Starting phenix.real_space_refine on Fri Jul 3 19:51:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byw_45046/07_2026/9byw_45046_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byw_45046/07_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_45046/07_2026/9byw_45046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byw_45046/07_2026/9byw_45046.map" model { file = "/net/cci-nas-00/data/ceres_data/9byw_45046/07_2026/9byw_45046_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byw_45046/07_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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.96, per 1000 atoms: 0.25 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: 1.35 Conformation dependent library (CDL) restraints added in 768.5 milliseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.516A 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: 2.79 Time building geometry restraints manager: 1.85 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 3.060 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.964 3.060 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 3.060 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 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: 1.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 16.570 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.780 ------------------------------------------------------------------------------- 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 : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 LEU cc_start: 0.9137 (mt) cc_final: 0.6541 (mt) REVERT: A 95 MET cc_start: 0.8221 (tpp) cc_final: 0.7891 (mmm) REVERT: A 136 LYS cc_start: 0.8133 (tptt) cc_final: 0.7434 (tttt) REVERT: A 143 LEU cc_start: 0.9004 (tp) cc_final: 0.8636 (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: 0.8751 (m) REVERT: A 166 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8433 (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: 0.6676 (mt) REVERT: A 181 ASP cc_start: 0.7470 (m-30) cc_final: 0.6965 (m-30) REVERT: A 190 MET cc_start: 0.7882 (mtt) cc_final: 0.7604 (mtt) REVERT: A 205 LYS cc_start: 0.7012 (mttp) cc_final: 0.6717 (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: 0.8354 (m) REVERT: A 550 MET cc_start: 0.6875 (mtm) cc_final: 0.6162 (mtp) REVERT: A 597 ILE cc_start: 0.8618 (pt) cc_final: 0.8413 (pt) REVERT: A 634 MET cc_start: 0.8480 (mmp) cc_final: 0.8018 (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: 0.6707 (tp-100) REVERT: A 650 GLN cc_start: 0.6815 (mt0) cc_final: 0.6452 (mt0) REVERT: A 655 THR cc_start: 0.7159 (m) cc_final: 0.6492 (m) REVERT: A 658 LEU cc_start: 0.8182 (mt) cc_final: 0.7623 (mt) REVERT: A 667 LEU cc_start: 0.8626 (tt) cc_final: 0.8222 (tp) REVERT: B 62 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8322 (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: 0.8884 (p) REVERT: B 125 VAL cc_start: 0.9205 (t) cc_final: 0.8976 (t) REVERT: B 143 LEU cc_start: 0.9058 (tp) cc_final: 0.8852 (tp) REVERT: B 179 LEU cc_start: 0.8385 (tp) cc_final: 0.8120 (tp) REVERT: B 191 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8215 (mm-40) REVERT: B 193 SER cc_start: 0.8165 (m) cc_final: 0.7937 (p) REVERT: B 200 SER cc_start: 0.8143 (t) cc_final: 0.7858 (m) REVERT: B 213 ILE cc_start: 0.8628 (mt) cc_final: 0.8241 (mp) REVERT: B 216 VAL cc_start: 0.8357 (OUTLIER) cc_final: 0.7795 (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: 0.7550 (mmmm) REVERT: B 282 VAL cc_start: 0.8805 (t) cc_final: 0.8495 (m) REVERT: B 288 PHE cc_start: 0.7211 (t80) cc_final: 0.6412 (t80) REVERT: B 319 MET cc_start: 0.7581 (tpp) cc_final: 0.6761 (tpp) REVERT: B 358 ILE cc_start: 0.8730 (mm) cc_final: 0.8283 (mm) REVERT: B 362 ASP cc_start: 0.5783 (m-30) cc_final: 0.4560 (m-30) REVERT: B 373 ILE cc_start: 0.9091 (mt) cc_final: 0.8005 (mt) REVERT: B 384 GLU cc_start: 0.6657 (pm20) cc_final: 0.6286 (pm20) REVERT: B 391 VAL cc_start: 0.9072 (p) cc_final: 0.8868 (p) REVERT: B 410 ASN cc_start: 0.8615 (OUTLIER) cc_final: 0.8111 (m-40) REVERT: B 411 LEU cc_start: 0.7569 (mp) cc_final: 0.7155 (mp) REVERT: B 417 LEU cc_start: 0.8670 (tp) cc_final: 0.7410 (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: 0.5306 (t80) REVERT: B 474 GLN cc_start: 0.8332 (mt0) cc_final: 0.8120 (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: 0.8447 (t) REVERT: B 589 SER cc_start: 0.8091 (m) cc_final: 0.7541 (t) REVERT: B 613 TYR cc_start: 0.7322 (t80) cc_final: 0.6635 (t80) REVERT: B 634 MET cc_start: 0.8149 (mmp) cc_final: 0.7805 (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: 0.4402 (mt) REVERT: C 151 ILE cc_start: 0.6601 (mm) cc_final: 0.6132 (mm) REVERT: C 208 LEU cc_start: 0.6294 (mt) cc_final: 0.5699 (mt) REVERT: D 126 LYS cc_start: 0.2376 (OUTLIER) cc_final: 0.1991 (tptp) REVERT: D 174 TYR cc_start: 0.1481 (t80) cc_final: 0.0312 (t80) REVERT: D 229 ILE cc_start: 0.5863 (mm) cc_final: 0.5620 (mm) REVERT: D 282 ILE cc_start: -0.1245 (OUTLIER) cc_final: -0.1504 (tp) outliers start: 23 outliers final: 5 residues processed: 799 average time/residue: 0.1437 time to fit residues: 167.0545 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 : 0.607 ------------------------------------------------------------------------------- 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 365 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.131520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.090687 restraints weight = 47867.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.094148 restraints weight = 30359.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.096574 restraints weight = 21039.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.098098 restraints weight = 16137.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.099247 restraints weight = 13240.595| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3420 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3420 r_free = 0.3420 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3417 r_free = 0.3417 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (13 function evaluations) r_final: 0.3417 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6772 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16386 Z= 0.207 Angle : 0.647 6.994 22134 Z= 0.348 Chirality : 0.044 0.251 2360 Planarity : 0.004 0.060 2818 Dihedral : 9.518 128.590 2290 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.29 % Allowed : 3.55 % 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: 1.42 (0.19), residues: 1932 helix: 1.39 (0.15), residues: 1117 sheet: -0.16 (0.40), residues: 152 loop : 0.68 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 207 TYR 0.026 0.002 TYR A 140 PHE 0.036 0.002 PHE D 178 TRP 0.027 0.002 TRP B 558 HIS 0.007 0.002 HIS B 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.21 (16386) covalent geometry : angle 0.64688 / 0.35 (22134) hydrogen bonds : bond 0.04692 / 2.94 ( 871) hydrogen bonds : angle 5.14610 / 3.65 ( 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 584 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 579 time to evaluate : 0.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 SER cc_start: 0.9262 (m) cc_final: 0.9052 (p) REVERT: A 128 PHE cc_start: 0.9159 (t80) cc_final: 0.8674 (t80) REVERT: A 143 LEU cc_start: 0.9117 (tp) cc_final: 0.8913 (tp) REVERT: A 147 GLN cc_start: 0.9080 (mt0) cc_final: 0.8593 (mt0) REVERT: A 168 VAL cc_start: 0.8565 (t) cc_final: 0.8292 (t) REVERT: A 172 LEU cc_start: 0.8898 (mp) cc_final: 0.8402 (mp) REVERT: A 173 LEU cc_start: 0.9107 (mt) cc_final: 0.8834 (mt) REVERT: A 259 ASN cc_start: 0.8202 (p0) cc_final: 0.7934 (p0) REVERT: A 270 ASP cc_start: 0.8744 (m-30) cc_final: 0.8084 (t70) REVERT: A 286 ASP cc_start: 0.8776 (m-30) cc_final: 0.8480 (m-30) REVERT: A 291 LEU cc_start: 0.8758 (mt) cc_final: 0.8484 (mt) REVERT: A 319 MET cc_start: 0.8998 (tpp) cc_final: 0.8724 (tpp) REVERT: A 322 MET cc_start: 0.8705 (mmm) cc_final: 0.7941 (mmm) REVERT: A 325 LYS cc_start: 0.9233 (mttt) cc_final: 0.8934 (mtmm) REVERT: A 348 MET cc_start: 0.9438 (ttp) cc_final: 0.9120 (ptp) REVERT: A 349 LEU cc_start: 0.8451 (tp) cc_final: 0.8215 (tp) REVERT: A 359 MET cc_start: 0.7957 (ttt) cc_final: 0.7677 (ttt) REVERT: A 361 GLN cc_start: 0.8273 (tp40) cc_final: 0.7724 (tp40) REVERT: A 375 LYS cc_start: 0.9094 (mmtm) cc_final: 0.8600 (mmtm) REVERT: A 406 ASP cc_start: 0.8216 (m-30) cc_final: 0.7960 (m-30) REVERT: A 407 ILE cc_start: 0.8848 (mt) cc_final: 0.8548 (mt) REVERT: A 425 ILE cc_start: 0.9410 (mt) cc_final: 0.9192 (mt) REVERT: A 444 ASP cc_start: 0.7872 (t0) cc_final: 0.6913 (t0) REVERT: A 493 MET cc_start: 0.9173 (tmm) cc_final: 0.8972 (tmm) REVERT: A 498 TYR cc_start: 0.8756 (m-80) cc_final: 0.8356 (m-80) REVERT: A 500 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9131 (mp) REVERT: A 512 GLU cc_start: 0.8449 (pm20) cc_final: 0.7967 (pm20) REVERT: A 546 LEU cc_start: 0.9387 (mt) cc_final: 0.9162 (mt) REVERT: A 550 MET cc_start: 0.7250 (mtm) cc_final: 0.6179 (mtp) REVERT: A 598 MET cc_start: 0.8919 (mtm) cc_final: 0.8546 (mtt) REVERT: A 599 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7183 (mm-30) REVERT: A 601 ILE cc_start: 0.8858 (tt) cc_final: 0.8585 (tt) REVERT: A 602 GLU cc_start: 0.8357 (pm20) cc_final: 0.6655 (mp0) REVERT: A 645 GLN cc_start: 0.8381 (tp40) cc_final: 0.8002 (tp-100) REVERT: A 650 GLN cc_start: 0.7720 (mt0) cc_final: 0.7079 (mt0) REVERT: A 655 THR cc_start: 0.7734 (m) cc_final: 0.6909 (m) REVERT: A 659 LYS cc_start: 0.8696 (mttt) cc_final: 0.8455 (mmmt) REVERT: A 672 LEU cc_start: 0.8907 (mt) cc_final: 0.8669 (mt) REVERT: B 8 LYS cc_start: 0.9439 (tttm) cc_final: 0.9195 (tppt) REVERT: B 12 LEU cc_start: 0.9557 (mt) cc_final: 0.9289 (mt) REVERT: B 95 MET cc_start: 0.8937 (tpp) cc_final: 0.7851 (tpp) REVERT: B 99 LYS cc_start: 0.9576 (mmmt) cc_final: 0.8827 (mmmt) REVERT: B 115 LEU cc_start: 0.8595 (mp) cc_final: 0.8324 (mp) REVERT: B 162 LYS cc_start: 0.8940 (tppt) cc_final: 0.8731 (ttmt) REVERT: B 229 LEU cc_start: 0.8053 (mp) cc_final: 0.7825 (mp) REVERT: B 288 PHE cc_start: 0.9340 (t80) cc_final: 0.8869 (t80) REVERT: B 322 MET cc_start: 0.8414 (mmm) cc_final: 0.8195 (mmt) REVERT: B 326 PHE cc_start: 0.9265 (m-80) cc_final: 0.8535 (m-80) REVERT: B 350 ARG cc_start: 0.7824 (mtm-85) cc_final: 0.7594 (mtm110) REVERT: B 358 ILE cc_start: 0.8508 (mm) cc_final: 0.8230 (mm) REVERT: B 394 TYR cc_start: 0.8741 (m-80) cc_final: 0.7934 (m-80) REVERT: B 413 SER cc_start: 0.9174 (m) cc_final: 0.8423 (t) REVERT: B 417 LEU cc_start: 0.9377 (tt) cc_final: 0.8945 (tt) REVERT: B 425 ILE cc_start: 0.9036 (mt) cc_final: 0.8652 (mt) REVERT: B 458 MET cc_start: 0.9281 (mmm) cc_final: 0.8893 (mmm) REVERT: B 479 TYR cc_start: 0.8304 (t80) cc_final: 0.7878 (t80) REVERT: B 493 MET cc_start: 0.9183 (tmm) cc_final: 0.8971 (tmm) REVERT: B 494 MET cc_start: 0.9459 (mtp) cc_final: 0.9058 (mtp) REVERT: B 512 GLU cc_start: 0.8575 (pm20) cc_final: 0.8319 (pm20) REVERT: B 645 GLN cc_start: 0.8921 (tp40) cc_final: 0.8647 (tp-100) REVERT: B 683 TYR cc_start: 0.8427 (t80) cc_final: 0.7759 (t80) REVERT: C 38 ASN cc_start: 0.7090 (m-40) cc_final: 0.6176 (p0) REVERT: C 93 MET cc_start: 0.8538 (mtm) cc_final: 0.8292 (mmt) REVERT: C 95 MET cc_start: 0.8135 (tmm) cc_final: 0.7725 (tmm) REVERT: C 96 MET cc_start: 0.8378 (mmm) cc_final: 0.7865 (mmm) REVERT: C 151 ILE cc_start: 0.8259 (mm) cc_final: 0.8013 (mm) REVERT: C 227 PHE cc_start: 0.7902 (t80) cc_final: 0.7586 (t80) REVERT: C 259 PHE cc_start: 0.6583 (t80) cc_final: 0.5786 (t80) REVERT: D 55 TYR cc_start: 0.8241 (t80) cc_final: 0.8008 (t80) REVERT: D 154 PHE cc_start: 0.8083 (t80) cc_final: 0.7815 (t80) REVERT: D 169 TYR cc_start: 0.7589 (m-80) cc_final: 0.6735 (m-80) REVERT: D 174 TYR cc_start: 0.1911 (t80) cc_final: 0.1275 (t80) REVERT: D 178 PHE cc_start: 0.7923 (m-80) cc_final: 0.7639 (m-80) outliers start: 5 outliers final: 0 residues processed: 581 average time/residue: 0.1241 time to fit residues: 108.1366 Evaluate side-chains 460 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 459 time to evaluate : 0.568 ------------------------------------------------------------------------------- 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: 2.9990 chunk 131 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 182 optimal weight: 20.0000 chunk 159 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 158 optimal weight: 20.0000 overall best weight: 3.1386 ------------------------------------------------------------------------------- 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 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN B 11 GLN B 61 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 D 71 ASN D 265 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.126614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.086890 restraints weight = 50912.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.090026 restraints weight = 31827.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.092150 restraints weight = 22434.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.093686 restraints weight = 17136.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.094664 restraints weight = 13935.211| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16386 Z= 0.212 Angle : 0.608 6.576 22134 Z= 0.328 Chirality : 0.043 0.172 2360 Planarity : 0.004 0.037 2818 Dihedral : 9.384 130.880 2290 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.23 % Allowed : 3.44 % Favored : 96.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.19), residues: 1932 helix: 1.26 (0.15), residues: 1133 sheet: -0.49 (0.39), residues: 160 loop : 0.62 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 161 TYR 0.019 0.002 TYR A 140 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 0.00447 / 0.21 (16386) covalent geometry : angle 0.60752 / 0.33 (22134) hydrogen bonds : bond 0.04342 / 2.70 ( 871) hydrogen bonds : angle 4.98232 / 3.52 ( 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 538 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 534 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.9268 (tp30) cc_final: 0.8865 (tp30) REVERT: A 71 LEU cc_start: 0.9413 (mt) cc_final: 0.9104 (mt) REVERT: A 81 PHE cc_start: 0.9443 (m-80) cc_final: 0.9101 (m-80) REVERT: A 99 LYS cc_start: 0.9263 (mmtp) cc_final: 0.8692 (mttt) REVERT: A 108 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.8896 (p) REVERT: A 117 ARG cc_start: 0.9109 (mmt90) cc_final: 0.8770 (mtp85) REVERT: A 119 GLU cc_start: 0.8651 (mp0) cc_final: 0.8436 (tm-30) REVERT: A 128 PHE cc_start: 0.9194 (t80) cc_final: 0.8814 (t80) REVERT: A 147 GLN cc_start: 0.9105 (mt0) cc_final: 0.8637 (mt0) REVERT: A 168 VAL cc_start: 0.8346 (t) cc_final: 0.8037 (p) REVERT: A 172 LEU cc_start: 0.8830 (mp) cc_final: 0.8272 (mp) REVERT: A 173 LEU cc_start: 0.9101 (mt) cc_final: 0.8868 (mt) REVERT: A 205 LYS cc_start: 0.7478 (mttt) cc_final: 0.7154 (mttt) REVERT: A 270 ASP cc_start: 0.8760 (m-30) cc_final: 0.8099 (t70) REVERT: A 349 LEU cc_start: 0.8571 (tp) cc_final: 0.8326 (tp) REVERT: A 359 MET cc_start: 0.7901 (ttt) cc_final: 0.7608 (ttt) REVERT: A 361 GLN cc_start: 0.8444 (tp40) cc_final: 0.7896 (tp40) REVERT: A 375 LYS cc_start: 0.9115 (mmtm) cc_final: 0.8671 (mmtm) REVERT: A 385 VAL cc_start: 0.8744 (t) cc_final: 0.8448 (p) REVERT: A 402 GLU cc_start: 0.8794 (mp0) cc_final: 0.8528 (mp0) REVERT: A 406 ASP cc_start: 0.8261 (m-30) cc_final: 0.8033 (m-30) REVERT: A 407 ILE cc_start: 0.8908 (mt) cc_final: 0.8502 (mt) REVERT: A 441 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8525 (mt-10) REVERT: A 466 MET cc_start: 0.9301 (ptt) cc_final: 0.9033 (ptp) REVERT: A 479 TYR cc_start: 0.8716 (t80) cc_final: 0.8507 (t80) REVERT: A 493 MET cc_start: 0.9095 (tmm) cc_final: 0.8854 (tmm) REVERT: A 498 TYR cc_start: 0.8916 (m-80) cc_final: 0.8511 (m-80) REVERT: A 550 MET cc_start: 0.7530 (mtm) cc_final: 0.6984 (mtm) REVERT: A 598 MET cc_start: 0.8858 (mtm) cc_final: 0.8473 (mtm) REVERT: A 599 GLU cc_start: 0.7873 (mm-30) cc_final: 0.7420 (mm-30) REVERT: A 602 GLU cc_start: 0.8942 (pm20) cc_final: 0.8093 (pm20) REVERT: A 615 MET cc_start: 0.8303 (mmp) cc_final: 0.7967 (mmp) REVERT: A 650 GLN cc_start: 0.7888 (mt0) cc_final: 0.7565 (mt0) REVERT: A 659 LYS cc_start: 0.8613 (mttt) cc_final: 0.8399 (mmmt) REVERT: B 8 LYS cc_start: 0.9477 (tttm) cc_final: 0.9189 (tppt) REVERT: B 12 LEU cc_start: 0.9553 (mt) cc_final: 0.9313 (mt) REVERT: B 24 PHE cc_start: 0.8699 (m-80) cc_final: 0.8345 (m-80) REVERT: B 40 TYR cc_start: 0.9222 (t80) cc_final: 0.8906 (t80) REVERT: B 67 GLU cc_start: 0.8684 (mp0) cc_final: 0.8439 (mp0) REVERT: B 95 MET cc_start: 0.9171 (tpp) cc_final: 0.8042 (tpp) REVERT: B 98 PHE cc_start: 0.9606 (t80) cc_final: 0.8969 (t80) REVERT: B 99 LYS cc_start: 0.9625 (mmmt) cc_final: 0.8973 (mmmt) REVERT: B 107 LYS cc_start: 0.8819 (mppt) cc_final: 0.8524 (mptt) REVERT: B 115 LEU cc_start: 0.8740 (mp) cc_final: 0.8447 (mp) REVERT: B 200 SER cc_start: 0.7193 (m) cc_final: 0.6910 (p) REVERT: B 228 LYS cc_start: 0.8132 (mmmm) cc_final: 0.7864 (tppt) REVERT: B 235 ARG cc_start: 0.7858 (mmt90) cc_final: 0.7448 (mmt90) REVERT: B 288 PHE cc_start: 0.9389 (t80) cc_final: 0.8894 (t80) REVERT: B 307 TYR cc_start: 0.9274 (t80) cc_final: 0.8838 (t80) REVERT: B 326 PHE cc_start: 0.9323 (m-80) cc_final: 0.8587 (m-80) REVERT: B 379 SER cc_start: 0.8309 (t) cc_final: 0.7934 (t) REVERT: B 394 TYR cc_start: 0.8903 (m-80) cc_final: 0.8628 (m-80) REVERT: B 413 SER cc_start: 0.9160 (m) cc_final: 0.8493 (t) REVERT: B 444 ASP cc_start: 0.9030 (t0) cc_final: 0.8816 (t70) REVERT: B 458 MET cc_start: 0.9269 (mmm) cc_final: 0.8994 (mmm) REVERT: B 466 MET cc_start: 0.8731 (ptp) cc_final: 0.8403 (ptp) REVERT: B 472 LEU cc_start: 0.9180 (mm) cc_final: 0.8894 (mm) REVERT: B 492 PHE cc_start: 0.9213 (m-80) cc_final: 0.8535 (m-80) REVERT: B 493 MET cc_start: 0.9313 (tmm) cc_final: 0.8801 (tmm) REVERT: B 494 MET cc_start: 0.9462 (mtp) cc_final: 0.8854 (mtp) REVERT: B 506 ILE cc_start: 0.9628 (mm) cc_final: 0.9300 (mm) REVERT: B 509 GLU cc_start: 0.9020 (pt0) cc_final: 0.8697 (pp20) REVERT: B 510 LYS cc_start: 0.9494 (mmtp) cc_final: 0.9220 (mmmm) REVERT: B 570 MET cc_start: 0.8492 (mtp) cc_final: 0.7960 (mmt) REVERT: B 597 ILE cc_start: 0.8994 (pt) cc_final: 0.8733 (pt) REVERT: B 615 MET cc_start: 0.8963 (mmp) cc_final: 0.8752 (mmm) REVERT: B 645 GLN cc_start: 0.9109 (tp40) cc_final: 0.8832 (tp-100) REVERT: C 95 MET cc_start: 0.8248 (tmm) cc_final: 0.7585 (tmm) REVERT: C 137 MET cc_start: 0.7011 (mpp) cc_final: 0.6269 (tpt) REVERT: C 149 ASP cc_start: 0.7975 (t0) cc_final: 0.7684 (t0) REVERT: C 151 ILE cc_start: 0.8305 (mm) cc_final: 0.8034 (mm) REVERT: C 227 PHE cc_start: 0.8043 (t80) cc_final: 0.7656 (t80) REVERT: C 259 PHE cc_start: 0.6332 (t80) cc_final: 0.5571 (t80) REVERT: C 276 TYR cc_start: 0.8152 (t80) cc_final: 0.7851 (t80) REVERT: D 169 TYR cc_start: 0.7859 (m-80) cc_final: 0.6895 (m-80) REVERT: D 178 PHE cc_start: 0.8294 (m-80) cc_final: 0.7967 (m-80) outliers start: 4 outliers final: 1 residues processed: 537 average time/residue: 0.1221 time to fit residues: 99.0530 Evaluate side-chains 451 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 449 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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: 0.0980 chunk 157 optimal weight: 0.9990 chunk 168 optimal weight: 8.9990 chunk 89 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 185 optimal weight: 5.9990 chunk 191 optimal weight: 9.9990 chunk 159 optimal weight: 7.9990 chunk 182 optimal weight: 20.0000 chunk 93 optimal weight: 0.7980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN ** 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** B 44 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.129266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.088346 restraints weight = 49240.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.091588 restraints weight = 30389.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.093700 restraints weight = 21185.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.095311 restraints weight = 16317.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.096034 restraints weight = 13255.598| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3372 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3372 r_free = 0.3372 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3372 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6950 moved from start: 0.5432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16386 Z= 0.149 Angle : 0.582 11.125 22134 Z= 0.309 Chirality : 0.042 0.177 2360 Planarity : 0.004 0.049 2818 Dihedral : 9.089 129.241 2290 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.06 % Allowed : 2.27 % Favored : 97.67 % 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: 1.22 (0.19), residues: 1932 helix: 1.25 (0.15), residues: 1131 sheet: -0.49 (0.41), residues: 150 loop : 0.58 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 161 TYR 0.019 0.002 TYR D 242 PHE 0.033 0.002 PHE B 81 TRP 0.028 0.001 TRP B 558 HIS 0.004 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (16386) covalent geometry : angle 0.58164 / 0.31 (22134) hydrogen bonds : bond 0.04017 / 2.51 ( 871) hydrogen bonds : angle 4.91430 / 3.48 ( 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 546 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 545 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.9205 (tp30) cc_final: 0.8689 (tp30) REVERT: A 71 LEU cc_start: 0.9442 (mt) cc_final: 0.8948 (mt) REVERT: A 99 LYS cc_start: 0.9276 (mmtp) cc_final: 0.8875 (mttt) REVERT: A 117 ARG cc_start: 0.9137 (mmt90) cc_final: 0.8764 (mtp85) REVERT: A 147 GLN cc_start: 0.9161 (mt0) cc_final: 0.8652 (mt0) REVERT: A 168 VAL cc_start: 0.8200 (t) cc_final: 0.7976 (p) REVERT: A 172 LEU cc_start: 0.8813 (mp) cc_final: 0.8267 (mp) REVERT: A 173 LEU cc_start: 0.9125 (mt) cc_final: 0.8900 (mt) REVERT: A 324 ASP cc_start: 0.9334 (p0) cc_final: 0.8878 (p0) REVERT: A 345 LYS cc_start: 0.9240 (mttp) cc_final: 0.8996 (mttt) REVERT: A 349 LEU cc_start: 0.8557 (tp) cc_final: 0.8318 (tp) REVERT: A 373 ILE cc_start: 0.9554 (mt) cc_final: 0.9077 (mt) REVERT: A 375 LYS cc_start: 0.9123 (mmtm) cc_final: 0.8684 (mmtm) REVERT: A 385 VAL cc_start: 0.8683 (t) cc_final: 0.8364 (p) REVERT: A 402 GLU cc_start: 0.8794 (mp0) cc_final: 0.8528 (mp0) REVERT: A 406 ASP cc_start: 0.8186 (m-30) cc_final: 0.7936 (m-30) REVERT: A 407 ILE cc_start: 0.8876 (mt) cc_final: 0.8484 (mt) REVERT: A 425 ILE cc_start: 0.9432 (mm) cc_final: 0.9157 (mm) REVERT: A 444 ASP cc_start: 0.7997 (t0) cc_final: 0.7438 (t0) REVERT: A 466 MET cc_start: 0.9315 (ptt) cc_final: 0.9039 (ptp) REVERT: A 479 TYR cc_start: 0.8479 (t80) cc_final: 0.8120 (t80) REVERT: A 494 MET cc_start: 0.9494 (mmp) cc_final: 0.9125 (mmm) REVERT: A 498 TYR cc_start: 0.8876 (m-80) cc_final: 0.8488 (m-80) REVERT: A 516 GLN cc_start: 0.9527 (mt0) cc_final: 0.9222 (tt0) REVERT: A 550 MET cc_start: 0.7520 (mtm) cc_final: 0.7000 (mtm) REVERT: A 598 MET cc_start: 0.8853 (mtm) cc_final: 0.8430 (mtm) REVERT: A 599 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7359 (mm-30) REVERT: A 602 GLU cc_start: 0.8989 (pm20) cc_final: 0.8483 (pm20) REVERT: A 640 MET cc_start: 0.9279 (tpt) cc_final: 0.9052 (tpp) REVERT: A 650 GLN cc_start: 0.7855 (mt0) cc_final: 0.7587 (mt0) REVERT: A 659 LYS cc_start: 0.8809 (mttt) cc_final: 0.8439 (mmmt) REVERT: B 8 LYS cc_start: 0.9453 (tttm) cc_final: 0.9171 (tppt) REVERT: B 12 LEU cc_start: 0.9570 (mt) cc_final: 0.9318 (mt) REVERT: B 17 MET cc_start: 0.8905 (mmm) cc_final: 0.8389 (mmt) REVERT: B 24 PHE cc_start: 0.8656 (m-80) cc_final: 0.7940 (m-80) REVERT: B 95 MET cc_start: 0.9063 (tpp) cc_final: 0.7844 (tpp) REVERT: B 98 PHE cc_start: 0.9574 (t80) cc_final: 0.8979 (t80) REVERT: B 99 LYS cc_start: 0.9634 (mmmt) cc_final: 0.8938 (mmmt) REVERT: B 100 PHE cc_start: 0.9405 (t80) cc_final: 0.9192 (t80) REVERT: B 116 GLU cc_start: 0.8722 (mm-30) cc_final: 0.8520 (mm-30) REVERT: B 228 LYS cc_start: 0.8041 (mmmm) cc_final: 0.7822 (tppt) REVERT: B 235 ARG cc_start: 0.8016 (mmt90) cc_final: 0.7716 (mmt90) REVERT: B 288 PHE cc_start: 0.9369 (t80) cc_final: 0.8898 (t80) REVERT: B 307 TYR cc_start: 0.9255 (t80) cc_final: 0.8783 (t80) REVERT: B 319 MET cc_start: 0.8952 (tpp) cc_final: 0.8351 (tpp) REVERT: B 326 PHE cc_start: 0.9340 (m-80) cc_final: 0.8309 (m-80) REVERT: B 370 ASN cc_start: 0.9372 (m-40) cc_final: 0.8951 (t0) REVERT: B 379 SER cc_start: 0.8318 (t) cc_final: 0.8055 (t) REVERT: B 413 SER cc_start: 0.9157 (m) cc_final: 0.8614 (t) REVERT: B 444 ASP cc_start: 0.8997 (t0) cc_final: 0.8771 (t70) REVERT: B 458 MET cc_start: 0.9245 (mmm) cc_final: 0.9019 (mmm) REVERT: B 459 LYS cc_start: 0.8712 (mttt) cc_final: 0.8433 (mtmt) REVERT: B 466 MET cc_start: 0.8759 (ptp) cc_final: 0.8400 (ptp) REVERT: B 472 LEU cc_start: 0.9201 (mm) cc_final: 0.8870 (mm) REVERT: B 492 PHE cc_start: 0.9180 (m-80) cc_final: 0.8436 (m-80) REVERT: B 493 MET cc_start: 0.9222 (tmm) cc_final: 0.8806 (tmm) REVERT: B 494 MET cc_start: 0.9245 (mtp) cc_final: 0.8717 (mtp) REVERT: B 506 ILE cc_start: 0.9583 (mm) cc_final: 0.9196 (mm) REVERT: B 509 GLU cc_start: 0.9023 (pt0) cc_final: 0.8765 (pp20) REVERT: B 510 LYS cc_start: 0.9495 (mmtp) cc_final: 0.9219 (mmmm) REVERT: B 597 ILE cc_start: 0.8928 (pt) cc_final: 0.8705 (pt) REVERT: B 645 GLN cc_start: 0.9075 (tp40) cc_final: 0.8806 (tp-100) REVERT: B 648 ILE cc_start: 0.9035 (mm) cc_final: 0.8812 (mm) REVERT: B 675 HIS cc_start: 0.8776 (t-90) cc_final: 0.8386 (t-90) REVERT: C 95 MET cc_start: 0.8064 (tmm) cc_final: 0.7337 (tmm) REVERT: C 137 MET cc_start: 0.7363 (mpp) cc_final: 0.6584 (tpt) REVERT: C 149 ASP cc_start: 0.8018 (t0) cc_final: 0.7734 (t0) REVERT: C 151 ILE cc_start: 0.8279 (mm) cc_final: 0.8017 (mm) REVERT: C 259 PHE cc_start: 0.6289 (t80) cc_final: 0.5542 (t80) REVERT: C 276 TYR cc_start: 0.8243 (t80) cc_final: 0.7951 (t80) REVERT: D 119 ASN cc_start: 0.7758 (m110) cc_final: 0.7492 (m110) REVERT: D 169 TYR cc_start: 0.7862 (m-80) cc_final: 0.7039 (m-80) REVERT: D 178 PHE cc_start: 0.8325 (m-80) cc_final: 0.7951 (m-80) REVERT: D 249 GLN cc_start: 0.7526 (pt0) cc_final: 0.7075 (pm20) REVERT: D 263 ASN cc_start: 0.6981 (p0) cc_final: 0.6586 (p0) outliers start: 1 outliers final: 0 residues processed: 545 average time/residue: 0.1237 time to fit residues: 102.1369 Evaluate side-chains 447 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 447 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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: 8.9990 chunk 46 optimal weight: 9.9990 chunk 120 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 126 optimal weight: 0.0980 chunk 129 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- 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 180 ASN A 313 HIS ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN B 218 ASN ** B 516 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 = 0.3888 r_free = 0.3888 target = 0.128361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.088447 restraints weight = 49538.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.091714 restraints weight = 31030.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.093926 restraints weight = 21437.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.095489 restraints weight = 16330.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.096554 restraints weight = 13358.062| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3396 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3396 r_free = 0.3396 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3396 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.5752 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= 0.137 Angle : 0.578 9.142 22134 Z= 0.306 Chirality : 0.042 0.187 2360 Planarity : 0.003 0.040 2818 Dihedral : 8.844 129.975 2290 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.12 % Allowed : 1.69 % Favored : 98.19 % 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: 1.17 (0.19), residues: 1932 helix: 1.29 (0.15), residues: 1113 sheet: -0.76 (0.39), residues: 164 loop : 0.52 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 161 TYR 0.017 0.001 TYR D 242 PHE 0.022 0.002 PHE A 81 TRP 0.014 0.001 TRP B 558 HIS 0.005 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (16386) covalent geometry : angle 0.57778 / 0.31 (22134) hydrogen bonds : bond 0.03852 / 2.43 ( 871) hydrogen bonds : angle 4.94688 / 3.52 ( 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 546 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 544 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.7896 (mp0) cc_final: 0.7465 (mp0) REVERT: A 67 GLU cc_start: 0.9166 (tp30) cc_final: 0.8686 (tp30) REVERT: A 71 LEU cc_start: 0.9446 (mt) cc_final: 0.9148 (mt) REVERT: A 99 LYS cc_start: 0.9405 (mmtp) cc_final: 0.8871 (mttt) REVERT: A 117 ARG cc_start: 0.9138 (mmt90) cc_final: 0.8747 (mtp85) REVERT: A 147 GLN cc_start: 0.9128 (mt0) cc_final: 0.8602 (mt0) REVERT: A 172 LEU cc_start: 0.8751 (mp) cc_final: 0.8251 (mp) REVERT: A 259 ASN cc_start: 0.8272 (p0) cc_final: 0.7832 (p0) REVERT: A 345 LYS cc_start: 0.9281 (mttp) cc_final: 0.8985 (mttt) REVERT: A 348 MET cc_start: 0.9353 (ttp) cc_final: 0.9122 (ptp) REVERT: A 349 LEU cc_start: 0.8521 (tp) cc_final: 0.8291 (tp) REVERT: A 375 LYS cc_start: 0.9116 (mmtm) cc_final: 0.8720 (mmtm) REVERT: A 385 VAL cc_start: 0.8865 (t) cc_final: 0.8289 (p) REVERT: A 402 GLU cc_start: 0.8802 (mp0) cc_final: 0.8521 (mp0) REVERT: A 407 ILE cc_start: 0.8840 (mt) cc_final: 0.8443 (mt) REVERT: A 466 MET cc_start: 0.9370 (ptt) cc_final: 0.9080 (ptp) REVERT: A 479 TYR cc_start: 0.8670 (t80) cc_final: 0.8456 (t80) REVERT: A 494 MET cc_start: 0.9477 (mmp) cc_final: 0.8964 (mmm) REVERT: A 498 TYR cc_start: 0.8835 (m-80) cc_final: 0.8467 (m-80) REVERT: A 515 ASP cc_start: 0.8532 (m-30) cc_final: 0.8329 (m-30) REVERT: A 550 MET cc_start: 0.7369 (mtm) cc_final: 0.7143 (mtm) REVERT: A 598 MET cc_start: 0.8856 (mtm) cc_final: 0.8571 (ttm) REVERT: A 599 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7385 (mm-30) REVERT: A 602 GLU cc_start: 0.8976 (pm20) cc_final: 0.8482 (pm20) REVERT: A 611 THR cc_start: 0.8798 (t) cc_final: 0.8186 (t) REVERT: A 615 MET cc_start: 0.8429 (mmp) cc_final: 0.8147 (mmm) REVERT: A 640 MET cc_start: 0.9318 (tpt) cc_final: 0.9095 (tpp) REVERT: B 8 LYS cc_start: 0.9436 (tttm) cc_final: 0.9150 (tppt) REVERT: B 12 LEU cc_start: 0.9598 (mt) cc_final: 0.9327 (mt) REVERT: B 17 MET cc_start: 0.8825 (mmm) cc_final: 0.8546 (mmm) REVERT: B 24 PHE cc_start: 0.8521 (m-80) cc_final: 0.7956 (m-80) REVERT: B 95 MET cc_start: 0.9048 (tpp) cc_final: 0.7804 (tpp) REVERT: B 98 PHE cc_start: 0.9565 (t80) cc_final: 0.9000 (t80) REVERT: B 99 LYS cc_start: 0.9651 (mmmt) cc_final: 0.8888 (mmmt) REVERT: B 124 ILE cc_start: 0.9206 (tp) cc_final: 0.8683 (tp) REVERT: B 200 SER cc_start: 0.6977 (m) cc_final: 0.6748 (p) REVERT: B 262 LEU cc_start: 0.8773 (mm) cc_final: 0.7956 (tp) REVERT: B 288 PHE cc_start: 0.9382 (t80) cc_final: 0.8927 (t80) REVERT: B 307 TYR cc_start: 0.9202 (t80) cc_final: 0.8704 (t80) REVERT: B 319 MET cc_start: 0.9109 (tpp) cc_final: 0.8895 (tpp) REVERT: B 326 PHE cc_start: 0.9129 (m-10) cc_final: 0.8400 (m-80) REVERT: B 370 ASN cc_start: 0.9388 (m-40) cc_final: 0.8968 (t0) REVERT: B 379 SER cc_start: 0.8190 (t) cc_final: 0.7864 (t) REVERT: B 417 LEU cc_start: 0.9317 (tt) cc_final: 0.8806 (tt) REVERT: B 444 ASP cc_start: 0.9004 (t0) cc_final: 0.8719 (t0) REVERT: B 459 LYS cc_start: 0.8681 (mttt) cc_final: 0.8420 (mtmt) REVERT: B 472 LEU cc_start: 0.9258 (mm) cc_final: 0.8844 (mt) REVERT: B 492 PHE cc_start: 0.9134 (m-80) cc_final: 0.8367 (m-80) REVERT: B 493 MET cc_start: 0.9230 (tmm) cc_final: 0.8600 (tmm) REVERT: B 494 MET cc_start: 0.9329 (mtp) cc_final: 0.8861 (mtp) REVERT: B 506 ILE cc_start: 0.9577 (mm) cc_final: 0.9246 (mm) REVERT: B 509 GLU cc_start: 0.9067 (pt0) cc_final: 0.8702 (pp20) REVERT: B 510 LYS cc_start: 0.9468 (mmtp) cc_final: 0.8965 (mmmm) REVERT: B 558 TRP cc_start: 0.8253 (m100) cc_final: 0.7576 (m100) REVERT: B 645 GLN cc_start: 0.9024 (tp40) cc_final: 0.8756 (tp-100) REVERT: B 648 ILE cc_start: 0.9056 (mm) cc_final: 0.8805 (mm) REVERT: B 675 HIS cc_start: 0.8814 (t-90) cc_final: 0.8466 (t-90) REVERT: C 95 MET cc_start: 0.7984 (tmm) cc_final: 0.7320 (tmm) REVERT: C 137 MET cc_start: 0.7472 (mpp) cc_final: 0.6681 (tpt) REVERT: C 149 ASP cc_start: 0.8033 (t0) cc_final: 0.7787 (t0) REVERT: C 151 ILE cc_start: 0.8250 (mm) cc_final: 0.7965 (mm) REVERT: C 227 PHE cc_start: 0.8497 (t80) cc_final: 0.8225 (t80) REVERT: C 259 PHE cc_start: 0.6218 (t80) cc_final: 0.5463 (t80) REVERT: C 276 TYR cc_start: 0.8237 (t80) cc_final: 0.7948 (t80) REVERT: D 169 TYR cc_start: 0.8068 (m-80) cc_final: 0.7294 (m-80) REVERT: D 178 PHE cc_start: 0.8131 (m-80) cc_final: 0.7919 (m-80) REVERT: D 201 HIS cc_start: 0.9327 (m90) cc_final: 0.9019 (m90) REVERT: D 249 GLN cc_start: 0.7456 (pt0) cc_final: 0.7071 (pm20) outliers start: 2 outliers final: 1 residues processed: 546 average time/residue: 0.1237 time to fit residues: 101.9170 Evaluate side-chains 451 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 450 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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: 7.9990 chunk 172 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 27 optimal weight: 6.9990 chunk 136 optimal weight: 8.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 313 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 238 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.131315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.092513 restraints weight = 49638.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.095798 restraints weight = 31997.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.097911 restraints weight = 22275.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.099347 restraints weight = 16959.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.100421 restraints weight = 13897.554| |-----------------------------------------------------------------------------| r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3410 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3410 r_free = 0.3410 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3410 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.6056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16386 Z= 0.127 Angle : 0.570 8.220 22134 Z= 0.301 Chirality : 0.041 0.212 2360 Planarity : 0.003 0.039 2818 Dihedral : 8.644 130.651 2290 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.06 % Allowed : 1.92 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.19), residues: 1932 helix: 1.28 (0.15), residues: 1117 sheet: -0.61 (0.39), residues: 162 loop : 0.36 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 161 TYR 0.033 0.001 TYR B 574 PHE 0.016 0.002 PHE A 360 TRP 0.011 0.001 TRP B 558 HIS 0.006 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (16386) covalent geometry : angle 0.57008 / 0.30 (22134) hydrogen bonds : bond 0.03787 / 2.41 ( 871) hydrogen bonds : angle 4.84995 / 3.44 ( 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 528 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 527 time to evaluate : 0.612 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.9173 (tp30) cc_final: 0.8715 (tp30) REVERT: A 71 LEU cc_start: 0.9445 (mt) cc_final: 0.9143 (mt) REVERT: A 99 LYS cc_start: 0.9431 (mmtp) cc_final: 0.8937 (mttt) REVERT: A 117 ARG cc_start: 0.9163 (mmt90) cc_final: 0.8808 (mtp85) REVERT: A 147 GLN cc_start: 0.8911 (mt0) cc_final: 0.8461 (mt0) REVERT: A 259 ASN cc_start: 0.8259 (p0) cc_final: 0.7764 (p0) REVERT: A 322 MET cc_start: 0.8494 (mmm) cc_final: 0.8122 (mmm) REVERT: A 345 LYS cc_start: 0.9261 (mttp) cc_final: 0.9003 (mttm) REVERT: A 349 LEU cc_start: 0.8547 (tp) cc_final: 0.8307 (tp) REVERT: A 361 GLN cc_start: 0.8905 (tp-100) cc_final: 0.8660 (tp-100) REVERT: A 375 LYS cc_start: 0.9063 (mmtm) cc_final: 0.8650 (mmtm) REVERT: A 385 VAL cc_start: 0.8938 (t) cc_final: 0.8734 (m) REVERT: A 386 LEU cc_start: 0.9236 (mt) cc_final: 0.9009 (mt) REVERT: A 400 GLU cc_start: 0.9430 (mm-30) cc_final: 0.9104 (tp30) REVERT: A 402 GLU cc_start: 0.8802 (mp0) cc_final: 0.8541 (mp0) REVERT: A 407 ILE cc_start: 0.8830 (mt) cc_final: 0.8593 (mt) REVERT: A 456 LYS cc_start: 0.8736 (mmtm) cc_final: 0.8330 (mmtm) REVERT: A 458 MET cc_start: 0.9127 (mmp) cc_final: 0.8904 (mmp) REVERT: A 466 MET cc_start: 0.9253 (ptt) cc_final: 0.9012 (ptp) REVERT: A 494 MET cc_start: 0.9492 (mmp) cc_final: 0.9190 (mmm) REVERT: A 498 TYR cc_start: 0.8833 (m-80) cc_final: 0.8499 (m-80) REVERT: A 598 MET cc_start: 0.8855 (mtm) cc_final: 0.8524 (ttm) REVERT: A 602 GLU cc_start: 0.9009 (pm20) cc_final: 0.8594 (pm20) REVERT: A 611 THR cc_start: 0.8819 (t) cc_final: 0.8240 (t) REVERT: A 615 MET cc_start: 0.8424 (mmp) cc_final: 0.8154 (mmm) REVERT: A 640 MET cc_start: 0.9312 (tpt) cc_final: 0.9069 (tpp) REVERT: B 8 LYS cc_start: 0.9437 (tttm) cc_final: 0.9147 (tppt) REVERT: B 12 LEU cc_start: 0.9596 (mt) cc_final: 0.9329 (mt) REVERT: B 17 MET cc_start: 0.8931 (mmm) cc_final: 0.8461 (mmt) REVERT: B 24 PHE cc_start: 0.8634 (m-80) cc_final: 0.7857 (m-80) REVERT: B 36 TYR cc_start: 0.9058 (t80) cc_final: 0.8577 (t80) REVERT: B 41 ILE cc_start: 0.9474 (mm) cc_final: 0.8718 (mm) REVERT: B 67 GLU cc_start: 0.8768 (mp0) cc_final: 0.8525 (mp0) REVERT: B 95 MET cc_start: 0.9035 (tpp) cc_final: 0.7630 (tpp) REVERT: B 98 PHE cc_start: 0.9568 (t80) cc_final: 0.8941 (t80) REVERT: B 99 LYS cc_start: 0.9668 (mmmt) cc_final: 0.8879 (mmmt) REVERT: B 107 LYS cc_start: 0.8977 (mppt) cc_final: 0.8603 (mptt) REVERT: B 124 ILE cc_start: 0.9232 (tp) cc_final: 0.8699 (tp) REVERT: B 200 SER cc_start: 0.7115 (m) cc_final: 0.6885 (p) REVERT: B 235 ARG cc_start: 0.7579 (mmm-85) cc_final: 0.6945 (mmt90) REVERT: B 288 PHE cc_start: 0.9367 (t80) cc_final: 0.8906 (t80) REVERT: B 307 TYR cc_start: 0.9195 (t80) cc_final: 0.8675 (t80) REVERT: B 319 MET cc_start: 0.9076 (tpp) cc_final: 0.8851 (tpp) REVERT: B 326 PHE cc_start: 0.9066 (m-10) cc_final: 0.8386 (m-80) REVERT: B 379 SER cc_start: 0.8242 (t) cc_final: 0.8007 (t) REVERT: B 386 LEU cc_start: 0.8864 (mt) cc_final: 0.8467 (mt) REVERT: B 394 TYR cc_start: 0.8893 (m-80) cc_final: 0.8581 (m-80) REVERT: B 444 ASP cc_start: 0.9018 (t0) cc_final: 0.8744 (t0) REVERT: B 459 LYS cc_start: 0.8676 (mttt) cc_final: 0.8397 (mtmt) REVERT: B 466 MET cc_start: 0.8786 (ptp) cc_final: 0.8296 (ptp) REVERT: B 472 LEU cc_start: 0.9294 (mm) cc_final: 0.8853 (mt) REVERT: B 492 PHE cc_start: 0.9207 (m-80) cc_final: 0.8441 (m-80) REVERT: B 493 MET cc_start: 0.9238 (tmm) cc_final: 0.8533 (tmm) REVERT: B 494 MET cc_start: 0.9318 (mtp) cc_final: 0.8891 (mtp) REVERT: B 506 ILE cc_start: 0.9589 (mm) cc_final: 0.9380 (mm) REVERT: B 558 TRP cc_start: 0.8309 (m100) cc_final: 0.7595 (m100) REVERT: B 604 ARG cc_start: 0.9233 (tpp80) cc_final: 0.8925 (ttm110) REVERT: B 645 GLN cc_start: 0.9076 (tp40) cc_final: 0.8790 (tp-100) REVERT: B 648 ILE cc_start: 0.9022 (mm) cc_final: 0.8784 (mm) REVERT: B 667 LEU cc_start: 0.8207 (tt) cc_final: 0.7923 (tt) REVERT: B 675 HIS cc_start: 0.8812 (t-90) cc_final: 0.8473 (t-90) REVERT: B 683 TYR cc_start: 0.8404 (t80) cc_final: 0.7789 (t80) REVERT: C 95 MET cc_start: 0.7780 (tmm) cc_final: 0.6929 (tmm) REVERT: C 96 MET cc_start: 0.8105 (mmm) cc_final: 0.7620 (mmm) REVERT: C 137 MET cc_start: 0.7574 (mpp) cc_final: 0.6903 (tpt) REVERT: C 149 ASP cc_start: 0.8104 (t0) cc_final: 0.7869 (t0) REVERT: C 151 ILE cc_start: 0.8209 (mm) cc_final: 0.7931 (mm) REVERT: C 198 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8403 (tp30) REVERT: C 227 PHE cc_start: 0.8568 (t80) cc_final: 0.8314 (t80) REVERT: C 259 PHE cc_start: 0.6247 (t80) cc_final: 0.5476 (t80) REVERT: C 276 TYR cc_start: 0.8292 (t80) cc_final: 0.8011 (t80) REVERT: D 169 TYR cc_start: 0.8301 (m-80) cc_final: 0.7628 (m-80) REVERT: D 178 PHE cc_start: 0.8200 (m-80) cc_final: 0.7973 (m-80) REVERT: D 201 HIS cc_start: 0.9146 (m90) cc_final: 0.8922 (m90) REVERT: D 208 LEU cc_start: 0.9118 (mt) cc_final: 0.8898 (mt) REVERT: D 249 GLN cc_start: 0.7446 (pt0) cc_final: 0.7101 (pm20) outliers start: 1 outliers final: 1 residues processed: 528 average time/residue: 0.1279 time to fit residues: 101.7534 Evaluate side-chains 459 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 458 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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: 4.9990 chunk 51 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 140 optimal weight: 0.9990 chunk 115 optimal weight: 9.9990 chunk 45 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 313 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 447 ASN D 24 GLN D 28 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.129033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.087895 restraints weight = 50456.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.091145 restraints weight = 31131.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.093411 restraints weight = 21468.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.094970 restraints weight = 16121.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.096112 restraints weight = 13039.497| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7015 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 : 0.004 0.070 16386 Z= 0.165 Angle : 0.598 7.150 22134 Z= 0.322 Chirality : 0.043 0.186 2360 Planarity : 0.003 0.040 2818 Dihedral : 8.698 132.255 2290 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.06 % Allowed : 1.11 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.19), residues: 1932 helix: 1.24 (0.15), residues: 1114 sheet: -0.64 (0.39), residues: 162 loop : 0.38 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 161 TYR 0.024 0.002 TYR B 574 PHE 0.025 0.002 PHE B 261 TRP 0.012 0.001 TRP B 558 HIS 0.008 0.001 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.17 (16386) covalent geometry : angle 0.59803 / 0.32 (22134) hydrogen bonds : bond 0.03871 / 2.45 ( 871) hydrogen bonds : angle 4.96671 / 3.53 ( 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 512 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 511 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.7963 (mp0) cc_final: 0.7621 (mp0) REVERT: A 67 GLU cc_start: 0.9217 (tp30) cc_final: 0.8781 (tp30) REVERT: A 71 LEU cc_start: 0.9411 (mt) cc_final: 0.9112 (mt) REVERT: A 99 LYS cc_start: 0.9475 (mmtp) cc_final: 0.8806 (mttt) REVERT: A 117 ARG cc_start: 0.9199 (mmt90) cc_final: 0.8843 (mtp85) REVERT: A 136 LYS cc_start: 0.9385 (tptt) cc_final: 0.9078 (ttpp) REVERT: A 147 GLN cc_start: 0.9035 (mt0) cc_final: 0.8633 (mt0) REVERT: A 202 ASN cc_start: 0.8605 (t0) cc_final: 0.8273 (t0) REVERT: A 259 ASN cc_start: 0.8252 (p0) cc_final: 0.7731 (p0) REVERT: A 345 LYS cc_start: 0.9263 (mttp) cc_final: 0.9022 (mttm) REVERT: A 349 LEU cc_start: 0.8536 (tp) cc_final: 0.8305 (tp) REVERT: A 361 GLN cc_start: 0.8860 (tp-100) cc_final: 0.8648 (tp-100) REVERT: A 373 ILE cc_start: 0.9560 (mt) cc_final: 0.9035 (mt) REVERT: A 375 LYS cc_start: 0.9044 (mmtm) cc_final: 0.8599 (mmtm) REVERT: A 402 GLU cc_start: 0.8671 (mp0) cc_final: 0.8458 (mp0) REVERT: A 407 ILE cc_start: 0.8982 (mt) cc_final: 0.8549 (mt) REVERT: A 444 ASP cc_start: 0.8291 (t0) cc_final: 0.7480 (t0) REVERT: A 452 ARG cc_start: 0.8795 (ttm170) cc_final: 0.8575 (tpp80) REVERT: A 455 ASN cc_start: 0.9059 (t0) cc_final: 0.8838 (t0) REVERT: A 456 LYS cc_start: 0.8854 (mmtm) cc_final: 0.8195 (mmtm) REVERT: A 466 MET cc_start: 0.9244 (ptt) cc_final: 0.8984 (ptp) REVERT: A 494 MET cc_start: 0.9509 (mmp) cc_final: 0.9122 (mmm) REVERT: A 498 TYR cc_start: 0.9065 (m-80) cc_final: 0.8742 (m-80) REVERT: A 501 GLN cc_start: 0.9159 (tp40) cc_final: 0.8788 (tp-100) REVERT: A 516 GLN cc_start: 0.9502 (mt0) cc_final: 0.9178 (tt0) REVERT: A 602 GLU cc_start: 0.9037 (pm20) cc_final: 0.8409 (pm20) REVERT: A 615 MET cc_start: 0.8499 (mmp) cc_final: 0.8083 (mmm) REVERT: A 640 MET cc_start: 0.9383 (tpt) cc_final: 0.9084 (tpp) REVERT: A 650 GLN cc_start: 0.6969 (mm-40) cc_final: 0.6635 (mm110) REVERT: A 655 THR cc_start: 0.8259 (m) cc_final: 0.8035 (t) REVERT: B 8 LYS cc_start: 0.9465 (tttm) cc_final: 0.9169 (tppt) REVERT: B 12 LEU cc_start: 0.9582 (mt) cc_final: 0.9346 (mt) REVERT: B 17 MET cc_start: 0.8883 (mmm) cc_final: 0.8576 (mmt) REVERT: B 24 PHE cc_start: 0.8751 (m-80) cc_final: 0.8282 (m-80) REVERT: B 41 ILE cc_start: 0.9508 (mm) cc_final: 0.9291 (mm) REVERT: B 95 MET cc_start: 0.9185 (tpp) cc_final: 0.7938 (tpp) REVERT: B 98 PHE cc_start: 0.9600 (t80) cc_final: 0.8974 (t80) REVERT: B 99 LYS cc_start: 0.9664 (mmmt) cc_final: 0.8951 (mmmt) REVERT: B 107 LYS cc_start: 0.9006 (mppt) cc_final: 0.8639 (mptt) REVERT: B 124 ILE cc_start: 0.9251 (tp) cc_final: 0.8745 (tp) REVERT: B 179 LEU cc_start: 0.9437 (tp) cc_final: 0.9218 (tp) REVERT: B 200 SER cc_start: 0.6983 (m) cc_final: 0.6779 (p) REVERT: B 235 ARG cc_start: 0.7673 (mmm-85) cc_final: 0.6968 (mmt90) REVERT: B 288 PHE cc_start: 0.9373 (t80) cc_final: 0.9076 (t80) REVERT: B 307 TYR cc_start: 0.9231 (t80) cc_final: 0.8683 (t80) REVERT: B 326 PHE cc_start: 0.9201 (m-10) cc_final: 0.8510 (m-80) REVERT: B 333 LYS cc_start: 0.8453 (ttpt) cc_final: 0.8050 (ttpt) REVERT: B 444 ASP cc_start: 0.8973 (t0) cc_final: 0.8714 (t0) REVERT: B 459 LYS cc_start: 0.8769 (mttt) cc_final: 0.8504 (mtmt) REVERT: B 472 LEU cc_start: 0.9289 (mm) cc_final: 0.9057 (mm) REVERT: B 492 PHE cc_start: 0.9251 (m-80) cc_final: 0.8555 (m-80) REVERT: B 493 MET cc_start: 0.9186 (tmm) cc_final: 0.8867 (tmm) REVERT: B 494 MET cc_start: 0.9350 (mtp) cc_final: 0.8942 (mtp) REVERT: B 604 ARG cc_start: 0.9257 (tpp80) cc_final: 0.8858 (ttm-80) REVERT: B 645 GLN cc_start: 0.9207 (tp40) cc_final: 0.8915 (tp-100) REVERT: B 648 ILE cc_start: 0.9140 (mm) cc_final: 0.8931 (mm) REVERT: B 675 HIS cc_start: 0.8847 (t-90) cc_final: 0.8510 (t-90) REVERT: B 683 TYR cc_start: 0.8611 (t80) cc_final: 0.8147 (t80) REVERT: C 95 MET cc_start: 0.7816 (tmm) cc_final: 0.6982 (tmm) REVERT: C 96 MET cc_start: 0.8120 (mmm) cc_final: 0.7613 (mmm) REVERT: C 137 MET cc_start: 0.7660 (mpp) cc_final: 0.6874 (tpt) REVERT: C 149 ASP cc_start: 0.8102 (t0) cc_final: 0.7892 (t0) REVERT: C 151 ILE cc_start: 0.8258 (mm) cc_final: 0.7986 (mm) REVERT: C 227 PHE cc_start: 0.8557 (t80) cc_final: 0.8295 (t80) REVERT: C 259 PHE cc_start: 0.6355 (t80) cc_final: 0.5616 (t80) REVERT: C 276 TYR cc_start: 0.8339 (t80) cc_final: 0.8102 (t80) REVERT: D 157 MET cc_start: 0.6864 (tmm) cc_final: 0.6555 (tmm) REVERT: D 169 TYR cc_start: 0.8451 (m-80) cc_final: 0.7798 (m-80) outliers start: 1 outliers final: 1 residues processed: 512 average time/residue: 0.1268 time to fit residues: 98.0608 Evaluate side-chains 428 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 427 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 7.9990 chunk 99 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 chunk 153 optimal weight: 30.0000 chunk 11 optimal weight: 10.0000 chunk 158 optimal weight: 20.0000 chunk 97 optimal weight: 6.9990 chunk 151 optimal weight: 20.0000 chunk 81 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- 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 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 ASN C 249 GLN D 24 GLN D 28 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.125044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.084950 restraints weight = 51782.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.088091 restraints weight = 31779.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.090077 restraints weight = 22037.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.091599 restraints weight = 16862.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.092733 restraints weight = 13714.696| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.6684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 16386 Z= 0.226 Angle : 0.666 10.042 22134 Z= 0.355 Chirality : 0.044 0.174 2360 Planarity : 0.004 0.042 2818 Dihedral : 8.986 131.653 2290 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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: 0.78 (0.19), residues: 1932 helix: 0.99 (0.15), residues: 1126 sheet: -0.74 (0.37), residues: 162 loop : 0.23 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG D 196 TYR 0.034 0.002 TYR B 574 PHE 0.022 0.002 PHE D 178 TRP 0.019 0.002 TRP B 558 HIS 0.008 0.001 HIS B 572 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.23 (16386) covalent geometry : angle 0.66638 / 0.35 (22134) hydrogen bonds : bond 0.04147 / 2.63 ( 871) hydrogen bonds : angle 5.13005 / 3.63 ( 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 491 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 491 time to evaluate : 0.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8064 (mp0) cc_final: 0.7561 (mp0) REVERT: A 67 GLU cc_start: 0.9241 (tp30) cc_final: 0.8959 (tp30) REVERT: A 117 ARG cc_start: 0.9112 (mmt90) cc_final: 0.8772 (mmt180) REVERT: A 136 LYS cc_start: 0.9468 (tptt) cc_final: 0.9172 (ttpp) REVERT: A 147 GLN cc_start: 0.9145 (mt0) cc_final: 0.8700 (mt0) REVERT: A 158 ASN cc_start: 0.8984 (m-40) cc_final: 0.8751 (m110) REVERT: A 236 TYR cc_start: 0.7250 (t80) cc_final: 0.6996 (t80) REVERT: A 252 ASN cc_start: 0.8546 (t0) cc_final: 0.8088 (t0) REVERT: A 259 ASN cc_start: 0.8115 (p0) cc_final: 0.7627 (p0) REVERT: A 270 ASP cc_start: 0.8733 (m-30) cc_final: 0.7913 (t0) REVERT: A 345 LYS cc_start: 0.9278 (mttp) cc_final: 0.9043 (mttt) REVERT: A 370 ASN cc_start: 0.9403 (m110) cc_final: 0.9109 (m110) REVERT: A 375 LYS cc_start: 0.9061 (mmtm) cc_final: 0.8595 (mmtm) REVERT: A 402 GLU cc_start: 0.8760 (mp0) cc_final: 0.8536 (mp0) REVERT: A 407 ILE cc_start: 0.9042 (mt) cc_final: 0.8672 (mt) REVERT: A 455 ASN cc_start: 0.9019 (t0) cc_final: 0.8744 (t0) REVERT: A 456 LYS cc_start: 0.8916 (mmtm) cc_final: 0.8439 (mmtm) REVERT: A 466 MET cc_start: 0.9287 (ptt) cc_final: 0.9082 (ptp) REVERT: A 493 MET cc_start: 0.8938 (tmm) cc_final: 0.8698 (tmm) REVERT: A 494 MET cc_start: 0.9479 (mmp) cc_final: 0.8793 (mmm) REVERT: A 498 TYR cc_start: 0.9139 (m-80) cc_final: 0.8854 (m-80) REVERT: A 501 GLN cc_start: 0.9291 (tp40) cc_final: 0.8826 (tp-100) REVERT: A 571 TYR cc_start: 0.9017 (t80) cc_final: 0.8673 (t80) REVERT: A 602 GLU cc_start: 0.9020 (pm20) cc_final: 0.8515 (pm20) REVERT: A 615 MET cc_start: 0.8515 (mmp) cc_final: 0.8119 (mmm) REVERT: A 640 MET cc_start: 0.9368 (tpt) cc_final: 0.9096 (tpp) REVERT: A 650 GLN cc_start: 0.7033 (mm-40) cc_final: 0.6535 (mm-40) REVERT: B 8 LYS cc_start: 0.9470 (tttm) cc_final: 0.9141 (tppt) REVERT: B 12 LEU cc_start: 0.9587 (mt) cc_final: 0.9349 (mt) REVERT: B 17 MET cc_start: 0.8906 (mmm) cc_final: 0.8637 (mmm) REVERT: B 24 PHE cc_start: 0.8987 (m-80) cc_final: 0.8486 (m-80) REVERT: B 41 ILE cc_start: 0.9458 (mm) cc_final: 0.9217 (mm) REVERT: B 95 MET cc_start: 0.9249 (tpp) cc_final: 0.7686 (tpp) REVERT: B 98 PHE cc_start: 0.9604 (t80) cc_final: 0.8320 (t80) REVERT: B 99 LYS cc_start: 0.9686 (mmmt) cc_final: 0.8861 (mmmt) REVERT: B 184 ARG cc_start: 0.8753 (mmm160) cc_final: 0.7985 (mmm160) REVERT: B 187 ASP cc_start: 0.9032 (t0) cc_final: 0.8598 (t0) REVERT: B 200 SER cc_start: 0.7148 (m) cc_final: 0.6947 (p) REVERT: B 215 ASP cc_start: 0.8495 (m-30) cc_final: 0.8239 (m-30) REVERT: B 235 ARG cc_start: 0.7797 (mmm-85) cc_final: 0.7026 (mmt180) REVERT: B 288 PHE cc_start: 0.9359 (t80) cc_final: 0.9107 (t80) REVERT: B 307 TYR cc_start: 0.9207 (t80) cc_final: 0.8672 (t80) REVERT: B 326 PHE cc_start: 0.9175 (m-10) cc_final: 0.8564 (m-80) REVERT: B 333 LYS cc_start: 0.8443 (ttpt) cc_final: 0.8013 (ttmt) REVERT: B 357 TYR cc_start: 0.8364 (m-10) cc_final: 0.8028 (m-10) REVERT: B 379 SER cc_start: 0.8314 (t) cc_final: 0.7919 (t) REVERT: B 444 ASP cc_start: 0.9047 (t0) cc_final: 0.8714 (t0) REVERT: B 458 MET cc_start: 0.9122 (mmm) cc_final: 0.8828 (mmm) REVERT: B 459 LYS cc_start: 0.8821 (mttt) cc_final: 0.8333 (mtmt) REVERT: B 472 LEU cc_start: 0.9284 (mm) cc_final: 0.9037 (mm) REVERT: B 492 PHE cc_start: 0.9336 (m-80) cc_final: 0.8883 (m-80) REVERT: B 493 MET cc_start: 0.9192 (tmm) cc_final: 0.8837 (tmm) REVERT: B 494 MET cc_start: 0.9317 (mtp) cc_final: 0.8918 (mtp) REVERT: B 604 ARG cc_start: 0.9265 (tpp80) cc_final: 0.8860 (ttm-80) REVERT: B 645 GLN cc_start: 0.9079 (tp40) cc_final: 0.8878 (tp-100) REVERT: B 675 HIS cc_start: 0.8836 (t-90) cc_final: 0.8507 (t-90) REVERT: B 683 TYR cc_start: 0.8620 (t80) cc_final: 0.7934 (t80) REVERT: C 95 MET cc_start: 0.7993 (tmm) cc_final: 0.7233 (tmm) REVERT: C 96 MET cc_start: 0.8188 (mmm) cc_final: 0.7754 (mmm) REVERT: C 137 MET cc_start: 0.7675 (mpp) cc_final: 0.6836 (tpp) REVERT: C 151 ILE cc_start: 0.8213 (mm) cc_final: 0.7884 (tp) REVERT: C 227 PHE cc_start: 0.8626 (t80) cc_final: 0.8332 (t80) REVERT: C 259 PHE cc_start: 0.6570 (t80) cc_final: 0.5773 (t80) REVERT: C 276 TYR cc_start: 0.8289 (t80) cc_final: 0.7863 (t80) REVERT: D 169 TYR cc_start: 0.8425 (m-80) cc_final: 0.7697 (m-80) outliers start: 0 outliers final: 0 residues processed: 491 average time/residue: 0.1247 time to fit residues: 92.6527 Evaluate side-chains 408 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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: 5.9990 chunk 133 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 16 optimal weight: 0.4980 chunk 114 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 100 optimal weight: 0.0770 chunk 88 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 25 GLN ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 GLN B 447 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN D 69 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.131583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.093463 restraints weight = 49450.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.096569 restraints weight = 32294.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.098653 restraints weight = 22756.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.099787 restraints weight = 17507.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.101144 restraints weight = 14249.906| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.6850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16386 Z= 0.127 Angle : 0.615 9.062 22134 Z= 0.326 Chirality : 0.042 0.168 2360 Planarity : 0.003 0.051 2818 Dihedral : 8.555 133.403 2290 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.06 % Allowed : 0.87 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.19), residues: 1932 helix: 1.09 (0.15), residues: 1129 sheet: -0.66 (0.38), residues: 162 loop : 0.19 (0.25), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 161 TYR 0.034 0.001 TYR D 174 PHE 0.015 0.001 PHE B 326 TRP 0.007 0.001 TRP A 623 HIS 0.010 0.001 HIS A 675 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (16386) covalent geometry : angle 0.61521 / 0.33 (22134) hydrogen bonds : bond 0.03959 / 2.54 ( 871) hydrogen bonds : angle 5.07449 / 3.63 ( 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 520 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 519 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9405 (t0) cc_final: 0.9195 (t70) REVERT: A 65 GLU cc_start: 0.8037 (mp0) cc_final: 0.7558 (mp0) REVERT: A 67 GLU cc_start: 0.9155 (tp30) cc_final: 0.8734 (tp30) REVERT: A 71 LEU cc_start: 0.9428 (mt) cc_final: 0.9130 (mt) REVERT: A 117 ARG cc_start: 0.9150 (mmt90) cc_final: 0.8766 (mtp85) REVERT: A 144 MET cc_start: 0.9178 (mmm) cc_final: 0.8961 (tpp) REVERT: A 147 GLN cc_start: 0.8971 (mt0) cc_final: 0.8527 (mt0) REVERT: A 169 SER cc_start: 0.8106 (p) cc_final: 0.7704 (t) REVERT: A 202 ASN cc_start: 0.8421 (t0) cc_final: 0.8044 (t0) REVERT: A 205 LYS cc_start: 0.7308 (mttt) cc_final: 0.7101 (mttt) REVERT: A 259 ASN cc_start: 0.8106 (p0) cc_final: 0.7547 (p0) REVERT: A 270 ASP cc_start: 0.8629 (m-30) cc_final: 0.7937 (p0) REVERT: A 312 GLN cc_start: 0.8536 (tp-100) cc_final: 0.8008 (tp-100) REVERT: A 322 MET cc_start: 0.8295 (mmm) cc_final: 0.8055 (mmm) REVERT: A 345 LYS cc_start: 0.9296 (mttp) cc_final: 0.9048 (mttm) REVERT: A 349 LEU cc_start: 0.8616 (tp) cc_final: 0.8382 (tp) REVERT: A 400 GLU cc_start: 0.9440 (mm-30) cc_final: 0.9154 (tp30) REVERT: A 402 GLU cc_start: 0.8824 (mp0) cc_final: 0.8556 (mp0) REVERT: A 407 ILE cc_start: 0.8886 (mt) cc_final: 0.8540 (mt) REVERT: A 456 LYS cc_start: 0.8953 (mmtm) cc_final: 0.8583 (mmtm) REVERT: A 466 MET cc_start: 0.9215 (ptt) cc_final: 0.8944 (ptp) REVERT: A 490 THR cc_start: 0.9394 (m) cc_final: 0.8309 (p) REVERT: A 493 MET cc_start: 0.8849 (tmm) cc_final: 0.8643 (tmm) REVERT: A 494 MET cc_start: 0.9438 (mmp) cc_final: 0.8763 (mmm) REVERT: A 498 TYR cc_start: 0.9117 (m-80) cc_final: 0.8795 (m-80) REVERT: A 501 GLN cc_start: 0.9249 (tp40) cc_final: 0.8815 (tp-100) REVERT: A 598 MET cc_start: 0.8339 (tpp) cc_final: 0.8120 (mmm) REVERT: A 602 GLU cc_start: 0.8881 (pm20) cc_final: 0.8680 (pm20) REVERT: A 640 MET cc_start: 0.9307 (tpt) cc_final: 0.9065 (tpp) REVERT: B 8 LYS cc_start: 0.9434 (tttm) cc_final: 0.9128 (tppt) REVERT: B 12 LEU cc_start: 0.9593 (mt) cc_final: 0.9352 (mt) REVERT: B 17 MET cc_start: 0.8935 (mmm) cc_final: 0.8702 (mmt) REVERT: B 24 PHE cc_start: 0.8784 (m-80) cc_final: 0.8315 (m-80) REVERT: B 36 TYR cc_start: 0.9002 (t80) cc_final: 0.8575 (t80) REVERT: B 41 ILE cc_start: 0.9378 (mm) cc_final: 0.8544 (mm) REVERT: B 67 GLU cc_start: 0.8875 (mp0) cc_final: 0.8658 (mp0) REVERT: B 95 MET cc_start: 0.8993 (tpp) cc_final: 0.7754 (tpp) REVERT: B 98 PHE cc_start: 0.9567 (t80) cc_final: 0.8907 (t80) REVERT: B 99 LYS cc_start: 0.9687 (mmmt) cc_final: 0.8932 (mmmt) REVERT: B 107 LYS cc_start: 0.9096 (mppt) cc_final: 0.8813 (mptt) REVERT: B 240 MET cc_start: 0.8593 (mpp) cc_final: 0.8020 (mpp) REVERT: B 256 ARG cc_start: 0.7981 (tmt-80) cc_final: 0.7441 (ttp80) REVERT: B 259 ASN cc_start: 0.8717 (m-40) cc_final: 0.8399 (p0) REVERT: B 307 TYR cc_start: 0.9147 (t80) cc_final: 0.8599 (t80) REVERT: B 326 PHE cc_start: 0.9138 (m-10) cc_final: 0.8505 (m-80) REVERT: B 333 LYS cc_start: 0.8559 (ttpt) cc_final: 0.8246 (ttmt) REVERT: B 357 TYR cc_start: 0.8297 (m-10) cc_final: 0.7957 (m-10) REVERT: B 359 MET cc_start: 0.7423 (tmm) cc_final: 0.7128 (tmm) REVERT: B 379 SER cc_start: 0.8205 (t) cc_final: 0.7866 (t) REVERT: B 444 ASP cc_start: 0.8955 (t0) cc_final: 0.8382 (t0) REVERT: B 446 ARG cc_start: 0.8845 (mpp80) cc_final: 0.8529 (ptp90) REVERT: B 447 ASN cc_start: 0.8478 (t160) cc_final: 0.8194 (t0) REVERT: B 458 MET cc_start: 0.9354 (mmm) cc_final: 0.8773 (mmm) REVERT: B 459 LYS cc_start: 0.8863 (mttt) cc_final: 0.8485 (mtmt) REVERT: B 472 LEU cc_start: 0.9300 (mm) cc_final: 0.8945 (mt) REVERT: B 492 PHE cc_start: 0.9240 (m-80) cc_final: 0.8595 (m-80) REVERT: B 493 MET cc_start: 0.9126 (tmm) cc_final: 0.8252 (tmm) REVERT: B 494 MET cc_start: 0.9285 (mtp) cc_final: 0.8867 (mtp) REVERT: B 558 TRP cc_start: 0.8113 (m100) cc_final: 0.7519 (m100) REVERT: B 574 TYR cc_start: 0.7739 (m-80) cc_final: 0.7457 (m-80) REVERT: B 675 HIS cc_start: 0.8744 (t-90) cc_final: 0.8448 (t-90) REVERT: B 683 TYR cc_start: 0.8615 (t80) cc_final: 0.7909 (t80) REVERT: C 95 MET cc_start: 0.7492 (tmm) cc_final: 0.6798 (tmm) REVERT: C 96 MET cc_start: 0.8098 (mmm) cc_final: 0.7373 (mmm) REVERT: C 110 MET cc_start: 0.7764 (mmp) cc_final: 0.7562 (mmp) REVERT: C 129 LYS cc_start: 0.8663 (tmtt) cc_final: 0.8447 (tmtt) REVERT: C 137 MET cc_start: 0.7760 (mpp) cc_final: 0.6746 (tpp) REVERT: C 151 ILE cc_start: 0.8329 (mm) cc_final: 0.8079 (mm) REVERT: C 227 PHE cc_start: 0.8529 (t80) cc_final: 0.8310 (t80) REVERT: C 259 PHE cc_start: 0.6396 (t80) cc_final: 0.5606 (t80) REVERT: C 276 TYR cc_start: 0.8219 (t80) cc_final: 0.7744 (t80) REVERT: D 74 MET cc_start: 0.7084 (ppp) cc_final: 0.5971 (ppp) REVERT: D 169 TYR cc_start: 0.8475 (m-80) cc_final: 0.7819 (m-80) REVERT: D 201 HIS cc_start: 0.9196 (m90) cc_final: 0.8824 (m90) outliers start: 1 outliers final: 0 residues processed: 520 average time/residue: 0.1246 time to fit residues: 97.9735 Evaluate side-chains 422 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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: 3.9990 chunk 62 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 189 optimal weight: 8.9990 chunk 181 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 ASN 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 = 0.3878 r_free = 0.3878 target = 0.128987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.090621 restraints weight = 51056.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.093563 restraints weight = 32332.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.095468 restraints weight = 22885.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.096898 restraints weight = 17734.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.097331 restraints weight = 14533.613| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7047 moved from start: 0.7063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16386 Z= 0.159 Angle : 0.661 15.663 22134 Z= 0.349 Chirality : 0.044 0.177 2360 Planarity : 0.004 0.051 2818 Dihedral : 8.641 135.180 2290 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.19), residues: 1932 helix: 1.04 (0.15), residues: 1126 sheet: -0.46 (0.43), residues: 128 loop : 0.09 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 196 TYR 0.036 0.002 TYR D 174 PHE 0.028 0.002 PHE A 81 TRP 0.010 0.001 TRP B 558 HIS 0.023 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.16 (16386) covalent geometry : angle 0.66148 / 0.35 (22134) hydrogen bonds : bond 0.04131 / 2.63 ( 871) hydrogen bonds : angle 5.16086 / 3.70 ( 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 491 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 491 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8013 (mp0) cc_final: 0.7547 (mp0) REVERT: A 67 GLU cc_start: 0.9259 (tp30) cc_final: 0.8901 (tp30) REVERT: A 71 LEU cc_start: 0.9408 (mt) cc_final: 0.9108 (mt) REVERT: A 117 ARG cc_start: 0.9184 (mmt90) cc_final: 0.8869 (mtp85) REVERT: A 147 GLN cc_start: 0.9062 (mt0) cc_final: 0.8851 (mt0) REVERT: A 158 ASN cc_start: 0.9012 (m110) cc_final: 0.8744 (m110) REVERT: A 169 SER cc_start: 0.8172 (p) cc_final: 0.7823 (t) REVERT: A 202 ASN cc_start: 0.8576 (t0) cc_final: 0.8215 (t0) REVERT: A 270 ASP cc_start: 0.8657 (m-30) cc_final: 0.8007 (t0) REVERT: A 322 MET cc_start: 0.8385 (mmm) cc_final: 0.8171 (mmm) REVERT: A 345 LYS cc_start: 0.9299 (mttp) cc_final: 0.9092 (mttt) REVERT: A 370 ASN cc_start: 0.9314 (m-40) cc_final: 0.9057 (m110) REVERT: A 400 GLU cc_start: 0.9464 (mm-30) cc_final: 0.9160 (tp30) REVERT: A 402 GLU cc_start: 0.8877 (mp0) cc_final: 0.8609 (mp0) REVERT: A 407 ILE cc_start: 0.8864 (mt) cc_final: 0.8654 (mt) REVERT: A 456 LYS cc_start: 0.8940 (mmtm) cc_final: 0.8481 (mmtm) REVERT: A 466 MET cc_start: 0.9205 (ptt) cc_final: 0.8964 (ptp) REVERT: A 468 LEU cc_start: 0.9438 (tp) cc_final: 0.9138 (tp) REVERT: A 494 MET cc_start: 0.9483 (mmp) cc_final: 0.8790 (mmm) REVERT: A 498 TYR cc_start: 0.9168 (m-80) cc_final: 0.8826 (m-80) REVERT: A 501 GLN cc_start: 0.9307 (tp40) cc_final: 0.8895 (tp-100) REVERT: A 571 TYR cc_start: 0.8961 (t80) cc_final: 0.8738 (t80) REVERT: A 595 MET cc_start: 0.7949 (ttt) cc_final: 0.7673 (ttt) REVERT: A 597 ILE cc_start: 0.8758 (pt) cc_final: 0.8503 (pt) REVERT: A 598 MET cc_start: 0.8359 (tpp) cc_final: 0.8055 (mmm) REVERT: A 602 GLU cc_start: 0.9015 (pm20) cc_final: 0.8415 (pm20) REVERT: A 611 THR cc_start: 0.8637 (t) cc_final: 0.8042 (t) REVERT: A 615 MET cc_start: 0.8300 (mmp) cc_final: 0.7899 (mmp) REVERT: A 650 GLN cc_start: 0.7062 (mm110) cc_final: 0.6821 (mm-40) REVERT: B 8 LYS cc_start: 0.9478 (tttm) cc_final: 0.9169 (tppt) REVERT: B 12 LEU cc_start: 0.9585 (mt) cc_final: 0.9369 (mt) REVERT: B 17 MET cc_start: 0.8956 (mmm) cc_final: 0.8256 (mmm) REVERT: B 24 PHE cc_start: 0.8912 (m-80) cc_final: 0.8648 (m-80) REVERT: B 36 TYR cc_start: 0.9141 (t80) cc_final: 0.8693 (t80) REVERT: B 64 TYR cc_start: 0.8638 (m-10) cc_final: 0.8424 (m-80) REVERT: B 95 MET cc_start: 0.9054 (tpp) cc_final: 0.7905 (tpp) REVERT: B 98 PHE cc_start: 0.9609 (t80) cc_final: 0.8941 (t80) REVERT: B 99 LYS cc_start: 0.9650 (mmmt) cc_final: 0.8943 (mmmt) REVERT: B 116 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8387 (mm-30) REVERT: B 256 ARG cc_start: 0.8303 (tmt-80) cc_final: 0.7629 (ttp80) REVERT: B 259 ASN cc_start: 0.8709 (m-40) cc_final: 0.8438 (p0) REVERT: B 288 PHE cc_start: 0.9454 (t80) cc_final: 0.9144 (t80) REVERT: B 307 TYR cc_start: 0.9193 (t80) cc_final: 0.8661 (t80) REVERT: B 333 LYS cc_start: 0.8497 (ttpt) cc_final: 0.8152 (ttpt) REVERT: B 357 TYR cc_start: 0.8262 (m-10) cc_final: 0.7823 (m-10) REVERT: B 359 MET cc_start: 0.7450 (tmm) cc_final: 0.7075 (tmm) REVERT: B 379 SER cc_start: 0.7977 (t) cc_final: 0.7602 (t) REVERT: B 458 MET cc_start: 0.9403 (mmm) cc_final: 0.8925 (mmm) REVERT: B 459 LYS cc_start: 0.8795 (mttt) cc_final: 0.8244 (mtmm) REVERT: B 492 PHE cc_start: 0.9330 (m-80) cc_final: 0.8750 (m-80) REVERT: B 493 MET cc_start: 0.9289 (tmm) cc_final: 0.8908 (tmm) REVERT: B 494 MET cc_start: 0.9371 (mtp) cc_final: 0.8799 (mtp) REVERT: B 584 ILE cc_start: 0.8792 (mt) cc_final: 0.8482 (mt) REVERT: B 615 MET cc_start: 0.8684 (mmp) cc_final: 0.8467 (mmm) REVERT: B 632 MET cc_start: 0.8355 (mtt) cc_final: 0.8047 (mtt) REVERT: B 634 MET cc_start: 0.9372 (mmp) cc_final: 0.9025 (mmp) REVERT: B 645 GLN cc_start: 0.9180 (tp40) cc_final: 0.8923 (tp-100) REVERT: B 675 HIS cc_start: 0.8875 (t-90) cc_final: 0.8336 (t70) REVERT: B 683 TYR cc_start: 0.8513 (t80) cc_final: 0.7929 (t80) REVERT: C 95 MET cc_start: 0.7713 (tmm) cc_final: 0.6763 (tmm) REVERT: C 96 MET cc_start: 0.8039 (mmm) cc_final: 0.7401 (mmm) REVERT: C 129 LYS cc_start: 0.8705 (tmtt) cc_final: 0.8497 (tmtt) REVERT: C 137 MET cc_start: 0.7816 (mpp) cc_final: 0.6848 (tpp) REVERT: C 151 ILE cc_start: 0.8236 (mm) cc_final: 0.7925 (tp) REVERT: C 259 PHE cc_start: 0.6531 (t80) cc_final: 0.5761 (t80) REVERT: C 276 TYR cc_start: 0.8315 (t80) cc_final: 0.8018 (t80) REVERT: D 74 MET cc_start: 0.7101 (ppp) cc_final: 0.5879 (ppp) REVERT: D 96 MET cc_start: 0.3946 (tpt) cc_final: 0.3692 (tpt) REVERT: D 137 MET cc_start: 0.0112 (mpp) cc_final: -0.0213 (ptp) REVERT: D 169 TYR cc_start: 0.8529 (m-80) cc_final: 0.7899 (m-80) REVERT: D 201 HIS cc_start: 0.9024 (m90) cc_final: 0.8791 (m90) outliers start: 0 outliers final: 0 residues processed: 491 average time/residue: 0.1261 time to fit residues: 93.1701 Evaluate side-chains 400 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 400 time to evaluate : 0.598 ------------------------------------------------------------------------------- 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: 3.9990 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 148 optimal weight: 20.0000 chunk 125 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 496 ASN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3866 r_free = 0.3866 target = 0.127564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.090002 restraints weight = 50566.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.092991 restraints weight = 32450.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.094150 restraints weight = 23134.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.096054 restraints weight = 18599.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.096954 restraints weight = 15312.132| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.7249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16386 Z= 0.162 Angle : 0.659 10.244 22134 Z= 0.348 Chirality : 0.044 0.182 2360 Planarity : 0.004 0.053 2818 Dihedral : 8.561 136.065 2290 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 0.73 (0.19), residues: 1932 helix: 0.93 (0.15), residues: 1141 sheet: -0.40 (0.44), residues: 128 loop : 0.10 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 161 TYR 0.033 0.002 TYR D 174 PHE 0.019 0.002 PHE B 254 TRP 0.011 0.001 TRP B 558 HIS 0.020 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (16386) covalent geometry : angle 0.65907 / 0.35 (22134) hydrogen bonds : bond 0.04131 / 2.61 ( 871) hydrogen bonds : angle 5.22263 / 3.74 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3188.70 seconds wall clock time: 56 minutes 14.35 seconds (3374.35 seconds total)