: 0.8564 (mptt) REVERT: B 115 LEU cc_start: 0.8724 (mp) cc_final: 0.8409 (mp) REVERT: B 200 SER cc_start: 0.7125 (m) cc_final: 0.6833 (p) REVERT: B 228 LYS cc_start: 0.8141 (mmmm) cc_final: 0.7869 (tppt) REVERT: B 288 PHE cc_start: 0.9393 (t80) cc_final: 0.8917 (t80) REVERT: B 307 TYR cc_start: 0.9281 (t80) cc_final: 0.8828 (t80) REVERT: B 326 PHE cc_start: 0.9322 (m-80) cc_final: 0.8589 (m-80) REVERT: B 379 SER cc_start: 0.8284 (t) cc_final: 0.7909 (t) REVERT: B 394 TYR cc_start: 0.8876 (m-80) cc_final: 0.8633 (m-80) REVERT: B 413 SER cc_start: 0.9167 (m) cc_final: 0.8495 (t) REVERT: B 458 MET cc_start: 0.9259 (mmm) cc_final: 0.9006 (mmm) REVERT: B 466 MET cc_start: 0.8708 (ptp) cc_final: 0.8423 (ptp) REVERT: B 492 PHE cc_start: 0.9216 (m-80) cc_final: 0.8542 (m-80) REVERT: B 493 MET cc_start: 0.9322 (tmm) cc_final: 0.8811 (tmm) REVERT: B 494 MET cc_start: 0.9475 (mtp) cc_final: 0.8890 (mtp) REVERT: B 506 ILE cc_start: 0.9624 (mm) cc_final: 0.9287 (mm) REVERT: B 509 GLU cc_start: 0.9016 (pt0) cc_final: 0.8714 (pp20) REVERT: B 510 LYS cc_start: 0.9507 (mmtp) cc_final: 0.9306 (mmmm) REVERT: B 512 GLU cc_start: 0.8540 (pm20) cc_final: 0.8312 (pm20) REVERT: B 522 TYR cc_start: 0.8598 (m-80) cc_final: 0.8222 (m-10) REVERT: B 597 ILE cc_start: 0.9002 (pt) cc_final: 0.8719 (pt) REVERT: B 615 MET cc_start: 0.9127 (mmp) cc_final: 0.8718 (mmm) REVERT: B 645 GLN cc_start: 0.9115 (tp40) cc_final: 0.8857 (tp-100) REVERT: C 74 MET cc_start: 0.7645 (ttm) cc_final: 0.6796 (ptm) REVERT: C 95 MET cc_start: 0.8175 (tmm) cc_final: 0.7482 (tmm) REVERT: C 137 MET cc_start: 0.6924 (mpp) cc_final: 0.6241 (tpt) REVERT: C 227 PHE cc_start: 0.8034 (t80) cc_final: 0.7631 (t80) REVERT: C 259 PHE cc_start: 0.6442 (t80) cc_final: 0.5696 (t80) REVERT: C 276 TYR cc_start: 0.8159 (t80) cc_final: 0.7859 (t80) REVERT: D 169 TYR cc_start: 0.7943 (m-80) cc_final: 0.7066 (m-80) REVERT: D 178 PHE cc_start: 0.8293 (m-80) cc_final: 0.7957 (m-80) REVERT: D 249 GLN cc_start: 0.7518 (pt0) cc_final: 0.7048 (pm20) outliers start: 4 outliers final: 1 residues processed: 538 average time/residue: 0.1223 time to fit residues: 99.9329 Evaluate side-chains 449 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 447 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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: 5.9990 chunk 157 optimal weight: 0.7980 chunk 168 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 185 optimal weight: 7.9990 chunk 191 optimal weight: 20.0000 chunk 159 optimal weight: 20.0000 chunk 182 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS A 455 ASN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 249 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.120608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.082637 restraints weight = 53925.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.085511 restraints weight = 34931.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.087461 restraints weight = 24920.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.088834 restraints weight = 19344.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.089826 restraints weight = 15946.252| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.6104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 16386 Z= 0.316 Angle : 0.742 10.071 22134 Z= 0.397 Chirality : 0.047 0.208 2360 Planarity : 0.005 0.054 2818 Dihedral : 9.932 121.339 2290 Min Nonbonded Distance : 1.694 Molprobity Statistics. All-atom Clashscore : 19.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.06 % Allowed : 3.79 % Favored : 96.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.18), residues: 1932 helix: 0.76 (0.15), residues: 1112 sheet: -0.58 (0.41), residues: 148 loop : 0.34 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 452 TYR 0.022 0.002 TYR D 169 PHE 0.038 0.003 PHE B 37 TRP 0.032 0.002 TRP B 558 HIS 0.019 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.32 (16386) covalent geometry : angle 0.74250 / 0.40 (22134) hydrogen bonds : bond 0.04706 / 2.94 ( 871) hydrogen bonds : angle 5.30716 / 3.74 ( 2571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 506 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 505 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.9326 (tp30) cc_final: 0.9029 (tp30) REVERT: A 99 LYS cc_start: 0.9174 (mmtp) cc_final: 0.8926 (mmtt) REVERT: A 147 GLN cc_start: 0.9164 (mt0) cc_final: 0.8740 (mt0) REVERT: A 148 GLU cc_start: 0.8373 (mp0) cc_final: 0.7602 (mm-30) REVERT: A 270 ASP cc_start: 0.8684 (m-30) cc_final: 0.7981 (t0) REVERT: A 322 MET cc_start: 0.8181 (mmm) cc_final: 0.7909 (mmm) REVERT: A 345 LYS cc_start: 0.9215 (mttp) cc_final: 0.8946 (mttm) REVERT: A 375 LYS cc_start: 0.9093 (mmtm) cc_final: 0.8681 (mmtm) REVERT: A 386 LEU cc_start: 0.9247 (mt) cc_final: 0.9027 (mt) REVERT: A 402 GLU cc_start: 0.8873 (mp0) cc_final: 0.8627 (mp0) REVERT: A 407 ILE cc_start: 0.8906 (mt) cc_final: 0.8394 (mt) REVERT: A 425 ILE cc_start: 0.9415 (mt) cc_final: 0.8995 (mm) REVERT: A 494 MET cc_start: 0.9546 (mmp) cc_final: 0.8948 (mmm) REVERT: A 498 TYR cc_start: 0.9000 (m-80) cc_final: 0.8557 (m-80) REVERT: A 550 MET cc_start: 0.7664 (mtm) cc_final: 0.6851 (mtm) REVERT: A 598 MET cc_start: 0.8647 (mtm) cc_final: 0.8205 (ttm) REVERT: A 599 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7313 (mm-30) REVERT: A 602 GLU cc_start: 0.9135 (pm20) cc_final: 0.8356 (pm20) REVERT: A 606 TYR cc_start: 0.8446 (m-80) cc_final: 0.8052 (m-80) REVERT: A 615 MET cc_start: 0.8475 (mmp) cc_final: 0.8127 (mmm) REVERT: A 650 GLN cc_start: 0.8004 (mt0) cc_final: 0.7418 (mt0) REVERT: A 659 LYS cc_start: 0.8767 (mttt) cc_final: 0.8431 (mmmt) REVERT: A 687 THR cc_start: 0.8765 (m) cc_final: 0.8436 (t) REVERT: B 8 LYS cc_start: 0.9466 (tttm) cc_final: 0.9186 (tppt) REVERT: B 12 LEU cc_start: 0.9649 (mt) cc_final: 0.9394 (mt) REVERT: B 24 PHE cc_start: 0.8821 (m-80) cc_final: 0.8598 (m-80) REVERT: B 95 MET cc_start: 0.9197 (tpp) cc_final: 0.8224 (tpp) REVERT: B 99 LYS cc_start: 0.9645 (mmmt) cc_final: 0.8939 (mmmt) REVERT: B 235 ARG cc_start: 0.7368 (mmt90) cc_final: 0.7050 (mmt90) REVERT: B 288 PHE cc_start: 0.9458 (t80) cc_final: 0.9065 (t80) REVERT: B 319 MET cc_start: 0.8877 (tpp) cc_final: 0.8535 (tpp) REVERT: B 326 PHE cc_start: 0.9288 (m-80) cc_final: 0.8475 (m-80) REVERT: B 386 LEU cc_start: 0.8903 (mt) cc_final: 0.8295 (mt) REVERT: B 458 MET cc_start: 0.9238 (mmm) cc_final: 0.9013 (mmm) REVERT: B 459 LYS cc_start: 0.8833 (mttt) cc_final: 0.8460 (mtmt) REVERT: B 472 LEU cc_start: 0.9251 (mm) cc_final: 0.8941 (mt) REVERT: B 492 PHE cc_start: 0.9379 (m-80) cc_final: 0.8949 (m-80) REVERT: B 493 MET cc_start: 0.9249 (tmm) cc_final: 0.8832 (tmm) REVERT: B 494 MET cc_start: 0.9333 (mtp) cc_final: 0.8817 (mtp) REVERT: B 506 ILE cc_start: 0.9648 (mm) cc_final: 0.9387 (mm) REVERT: B 615 MET cc_start: 0.8784 (mmp) cc_final: 0.8525 (mmm) REVERT: B 645 GLN cc_start: 0.9041 (tp40) cc_final: 0.8830 (tp-100) REVERT: B 648 ILE cc_start: 0.9059 (mm) cc_final: 0.8835 (mm) REVERT: C 95 MET cc_start: 0.8384 (tmm) cc_final: 0.8045 (tmm) REVERT: C 96 MET cc_start: 0.8465 (mmm) cc_final: 0.8183 (mmm) REVERT: C 98 ASN cc_start: 0.7251 (m110) cc_final: 0.6816 (m110) REVERT: C 149 ASP cc_start: 0.8109 (t0) cc_final: 0.7815 (t0) REVERT: C 151 ILE cc_start: 0.8270 (mm) cc_final: 0.7908 (tp) REVERT: C 259 PHE cc_start: 0.6455 (t80) cc_final: 0.5683 (t80) REVERT: C 276 TYR cc_start: 0.8236 (t80) cc_final: 0.7796 (t80) REVERT: D 178 PHE cc_start: 0.8463 (m-80) cc_final: 0.8087 (m-80) outliers start: 1 outliers final: 0 residues processed: 506 average time/residue: 0.1247 time to fit residues: 94.9641 Evaluate side-chains 396 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 0.9990 chunk 46 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 126 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 122 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 168 optimal weight: 6.9990 chunk 157 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN A 455 ASN B 11 GLN ** B 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN B 496 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.123783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.083580 restraints weight = 51967.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.086715 restraints weight = 31739.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.088887 restraints weight = 22034.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.090403 restraints weight = 16636.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.091559 restraints weight = 13451.960| |-----------------------------------------------------------------------------| r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (11 function evaluations) r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.6328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 16386 Z= 0.210 Angle : 0.648 8.615 22134 Z= 0.346 Chirality : 0.044 0.179 2360 Planarity : 0.004 0.048 2818 Dihedral : 9.547 120.859 2290 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % 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: 0.69 (0.19), residues: 1932 helix: 0.87 (0.15), residues: 1113 sheet: -0.70 (0.39), residues: 154 loop : 0.28 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 161 TYR 0.024 0.002 TYR B 574 PHE 0.023 0.002 PHE A 100 TRP 0.018 0.002 TRP B 558 HIS 0.013 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.21 (16386) covalent geometry : angle 0.64761 / 0.35 (22134) hydrogen bonds : bond 0.04216 / 2.62 ( 871) hydrogen bonds : angle 5.13445 / 3.64 ( 2571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 0.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.9276 (tp30) cc_final: 0.8905 (tp30) REVERT: A 71 LEU cc_start: 0.9380 (mt) cc_final: 0.9076 (mt) REVERT: A 99 LYS cc_start: 0.9165 (mmtp) cc_final: 0.8870 (mmmm) REVERT: A 147 GLN cc_start: 0.9123 (mt0) cc_final: 0.8638 (mt0) REVERT: A 148 GLU cc_start: 0.8290 (mp0) cc_final: 0.7707 (mm-30) REVERT: A 270 ASP cc_start: 0.8687 (m-30) cc_final: 0.7999 (t0) REVERT: A 345 LYS cc_start: 0.9293 (mttp) cc_final: 0.9065 (mttt) REVERT: A 375 LYS cc_start: 0.9089 (mmtm) cc_final: 0.8680 (mmtm) REVERT: A 385 VAL cc_start: 0.8896 (t) cc_final: 0.8607 (m) REVERT: A 386 LEU cc_start: 0.9177 (mt) cc_final: 0.8931 (mt) REVERT: A 402 GLU cc_start: 0.8866 (mp0) cc_final: 0.8599 (mp0) REVERT: A 405 LEU cc_start: 0.8451 (mt) cc_final: 0.8241 (mp) REVERT: A 407 ILE cc_start: 0.9001 (mt) cc_final: 0.8663 (mt) REVERT: A 425 ILE cc_start: 0.9385 (mt) cc_final: 0.8855 (mm) REVERT: A 494 MET cc_start: 0.9509 (mmp) cc_final: 0.8854 (mmm) REVERT: A 498 TYR cc_start: 0.9130 (m-80) cc_final: 0.8739 (m-80) REVERT: A 501 GLN cc_start: 0.9103 (tp-100) cc_final: 0.8732 (tp-100) REVERT: A 546 LEU cc_start: 0.9467 (mt) cc_final: 0.9258 (mt) REVERT: A 550 MET cc_start: 0.7580 (mtm) cc_final: 0.6704 (mtm) REVERT: A 595 MET cc_start: 0.8788 (tpp) cc_final: 0.8572 (mmm) REVERT: A 598 MET cc_start: 0.8564 (mtm) cc_final: 0.8078 (ttm) REVERT: A 602 GLU cc_start: 0.9045 (pm20) cc_final: 0.8408 (pm20) REVERT: A 615 MET cc_start: 0.8487 (mmp) cc_final: 0.8200 (mmp) REVERT: A 650 GLN cc_start: 0.7929 (mt0) cc_final: 0.7456 (mt0) REVERT: A 658 LEU cc_start: 0.9337 (mt) cc_final: 0.9104 (mt) REVERT: A 659 LYS cc_start: 0.8918 (mttt) cc_final: 0.8543 (mmmt) REVERT: A 687 THR cc_start: 0.8835 (m) cc_final: 0.8425 (t) REVERT: B 8 LYS cc_start: 0.9437 (tttm) cc_final: 0.9141 (tppt) REVERT: B 12 LEU cc_start: 0.9653 (mt) cc_final: 0.9359 (mt) REVERT: B 17 MET cc_start: 0.9056 (mmm) cc_final: 0.8546 (mmt) REVERT: B 24 PHE cc_start: 0.9011 (m-80) cc_final: 0.8219 (m-80) REVERT: B 95 MET cc_start: 0.9000 (tpp) cc_final: 0.7703 (tpp) REVERT: B 98 PHE cc_start: 0.9445 (t80) cc_final: 0.8455 (t80) REVERT: B 99 LYS cc_start: 0.9645 (mmmt) cc_final: 0.8825 (mmmt) REVERT: B 184 ARG cc_start: 0.8731 (mmm160) cc_final: 0.7969 (mmm160) REVERT: B 187 ASP cc_start: 0.9057 (t0) cc_final: 0.8583 (t0) REVERT: B 235 ARG cc_start: 0.7522 (mmt90) cc_final: 0.7230 (mmt90) REVERT: B 238 ASP cc_start: 0.7123 (t0) cc_final: 0.6741 (t70) REVERT: B 288 PHE cc_start: 0.9425 (t80) cc_final: 0.9154 (t80) REVERT: B 307 TYR cc_start: 0.9253 (t80) cc_final: 0.8739 (t80) REVERT: B 319 MET cc_start: 0.9010 (tpp) cc_final: 0.8797 (tpp) REVERT: B 326 PHE cc_start: 0.9158 (m-10) cc_final: 0.8437 (m-80) REVERT: B 333 LYS cc_start: 0.8517 (ttpt) cc_final: 0.8066 (ttpt) REVERT: B 350 ARG cc_start: 0.7412 (mtm-85) cc_final: 0.7107 (mtm-85) REVERT: B 379 SER cc_start: 0.8202 (t) cc_final: 0.7990 (t) REVERT: B 446 ARG cc_start: 0.8897 (mpp80) cc_final: 0.8472 (mtm-85) REVERT: B 459 LYS cc_start: 0.8874 (mttt) cc_final: 0.8350 (mtpt) REVERT: B 472 LEU cc_start: 0.9240 (mm) cc_final: 0.8904 (mt) REVERT: B 492 PHE cc_start: 0.9317 (m-80) cc_final: 0.8822 (m-80) REVERT: B 493 MET cc_start: 0.9246 (tmm) cc_final: 0.8860 (tmm) REVERT: B 494 MET cc_start: 0.9331 (mtp) cc_final: 0.8886 (mtp) REVERT: B 615 MET cc_start: 0.8811 (mmp) cc_final: 0.8523 (mmm) REVERT: B 640 MET cc_start: 0.9086 (mmp) cc_final: 0.8885 (mmp) REVERT: B 675 HIS cc_start: 0.8892 (t-90) cc_final: 0.8533 (t-90) REVERT: C 95 MET cc_start: 0.8321 (tmm) cc_final: 0.7835 (tmm) REVERT: C 96 MET cc_start: 0.8460 (mmm) cc_final: 0.8037 (mmm) REVERT: C 137 MET cc_start: 0.7440 (mpp) cc_final: 0.6821 (tpp) REVERT: C 149 ASP cc_start: 0.7997 (t0) cc_final: 0.7700 (t0) REVERT: C 151 ILE cc_start: 0.8246 (mm) cc_final: 0.7885 (tp) REVERT: C 227 PHE cc_start: 0.8035 (t80) cc_final: 0.7767 (t80) REVERT: C 259 PHE cc_start: 0.6521 (t80) cc_final: 0.5781 (t80) REVERT: C 276 TYR cc_start: 0.8284 (t80) cc_final: 0.8008 (t80) REVERT: D 96 MET cc_start: 0.4721 (tpt) cc_final: 0.4509 (tpt) REVERT: D 178 PHE cc_start: 0.8327 (m-80) cc_final: 0.8121 (m-80) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.1212 time to fit residues: 94.6450 Evaluate side-chains 413 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 413 time to evaluate : 0.618 ------------------------------------------------------------------------------- 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: 3.9990 chunk 183 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 172 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 4 optimal weight: 0.2980 chunk 77 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 overall best weight: 0.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 180 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN A 447 ASN A 646 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 545 ASN B 645 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.128825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.090644 restraints weight = 50810.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.093667 restraints weight = 32301.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.095685 restraints weight = 22660.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.096541 restraints weight = 17342.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.097869 restraints weight = 14787.994| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3358 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3358 r_free = 0.3358 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3358 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.6494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16386 Z= 0.126 Angle : 0.587 7.084 22134 Z= 0.313 Chirality : 0.042 0.179 2360 Planarity : 0.003 0.045 2818 Dihedral : 9.020 119.994 2290 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.12 % Allowed : 1.63 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.19), residues: 1932 helix: 1.13 (0.15), residues: 1123 sheet: -0.60 (0.39), residues: 150 loop : 0.42 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 161 TYR 0.017 0.001 TYR B 498 PHE 0.019 0.002 PHE A 261 TRP 0.013 0.001 TRP B 558 HIS 0.009 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.13 (16386) covalent geometry : angle 0.58708 / 0.31 (22134) hydrogen bonds : bond 0.03869 / 2.44 ( 871) hydrogen bonds : angle 4.97792 / 3.54 ( 2571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 524 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8220 (mp0) cc_final: 0.7689 (mp0) REVERT: A 67 GLU cc_start: 0.9233 (tp30) cc_final: 0.8818 (tp30) REVERT: A 71 LEU cc_start: 0.9427 (mt) cc_final: 0.9111 (mt) REVERT: A 158 ASN cc_start: 0.9087 (m110) cc_final: 0.8770 (m110) REVERT: A 259 ASN cc_start: 0.8296 (p0) cc_final: 0.7785 (p0) REVERT: A 270 ASP cc_start: 0.8710 (m-30) cc_final: 0.8030 (t0) REVERT: A 345 LYS cc_start: 0.9274 (mttp) cc_final: 0.9041 (mttt) REVERT: A 361 GLN cc_start: 0.9030 (tp40) cc_final: 0.8734 (tp-100) REVERT: A 375 LYS cc_start: 0.9128 (mmtm) cc_final: 0.8710 (mmtm) REVERT: A 386 LEU cc_start: 0.9066 (mt) cc_final: 0.8866 (mt) REVERT: A 400 GLU cc_start: 0.9398 (mm-30) cc_final: 0.9068 (tp30) REVERT: A 402 GLU cc_start: 0.8836 (mp0) cc_final: 0.8546 (mp0) REVERT: A 407 ILE cc_start: 0.8901 (mt) cc_final: 0.8642 (mt) REVERT: A 458 MET cc_start: 0.9146 (mmp) cc_final: 0.8805 (mmp) REVERT: A 466 MET cc_start: 0.9024 (ptm) cc_final: 0.8518 (ptp) REVERT: A 468 LEU cc_start: 0.9404 (tp) cc_final: 0.9183 (tp) REVERT: A 479 TYR cc_start: 0.8224 (t80) cc_final: 0.7157 (t80) REVERT: A 494 MET cc_start: 0.9534 (mmp) cc_final: 0.8983 (mmm) REVERT: A 498 TYR cc_start: 0.9114 (m-80) cc_final: 0.8866 (m-80) REVERT: A 550 MET cc_start: 0.7549 (mtm) cc_final: 0.6588 (mtm) REVERT: A 598 MET cc_start: 0.8597 (mtm) cc_final: 0.8109 (ttm) REVERT: A 602 GLU cc_start: 0.8962 (pm20) cc_final: 0.8385 (pm20) REVERT: A 611 THR cc_start: 0.8708 (t) cc_final: 0.8444 (t) REVERT: A 650 GLN cc_start: 0.7792 (mt0) cc_final: 0.7590 (mt0) REVERT: A 659 LYS cc_start: 0.8962 (mttt) cc_final: 0.8744 (mmmm) REVERT: A 675 HIS cc_start: 0.9161 (t70) cc_final: 0.8808 (t70) REVERT: B 8 LYS cc_start: 0.9460 (tttm) cc_final: 0.9164 (tppt) REVERT: B 12 LEU cc_start: 0.9643 (mt) cc_final: 0.9349 (mt) REVERT: B 17 MET cc_start: 0.9076 (mmm) cc_final: 0.8541 (mmt) REVERT: B 24 PHE cc_start: 0.8934 (m-80) cc_final: 0.8211 (m-80) REVERT: B 41 ILE cc_start: 0.9428 (mm) cc_final: 0.8985 (mm) REVERT: B 95 MET cc_start: 0.8954 (tpp) cc_final: 0.7663 (tpp) REVERT: B 99 LYS cc_start: 0.9625 (mmmt) cc_final: 0.8791 (mmmt) REVERT: B 115 LEU cc_start: 0.8678 (mp) cc_final: 0.8229 (mp) REVERT: B 122 ILE cc_start: 0.9218 (mt) cc_final: 0.8982 (mt) REVERT: B 200 SER cc_start: 0.7340 (m) cc_final: 0.6918 (p) REVERT: B 235 ARG cc_start: 0.7523 (mmt90) cc_final: 0.7303 (mmt90) REVERT: B 259 ASN cc_start: 0.8673 (m-40) cc_final: 0.8426 (p0) REVERT: B 280 ILE cc_start: 0.8501 (pt) cc_final: 0.8286 (pt) REVERT: B 288 PHE cc_start: 0.9365 (t80) cc_final: 0.9104 (t80) REVERT: B 307 TYR cc_start: 0.9218 (t80) cc_final: 0.8724 (t80) REVERT: B 319 MET cc_start: 0.9108 (tpp) cc_final: 0.8728 (tpp) REVERT: B 322 MET cc_start: 0.8885 (tpt) cc_final: 0.8483 (mmm) REVERT: B 326 PHE cc_start: 0.9124 (m-10) cc_final: 0.8341 (m-80) REVERT: B 333 LYS cc_start: 0.8512 (ttpt) cc_final: 0.8136 (ttpt) REVERT: B 359 MET cc_start: 0.7525 (tmm) cc_final: 0.7275 (tmm) REVERT: B 375 LYS cc_start: 0.9071 (mmtm) cc_final: 0.8853 (mmtm) REVERT: B 379 SER cc_start: 0.8119 (t) cc_final: 0.7736 (t) REVERT: B 403 ILE cc_start: 0.8954 (mp) cc_final: 0.8561 (tp) REVERT: B 446 ARG cc_start: 0.9019 (mpp80) cc_final: 0.8630 (mtm-85) REVERT: B 466 MET cc_start: 0.8784 (ptp) cc_final: 0.8259 (ptp) REVERT: B 472 LEU cc_start: 0.9285 (mm) cc_final: 0.8915 (mt) REVERT: B 492 PHE cc_start: 0.9290 (m-80) cc_final: 0.8678 (m-80) REVERT: B 493 MET cc_start: 0.9218 (tmm) cc_final: 0.8461 (tmm) REVERT: B 494 MET cc_start: 0.9418 (mtp) cc_final: 0.8946 (mtp) REVERT: B 506 ILE cc_start: 0.9629 (mm) cc_final: 0.9426 (mm) REVERT: B 558 TRP cc_start: 0.8433 (m100) cc_final: 0.7760 (m100) REVERT: B 584 ILE cc_start: 0.8867 (mt) cc_final: 0.8608 (mt) REVERT: B 627 LYS cc_start: 0.8777 (ttpp) cc_final: 0.8442 (ptmm) REVERT: B 645 GLN cc_start: 0.9252 (tp40) cc_final: 0.9028 (tp-100) REVERT: B 675 HIS cc_start: 0.8857 (t-90) cc_final: 0.8537 (t-90) REVERT: C 95 MET cc_start: 0.7890 (tmm) cc_final: 0.7164 (tmm) REVERT: C 137 MET cc_start: 0.7397 (mpp) cc_final: 0.6892 (tpt) REVERT: C 149 ASP cc_start: 0.7995 (t0) cc_final: 0.7726 (t0) REVERT: C 151 ILE cc_start: 0.8320 (mm) cc_final: 0.7958 (tp) REVERT: C 259 PHE cc_start: 0.6468 (t80) cc_final: 0.5710 (t80) REVERT: C 276 TYR cc_start: 0.8358 (t80) cc_final: 0.7903 (t80) REVERT: D 96 MET cc_start: 0.4517 (tpt) cc_final: 0.4098 (tpp) REVERT: D 157 MET cc_start: 0.6758 (tmm) cc_final: 0.6415 (tmm) REVERT: D 169 TYR cc_start: 0.8214 (m-80) cc_final: 0.7423 (m-80) REVERT: D 201 HIS cc_start: 0.7916 (m90) cc_final: 0.7598 (m90) outliers start: 2 outliers final: 1 residues processed: 526 average time/residue: 0.1165 time to fit residues: 92.4665 Evaluate side-chains 416 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 415 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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: 5.9990 chunk 51 optimal weight: 4.9990 chunk 74 optimal weight: 0.6980 chunk 105 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 186 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 115 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN A 455 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.124719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.085590 restraints weight = 50083.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.088721 restraints weight = 31249.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.090646 restraints weight = 22289.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.092172 restraints weight = 16830.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.093283 restraints weight = 13540.523| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.6737 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= 0.156 Angle : 0.609 7.254 22134 Z= 0.325 Chirality : 0.043 0.166 2360 Planarity : 0.004 0.040 2818 Dihedral : 8.895 120.929 2290 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.06 % Allowed : 1.52 % Favored : 98.43 % 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: 0.96 (0.19), residues: 1932 helix: 1.13 (0.15), residues: 1111 sheet: -0.72 (0.38), residues: 156 loop : 0.36 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 161 TYR 0.024 0.002 TYR A 118 PHE 0.047 0.002 PHE D 178 TRP 0.015 0.002 TRP B 558 HIS 0.015 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.16 (16386) covalent geometry : angle 0.60887 / 0.33 (22134) hydrogen bonds : bond 0.03938 / 2.50 ( 871) hydrogen bonds : angle 5.08972 / 3.64 ( 2571) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 485 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.9246 (tp30) cc_final: 0.8949 (tp30) REVERT: A 99 LYS cc_start: 0.9507 (mmtt) cc_final: 0.9045 (mttt) REVERT: A 147 GLN cc_start: 0.8962 (mt0) cc_final: 0.8515 (mt0) REVERT: A 259 ASN cc_start: 0.8257 (p0) cc_final: 0.7713 (p0) REVERT: A 270 ASP cc_start: 0.8672 (m-30) cc_final: 0.7971 (t0) REVERT: A 322 MET cc_start: 0.8214 (mmm) cc_final: 0.7908 (mmm) REVERT: A 345 LYS cc_start: 0.9273 (mttp) cc_final: 0.9020 (mttm) REVERT: A 361 GLN cc_start: 0.9065 (tp40) cc_final: 0.8786 (tp-100) REVERT: A 375 LYS cc_start: 0.9112 (mmtm) cc_final: 0.8664 (mmtm) REVERT: A 402 GLU cc_start: 0.8862 (mp0) cc_final: 0.8581 (mp0) REVERT: A 407 ILE cc_start: 0.8957 (mt) cc_final: 0.8645 (mt) REVERT: A 425 ILE cc_start: 0.9383 (mm) cc_final: 0.8750 (mm) REVERT: A 458 MET cc_start: 0.9143 (mmp) cc_final: 0.8798 (mmp) REVERT: A 468 LEU cc_start: 0.9491 (tp) cc_final: 0.9285 (tp) REVERT: A 479 TYR cc_start: 0.8364 (t80) cc_final: 0.7848 (t80) REVERT: A 494 MET cc_start: 0.9520 (mmp) cc_final: 0.8954 (mmm) REVERT: A 498 TYR cc_start: 0.9188 (m-80) cc_final: 0.8927 (m-80) REVERT: A 550 MET cc_start: 0.7567 (mtm) cc_final: 0.6873 (mtm) REVERT: A 598 MET cc_start: 0.8596 (mtm) cc_final: 0.8191 (ttm) REVERT: A 602 GLU cc_start: 0.8866 (pm20) cc_final: 0.8662 (pm20) REVERT: A 611 THR cc_start: 0.8865 (t) cc_final: 0.7976 (t) REVERT: A 615 MET cc_start: 0.8512 (mmp) cc_final: 0.8112 (mmm) REVERT: A 650 GLN cc_start: 0.7950 (mt0) cc_final: 0.7391 (mt0) REVERT: A 659 LYS cc_start: 0.8838 (mttt) cc_final: 0.8630 (mmmm) REVERT: B 8 LYS cc_start: 0.9464 (tttm) cc_final: 0.9153 (tppt) REVERT: B 12 LEU cc_start: 0.9675 (mt) cc_final: 0.9384 (mt) REVERT: B 17 MET cc_start: 0.9049 (mmm) cc_final: 0.8767 (mmp) REVERT: B 24 PHE cc_start: 0.8945 (m-80) cc_final: 0.8433 (m-80) REVERT: B 95 MET cc_start: 0.9013 (tpp) cc_final: 0.7756 (tpp) REVERT: B 98 PHE cc_start: 0.9428 (t80) cc_final: 0.8638 (t80) REVERT: B 99 LYS cc_start: 0.9649 (mmmt) cc_final: 0.8776 (mmmt) REVERT: B 122 ILE cc_start: 0.9138 (mt) cc_final: 0.8863 (mt) REVERT: B 235 ARG cc_start: 0.7631 (mmt90) cc_final: 0.7345 (mmt90) REVERT: B 256 ARG cc_start: 0.8360 (tmt-80) cc_final: 0.8100 (ttp80) REVERT: B 288 PHE cc_start: 0.9361 (t80) cc_final: 0.9118 (t80) REVERT: B 307 TYR cc_start: 0.9232 (t80) cc_final: 0.8727 (t80) REVERT: B 319 MET cc_start: 0.9039 (tpp) cc_final: 0.8747 (tpp) REVERT: B 322 MET cc_start: 0.8980 (tpt) cc_final: 0.8685 (mmm) REVERT: B 326 PHE cc_start: 0.9181 (m-10) cc_final: 0.8506 (m-80) REVERT: B 333 LYS cc_start: 0.8494 (ttpt) cc_final: 0.8159 (ttpt) REVERT: B 358 ILE cc_start: 0.8604 (mm) cc_final: 0.8396 (mm) REVERT: B 375 LYS cc_start: 0.9061 (mmtm) cc_final: 0.8832 (mmtm) REVERT: B 379 SER cc_start: 0.8181 (t) cc_final: 0.7780 (t) REVERT: B 403 ILE cc_start: 0.9004 (mp) cc_final: 0.8639 (tp) REVERT: B 407 ILE cc_start: 0.8410 (mt) cc_final: 0.8198 (mt) REVERT: B 444 ASP cc_start: 0.8837 (t70) cc_final: 0.8627 (t70) REVERT: B 458 MET cc_start: 0.9249 (mmm) cc_final: 0.9029 (mmm) REVERT: B 459 LYS cc_start: 0.8953 (mtmt) cc_final: 0.8614 (mtpt) REVERT: B 466 MET cc_start: 0.8747 (ptp) cc_final: 0.8232 (ptp) REVERT: B 472 LEU cc_start: 0.9263 (mm) cc_final: 0.9027 (mm) REVERT: B 492 PHE cc_start: 0.9351 (m-80) cc_final: 0.8747 (m-80) REVERT: B 493 MET cc_start: 0.9221 (tmm) cc_final: 0.8865 (tmm) REVERT: B 494 MET cc_start: 0.9422 (mtp) cc_final: 0.8919 (mtp) REVERT: B 529 ASP cc_start: 0.8980 (p0) cc_final: 0.8724 (m-30) REVERT: B 640 MET cc_start: 0.9282 (mmp) cc_final: 0.9002 (mmp) REVERT: B 675 HIS cc_start: 0.8913 (t-90) cc_final: 0.8618 (t-90) REVERT: C 95 MET cc_start: 0.8004 (tmm) cc_final: 0.7401 (tmm) REVERT: C 96 MET cc_start: 0.8399 (mmm) cc_final: 0.7960 (mmm) REVERT: C 137 MET cc_start: 0.7620 (mpp) cc_final: 0.6992 (tpt) REVERT: C 149 ASP cc_start: 0.7905 (t0) cc_final: 0.7658 (t0) REVERT: C 151 ILE cc_start: 0.8372 (mm) cc_final: 0.8004 (tp) REVERT: C 259 PHE cc_start: 0.6547 (t80) cc_final: 0.5785 (t80) REVERT: C 276 TYR cc_start: 0.8351 (t80) cc_final: 0.8051 (t80) REVERT: D 74 MET cc_start: 0.7278 (ttp) cc_final: 0.7033 (ptm) REVERT: D 96 MET cc_start: 0.4934 (tpt) cc_final: 0.4339 (tpp) REVERT: D 157 MET cc_start: 0.6627 (tmm) cc_final: 0.6359 (tmm) REVERT: D 169 TYR cc_start: 0.8310 (m-80) cc_final: 0.7593 (m-80) REVERT: D 179 TYR cc_start: 0.8308 (t80) cc_final: 0.8094 (t80) REVERT: D 201 HIS cc_start: 0.7890 (m90) cc_final: 0.7679 (m90) outliers start: 1 outliers final: 0 residues processed: 486 average time/residue: 0.1228 time to fit residues: 90.2409 Evaluate side-chains 397 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 0.690 ------------------------------------------------------------------------------- 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: 0.9990 chunk 99 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 19 optimal weight: 8.9990 chunk 134 optimal weight: 8.9990 chunk 153 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 158 optimal weight: 8.9990 chunk 97 optimal weight: 0.9980 chunk 151 optimal weight: 20.0000 chunk 81 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 GLN B 645 GLN C 238 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.127586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.087342 restraints weight = 50369.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.090570 restraints weight = 31369.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.092666 restraints weight = 22575.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.093666 restraints weight = 16893.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.095207 restraints weight = 14094.085| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3371 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3371 r_free = 0.3371 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3371 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.6910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16386 Z= 0.129 Angle : 0.599 9.299 22134 Z= 0.319 Chirality : 0.042 0.182 2360 Planarity : 0.004 0.051 2818 Dihedral : 8.638 120.772 2290 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % 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: 0.97 (0.19), residues: 1932 helix: 1.08 (0.15), residues: 1123 sheet: -0.37 (0.41), residues: 138 loop : 0.32 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 161 TYR 0.027 0.001 TYR A 571 PHE 0.030 0.002 PHE D 178 TRP 0.012 0.001 TRP B 558 HIS 0.013 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (16386) covalent geometry : angle 0.59925 / 0.32 (22134) hydrogen bonds : bond 0.03921 / 2.50 ( 871) hydrogen bonds : angle 5.06764 / 3.62 ( 2571) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.9235 (tp30) cc_final: 0.8866 (tp30) REVERT: A 71 LEU cc_start: 0.9404 (mt) cc_final: 0.9106 (mt) REVERT: A 99 LYS cc_start: 0.9491 (mmtt) cc_final: 0.9102 (mttt) REVERT: A 158 ASN cc_start: 0.9064 (m110) cc_final: 0.8739 (m110) REVERT: A 169 SER cc_start: 0.8120 (p) cc_final: 0.7806 (t) REVERT: A 187 ASP cc_start: 0.9221 (t70) cc_final: 0.8908 (t70) REVERT: A 202 ASN cc_start: 0.8675 (t0) cc_final: 0.8244 (t0) REVERT: A 236 TYR cc_start: 0.7255 (t80) cc_final: 0.7016 (t80) REVERT: A 259 ASN cc_start: 0.8218 (p0) cc_final: 0.7672 (p0) REVERT: A 270 ASP cc_start: 0.8695 (m-30) cc_final: 0.8205 (t0) REVERT: A 322 MET cc_start: 0.8329 (mmm) cc_final: 0.8080 (mmm) REVERT: A 345 LYS cc_start: 0.9277 (mttp) cc_final: 0.9035 (mttm) REVERT: A 361 GLN cc_start: 0.9086 (tp40) cc_final: 0.8811 (tp-100) REVERT: A 375 LYS cc_start: 0.9108 (mmtm) cc_final: 0.8680 (mmtm) REVERT: A 400 GLU cc_start: 0.9364 (mm-30) cc_final: 0.9077 (tp30) REVERT: A 402 GLU cc_start: 0.8820 (mp0) cc_final: 0.8553 (mp0) REVERT: A 407 ILE cc_start: 0.8983 (mt) cc_final: 0.8678 (mt) REVERT: A 455 ASN cc_start: 0.8934 (t0) cc_final: 0.8715 (t0) REVERT: A 468 LEU cc_start: 0.9495 (tp) cc_final: 0.9185 (tp) REVERT: A 479 TYR cc_start: 0.8202 (t80) cc_final: 0.7267 (t80) REVERT: A 494 MET cc_start: 0.9491 (mmp) cc_final: 0.9042 (mmm) REVERT: A 498 TYR cc_start: 0.9159 (m-80) cc_final: 0.8923 (m-80) REVERT: A 550 MET cc_start: 0.7829 (mtm) cc_final: 0.6965 (mtm) REVERT: A 571 TYR cc_start: 0.8842 (t80) cc_final: 0.8492 (t80) REVERT: A 595 MET cc_start: 0.8548 (tpp) cc_final: 0.8335 (mmm) REVERT: A 611 THR cc_start: 0.8785 (t) cc_final: 0.8138 (t) REVERT: A 650 GLN cc_start: 0.7976 (mt0) cc_final: 0.7375 (mm-40) REVERT: B 8 LYS cc_start: 0.9490 (tttm) cc_final: 0.9201 (tppt) REVERT: B 12 LEU cc_start: 0.9676 (mt) cc_final: 0.9392 (mt) REVERT: B 17 MET cc_start: 0.9090 (mmm) cc_final: 0.8788 (mmp) REVERT: B 24 PHE cc_start: 0.8980 (m-80) cc_final: 0.8511 (m-80) REVERT: B 95 MET cc_start: 0.8973 (tpp) cc_final: 0.7673 (tpp) REVERT: B 99 LYS cc_start: 0.9663 (mmmt) cc_final: 0.8803 (mmmt) REVERT: B 122 ILE cc_start: 0.9210 (mt) cc_final: 0.9007 (mt) REVERT: B 256 ARG cc_start: 0.8277 (tmt-80) cc_final: 0.7590 (ttp80) REVERT: B 259 ASN cc_start: 0.8681 (m-40) cc_final: 0.8447 (p0) REVERT: B 288 PHE cc_start: 0.9345 (t80) cc_final: 0.9095 (t80) REVERT: B 307 TYR cc_start: 0.9209 (t80) cc_final: 0.8650 (t80) REVERT: B 319 MET cc_start: 0.9066 (tpp) cc_final: 0.8770 (tpp) REVERT: B 322 MET cc_start: 0.9017 (tpt) cc_final: 0.8765 (mmm) REVERT: B 326 PHE cc_start: 0.9184 (m-10) cc_final: 0.8433 (m-80) REVERT: B 333 LYS cc_start: 0.8525 (ttpt) cc_final: 0.8163 (ttpt) REVERT: B 375 LYS cc_start: 0.9031 (mmtm) cc_final: 0.8814 (mmtm) REVERT: B 384 GLU cc_start: 0.6605 (pm20) cc_final: 0.6328 (pm20) REVERT: B 403 ILE cc_start: 0.9016 (mp) cc_final: 0.8671 (tp) REVERT: B 444 ASP cc_start: 0.8862 (t70) cc_final: 0.8641 (t70) REVERT: B 458 MET cc_start: 0.9297 (mmm) cc_final: 0.8942 (mmm) REVERT: B 459 LYS cc_start: 0.8918 (mtmt) cc_final: 0.8541 (mtpt) REVERT: B 466 MET cc_start: 0.8732 (ptp) cc_final: 0.8103 (ptp) REVERT: B 472 LEU cc_start: 0.9299 (mm) cc_final: 0.8961 (mt) REVERT: B 492 PHE cc_start: 0.9277 (m-80) cc_final: 0.8757 (m-80) REVERT: B 493 MET cc_start: 0.9196 (tmm) cc_final: 0.8842 (tmm) REVERT: B 494 MET cc_start: 0.9452 (mtp) cc_final: 0.8884 (mtp) REVERT: B 584 ILE cc_start: 0.8920 (mt) cc_final: 0.8358 (mt) REVERT: B 640 MET cc_start: 0.9274 (mmp) cc_final: 0.8970 (mmp) REVERT: B 675 HIS cc_start: 0.8887 (t-90) cc_final: 0.8515 (t-90) REVERT: C 95 MET cc_start: 0.7740 (tmm) cc_final: 0.7022 (tmm) REVERT: C 96 MET cc_start: 0.8403 (mmm) cc_final: 0.8116 (mmm) REVERT: C 137 MET cc_start: 0.7658 (mpp) cc_final: 0.6906 (tpp) REVERT: C 151 ILE cc_start: 0.8351 (mm) cc_final: 0.7978 (tp) REVERT: C 227 PHE cc_start: 0.8619 (t80) cc_final: 0.8385 (t80) REVERT: C 259 PHE cc_start: 0.6525 (t80) cc_final: 0.5757 (t80) REVERT: C 276 TYR cc_start: 0.8364 (t80) cc_final: 0.8059 (t80) REVERT: D 74 MET cc_start: 0.7053 (ttp) cc_final: 0.6610 (ttp) REVERT: D 96 MET cc_start: 0.4632 (tpt) cc_final: 0.4173 (tpp) REVERT: D 157 MET cc_start: 0.6569 (tmm) cc_final: 0.6335 (tmm) REVERT: D 169 TYR cc_start: 0.8468 (m-80) cc_final: 0.7816 (m-80) outliers start: 0 outliers final: 0 residues processed: 504 average time/residue: 0.1191 time to fit residues: 91.4132 Evaluate side-chains 381 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 381 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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: 6.9990 chunk 133 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 114 optimal weight: 6.9990 chunk 86 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 100 optimal weight: 0.1980 chunk 88 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN D 69 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.128375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.089503 restraints weight = 49755.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.092551 restraints weight = 31267.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.094428 restraints weight = 22606.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.095961 restraints weight = 17154.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.097002 restraints weight = 13889.627| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3461 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.7121 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= 0.131 Angle : 0.624 9.161 22134 Z= 0.333 Chirality : 0.044 0.352 2360 Planarity : 0.004 0.051 2818 Dihedral : 8.549 120.910 2290 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.06 % Allowed : 0.41 % Favored : 99.53 % 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: 0.99 (0.15), residues: 1136 sheet: -0.15 (0.44), residues: 138 loop : 0.20 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 161 TYR 0.035 0.002 TYR B 498 PHE 0.028 0.002 PHE D 259 TRP 0.011 0.001 TRP B 558 HIS 0.013 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (16386) covalent geometry : angle 0.62362 / 0.33 (22134) hydrogen bonds : bond 0.03962 / 2.53 ( 871) hydrogen bonds : angle 5.13657 / 3.66 ( 2571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 491 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8271 (mp0) cc_final: 0.6492 (mp0) REVERT: A 67 GLU cc_start: 0.9232 (tp30) cc_final: 0.8934 (tp30) REVERT: A 80 VAL cc_start: 0.9617 (t) cc_final: 0.9178 (t) REVERT: A 139 GLU cc_start: 0.9286 (mp0) cc_final: 0.9063 (pm20) REVERT: A 147 GLN cc_start: 0.8765 (mm-40) cc_final: 0.8518 (tp40) REVERT: A 158 ASN cc_start: 0.8965 (m110) cc_final: 0.8670 (m110) REVERT: A 169 SER cc_start: 0.8191 (p) cc_final: 0.7955 (t) REVERT: A 187 ASP cc_start: 0.9238 (t70) cc_final: 0.8938 (t70) REVERT: A 202 ASN cc_start: 0.8608 (t0) cc_final: 0.8102 (t0) REVERT: A 236 TYR cc_start: 0.7144 (t80) cc_final: 0.6936 (t80) REVERT: A 259 ASN cc_start: 0.8186 (p0) cc_final: 0.7704 (p0) REVERT: A 270 ASP cc_start: 0.8801 (m-30) cc_final: 0.8188 (p0) REVERT: A 322 MET cc_start: 0.8343 (mmm) cc_final: 0.8101 (mmm) REVERT: A 345 LYS cc_start: 0.9296 (mttp) cc_final: 0.9039 (mttm) REVERT: A 375 LYS cc_start: 0.9124 (mmtm) cc_final: 0.8701 (mmtm) REVERT: A 400 GLU cc_start: 0.9413 (mm-30) cc_final: 0.9070 (tp30) REVERT: A 402 GLU cc_start: 0.8803 (mp0) cc_final: 0.8533 (mp0) REVERT: A 407 ILE cc_start: 0.8974 (mt) cc_final: 0.8647 (mt) REVERT: A 427 LYS cc_start: 0.9347 (mmpt) cc_final: 0.8893 (mmpt) REVERT: A 479 TYR cc_start: 0.8477 (t80) cc_final: 0.7998 (t80) REVERT: A 483 GLU cc_start: 0.9350 (mp0) cc_final: 0.8913 (mp0) REVERT: A 494 MET cc_start: 0.9489 (mmp) cc_final: 0.8923 (mmm) REVERT: A 498 TYR cc_start: 0.9120 (m-80) cc_final: 0.8887 (m-80) REVERT: A 611 THR cc_start: 0.8889 (t) cc_final: 0.8434 (t) REVERT: A 650 GLN cc_start: 0.7948 (mt0) cc_final: 0.7355 (mm-40) REVERT: A 679 ILE cc_start: 0.9358 (mm) cc_final: 0.9123 (mm) REVERT: B 8 LYS cc_start: 0.9487 (tttm) cc_final: 0.9194 (tppt) REVERT: B 12 LEU cc_start: 0.9691 (mt) cc_final: 0.9396 (mt) REVERT: B 24 PHE cc_start: 0.8916 (m-80) cc_final: 0.8500 (m-80) REVERT: B 95 MET cc_start: 0.8987 (tpp) cc_final: 0.7620 (tpp) REVERT: B 99 LYS cc_start: 0.9675 (mmmt) cc_final: 0.8879 (mmmt) REVERT: B 122 ILE cc_start: 0.9104 (mt) cc_final: 0.8879 (mt) REVERT: B 256 ARG cc_start: 0.8261 (tmt-80) cc_final: 0.8033 (ttp80) REVERT: B 259 ASN cc_start: 0.8703 (m-40) cc_final: 0.8456 (p0) REVERT: B 307 TYR cc_start: 0.9181 (t80) cc_final: 0.8605 (t80) REVERT: B 319 MET cc_start: 0.9152 (tpp) cc_final: 0.8907 (tpp) REVERT: B 326 PHE cc_start: 0.9210 (m-10) cc_final: 0.8573 (m-80) REVERT: B 333 LYS cc_start: 0.8546 (ttpt) cc_final: 0.8184 (ttpt) REVERT: B 359 MET cc_start: 0.7609 (tmm) cc_final: 0.7067 (tmm) REVERT: B 361 GLN cc_start: 0.8795 (tt0) cc_final: 0.8265 (tt0) REVERT: B 403 ILE cc_start: 0.8998 (mp) cc_final: 0.8605 (tp) REVERT: B 441 GLU cc_start: 0.9251 (pt0) cc_final: 0.8837 (pt0) REVERT: B 458 MET cc_start: 0.9289 (mmm) cc_final: 0.8950 (mmm) REVERT: B 459 LYS cc_start: 0.8856 (mtmt) cc_final: 0.8498 (mtpt) REVERT: B 466 MET cc_start: 0.8757 (ptp) cc_final: 0.8131 (ptp) REVERT: B 472 LEU cc_start: 0.9340 (mm) cc_final: 0.9045 (mt) REVERT: B 492 PHE cc_start: 0.9290 (m-80) cc_final: 0.8825 (m-80) REVERT: B 493 MET cc_start: 0.9240 (tmm) cc_final: 0.8930 (tmm) REVERT: B 494 MET cc_start: 0.9355 (mtp) cc_final: 0.8786 (tpp) REVERT: B 640 MET cc_start: 0.9311 (mmp) cc_final: 0.8940 (mmp) REVERT: B 675 HIS cc_start: 0.8932 (t-90) cc_final: 0.8653 (t-90) REVERT: C 95 MET cc_start: 0.7757 (tmm) cc_final: 0.7026 (tmm) REVERT: C 96 MET cc_start: 0.8359 (mmm) cc_final: 0.7981 (mmm) REVERT: C 137 MET cc_start: 0.7624 (mpp) cc_final: 0.6820 (tpp) REVERT: C 149 ASP cc_start: 0.7881 (t0) cc_final: 0.7554 (t0) REVERT: C 151 ILE cc_start: 0.8241 (mm) cc_final: 0.7888 (tp) REVERT: C 259 PHE cc_start: 0.6520 (t80) cc_final: 0.5744 (t80) REVERT: C 276 TYR cc_start: 0.8378 (t80) cc_final: 0.8085 (t80) REVERT: D 74 MET cc_start: 0.7138 (ttp) cc_final: 0.6296 (ttp) REVERT: D 96 MET cc_start: 0.4496 (tpt) cc_final: 0.4003 (tpp) REVERT: D 157 MET cc_start: 0.6341 (tmm) cc_final: 0.6074 (tmm) REVERT: D 169 TYR cc_start: 0.8499 (m-80) cc_final: 0.7863 (m-80) outliers start: 1 outliers final: 0 residues processed: 492 average time/residue: 0.1239 time to fit residues: 92.9019 Evaluate side-chains 393 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 393 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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: 0.9980 chunk 62 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 189 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 54 optimal weight: 0.0370 chunk 132 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN A 158 ASN ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 GLN B 608 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.130246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.090839 restraints weight = 50620.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.093977 restraints weight = 31857.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.096013 restraints weight = 22707.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.097586 restraints weight = 16981.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.098674 restraints weight = 13642.034| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (16 function evaluations) r_final: 0.3479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 moved from start: 0.7302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16386 Z= 0.131 Angle : 0.632 8.991 22134 Z= 0.335 Chirality : 0.043 0.252 2360 Planarity : 0.004 0.077 2818 Dihedral : 8.511 121.655 2290 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.06 % Allowed : 0.23 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.19), residues: 1932 helix: 0.95 (0.15), residues: 1136 sheet: -0.24 (0.43), residues: 148 loop : 0.19 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 196 TYR 0.023 0.002 TYR B 498 PHE 0.024 0.002 PHE D 259 TRP 0.012 0.001 TRP B 623 HIS 0.013 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (16386) covalent geometry : angle 0.63225 / 0.34 (22134) hydrogen bonds : bond 0.03922 / 2.51 ( 871) hydrogen bonds : angle 5.13118 / 3.65 ( 2571) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 489 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8059 (mp0) cc_final: 0.7737 (mp0) REVERT: A 67 GLU cc_start: 0.9241 (tp30) cc_final: 0.8902 (tp30) REVERT: A 139 GLU cc_start: 0.9261 (mp0) cc_final: 0.9018 (mp0) REVERT: A 147 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8278 (mm-40) REVERT: A 169 SER cc_start: 0.8238 (p) cc_final: 0.8023 (t) REVERT: A 187 ASP cc_start: 0.9342 (t70) cc_final: 0.9095 (t70) REVERT: A 202 ASN cc_start: 0.8657 (t0) cc_final: 0.8156 (t0) REVERT: A 236 TYR cc_start: 0.7065 (t80) cc_final: 0.6839 (t80) REVERT: A 259 ASN cc_start: 0.8150 (p0) cc_final: 0.7507 (p0) REVERT: A 270 ASP cc_start: 0.8848 (m-30) cc_final: 0.8172 (p0) REVERT: A 322 MET cc_start: 0.8326 (mmm) cc_final: 0.8084 (mmm) REVERT: A 345 LYS cc_start: 0.9302 (mttp) cc_final: 0.9053 (mttm) REVERT: A 361 GLN cc_start: 0.9011 (tp-100) cc_final: 0.8789 (tp-100) REVERT: A 375 LYS cc_start: 0.9111 (mmtm) cc_final: 0.8726 (mmtm) REVERT: A 400 GLU cc_start: 0.9380 (mm-30) cc_final: 0.9038 (tp30) REVERT: A 402 GLU cc_start: 0.8772 (mp0) cc_final: 0.8509 (mp0) REVERT: A 418 ASN cc_start: 0.9462 (m-40) cc_final: 0.9210 (m-40) REVERT: A 479 TYR cc_start: 0.7903 (t80) cc_final: 0.7319 (t80) REVERT: A 483 GLU cc_start: 0.9331 (mp0) cc_final: 0.9104 (mp0) REVERT: A 490 THR cc_start: 0.9404 (m) cc_final: 0.8556 (p) REVERT: A 494 MET cc_start: 0.9483 (mmp) cc_final: 0.8962 (mmm) REVERT: A 498 TYR cc_start: 0.9110 (m-80) cc_final: 0.8885 (m-80) REVERT: A 611 THR cc_start: 0.8976 (t) cc_final: 0.8441 (t) REVERT: A 650 GLN cc_start: 0.8009 (mt0) cc_final: 0.7382 (mm-40) REVERT: A 679 ILE cc_start: 0.9344 (mm) cc_final: 0.9088 (mm) REVERT: B 8 LYS cc_start: 0.9509 (tttm) cc_final: 0.9208 (tppt) REVERT: B 12 LEU cc_start: 0.9700 (mt) cc_final: 0.9409 (mt) REVERT: B 17 MET cc_start: 0.9141 (mmm) cc_final: 0.8461 (mmt) REVERT: B 24 PHE cc_start: 0.8915 (m-80) cc_final: 0.8237 (m-80) REVERT: B 41 ILE cc_start: 0.9443 (mm) cc_final: 0.9242 (mm) REVERT: B 95 MET cc_start: 0.8903 (tpp) cc_final: 0.7581 (tpp) REVERT: B 99 LYS cc_start: 0.9681 (mmmt) cc_final: 0.8851 (mmmt) REVERT: B 256 ARG cc_start: 0.8276 (tmt-80) cc_final: 0.8069 (ttp80) REVERT: B 259 ASN cc_start: 0.8696 (m-40) cc_final: 0.8463 (p0) REVERT: B 307 TYR cc_start: 0.9154 (t80) cc_final: 0.8584 (t80) REVERT: B 319 MET cc_start: 0.9202 (tpp) cc_final: 0.8987 (tpp) REVERT: B 326 PHE cc_start: 0.9160 (m-10) cc_final: 0.8743 (m-80) REVERT: B 333 LYS cc_start: 0.8578 (ttpt) cc_final: 0.8208 (ttpt) REVERT: B 359 MET cc_start: 0.7740 (tmm) cc_final: 0.7344 (tmm) REVERT: B 361 GLN cc_start: 0.8714 (tt0) cc_final: 0.8495 (tt0) REVERT: B 403 ILE cc_start: 0.9031 (mp) cc_final: 0.8640 (tp) REVERT: B 441 GLU cc_start: 0.9239 (pt0) cc_final: 0.8807 (pt0) REVERT: B 446 ARG cc_start: 0.8946 (mpp80) cc_final: 0.8563 (mtm-85) REVERT: B 447 ASN cc_start: 0.8705 (m-40) cc_final: 0.8468 (t0) REVERT: B 458 MET cc_start: 0.9259 (mmm) cc_final: 0.8959 (mmm) REVERT: B 459 LYS cc_start: 0.8878 (mtmt) cc_final: 0.8525 (mtpt) REVERT: B 472 LEU cc_start: 0.9333 (mm) cc_final: 0.9050 (mt) REVERT: B 493 MET cc_start: 0.9241 (tmm) cc_final: 0.8937 (tmm) REVERT: B 494 MET cc_start: 0.9397 (mtp) cc_final: 0.8790 (tpp) REVERT: B 613 TYR cc_start: 0.8345 (t80) cc_final: 0.8056 (t80) REVERT: B 640 MET cc_start: 0.9300 (mmp) cc_final: 0.8886 (mmp) REVERT: B 675 HIS cc_start: 0.8848 (t-90) cc_final: 0.8578 (t-90) REVERT: C 95 MET cc_start: 0.7698 (tmm) cc_final: 0.6961 (tmm) REVERT: C 96 MET cc_start: 0.8288 (mmm) cc_final: 0.7921 (mmm) REVERT: C 137 MET cc_start: 0.7732 (mpp) cc_final: 0.6925 (tpp) REVERT: C 151 ILE cc_start: 0.8268 (mm) cc_final: 0.7972 (tp) REVERT: C 227 PHE cc_start: 0.8632 (t80) cc_final: 0.8426 (t80) REVERT: C 259 PHE cc_start: 0.6544 (t80) cc_final: 0.5788 (t80) REVERT: C 276 TYR cc_start: 0.8383 (t80) cc_final: 0.8090 (t80) REVERT: D 74 MET cc_start: 0.7013 (ttp) cc_final: 0.6385 (ttp) REVERT: D 96 MET cc_start: 0.4329 (tpt) cc_final: 0.3777 (tpp) REVERT: D 157 MET cc_start: 0.6293 (tmm) cc_final: 0.6045 (tmm) REVERT: D 169 TYR cc_start: 0.8565 (m-80) cc_final: 0.7960 (m-80) outliers start: 1 outliers final: 0 residues processed: 490 average time/residue: 0.1297 time to fit residues: 95.9682 Evaluate side-chains 375 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 375 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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: 2.9990 chunk 1 optimal weight: 0.6980 chunk 48 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 25 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 28 optimal weight: 0.2980 chunk 34 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 572 HIS ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.129690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.091251 restraints weight = 50144.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.094198 restraints weight = 31568.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.096189 restraints weight = 22243.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.097622 restraints weight = 17277.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.098643 restraints weight = 14150.210| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3428 r_free = 0.3428 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3428 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7051 moved from start: 0.7466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16386 Z= 0.130 Angle : 0.647 8.747 22134 Z= 0.341 Chirality : 0.043 0.215 2360 Planarity : 0.004 0.044 2818 Dihedral : 8.344 122.274 2290 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.19), residues: 1932 helix: 0.96 (0.15), residues: 1131 sheet: -0.22 (0.43), residues: 148 loop : 0.09 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 164 TYR 0.028 0.002 TYR D 174 PHE 0.024 0.002 PHE B 261 TRP 0.011 0.001 TRP B 558 HIS 0.012 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (16386) covalent geometry : angle 0.64671 / 0.34 (22134) hydrogen bonds : bond 0.03935 / 2.54 ( 871) hydrogen bonds : angle 5.15236 / 3.66 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3156.94 seconds wall clock time: 55 minutes 33.28 seconds (3333.28 seconds total)