Starting phenix.real_space_refine on Thu Aug 6 15:11:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byx_45047/08_2026/9byx_45047_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byx_45047/08_2026/9byx_45047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9byx_45047/08_2026/9byx_45047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byx_45047/08_2026/9byx_45047.map" model { file = "/net/cci-nas-00/data/ceres_data/9byx_45047/08_2026/9byx_45047_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byx_45047/08_2026/9byx_45047_neut.cif" } resolution = 3.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.39, per 1000 atoms: 0.21 Number of scatterers: 16038 At special positions: 0 Unit cell: (95.598, 132.21, 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: 1.23 Conformation dependent library (CDL) restraints added in 691.0 milliseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 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: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.985A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.954A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.664A 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: 3.949A 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: 5.393A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.627A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.580A 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: 3.878A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.027A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.068A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.514A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.668A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A 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: 4.876A 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: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.478A 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: 6.709A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.228A 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: 7.906A 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: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 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: 2.94 Time building geometry restraints manager: 1.70 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: 4824 1.34 - 1.46: 3048 1.46 - 1.58: 8332 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 4.83e+01 bond pdb=" O3B TTP A 803 " pdb=" PG TTP A 803 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.25e-02 6.40e+03 2.38e+01 bond pdb=" O3A TTP A 803 " pdb=" PB TTP A 803 " ideal model delta sigma weight residual 1.675 1.606 0.069 2.00e-02 2.50e+03 1.18e+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: 21520 2.09 - 4.18: 532 4.18 - 6.27: 65 6.27 - 8.37: 8 8.37 - 10.46: 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 110.54 116.61 -6.07 1.36e+00 5.41e-01 1.99e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.17 -4.46 1.15e+00 7.56e-01 1.50e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.89 -4.39 1.23e+00 6.61e-01 1.27e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.71 -4.00 1.15e+00 7.56e-01 1.21e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.52 3.67 1.06e+00 8.90e-01 1.20e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.05: 9091 25.05 - 50.10: 652 50.10 - 75.15: 127 75.15 - 100.20: 26 100.20 - 125.25: 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 -98.23 125.25 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" O4' GDP B 804 " pdb=" C1' GDP B 804 " pdb=" N9 GDP B 804 " pdb=" C8 GDP B 804 " ideal model delta sinusoidal sigma weight residual 27.02 -95.66 122.68 1 2.00e+01 2.50e-03 3.70e+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 -134.27 12.27 0 2.50e+00 1.60e-01 2.41e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2138 0.093 - 0.186: 187 0.186 - 0.279: 30 0.279 - 0.372: 3 0.372 - 0.464: 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 5.39e+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 4.64e+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 2.96e+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 4.14e-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 1.11e-02 2.16e+00 pdb=" CG PHE D 92 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 169 " 0.017 2.00e-02 2.50e+03 9.81e-03 1.93e+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: 11558 3.11 - 3.70: 27040 3.70 - 4.30: 41539 4.30 - 4.90: 65436 Nonbonded interactions: 145702 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 145697 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: 1.310 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.160 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6506 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 : 0.787 10.457 22134 Z= 0.471 Chirality : 0.058 0.464 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.658 125.250 6202 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.28 % Allowed : 15.27 % Favored : 83.45 % 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 C 169 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 0.78738 / 0.47 (22134) hydrogen bonds : bond 0.15421 / 9.51 ( 871) hydrogen bonds : angle 6.51788 / 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 834 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 812 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8331 (t0) cc_final: 0.8127 (t70) REVERT: A 68 PHE cc_start: 0.8345 (p90) cc_final: 0.8028 (p90) REVERT: A 76 ASP cc_start: 0.7983 (m-30) cc_final: 0.7597 (m-30) REVERT: A 106 LEU cc_start: 0.8438 (tp) cc_final: 0.8029 (tp) REVERT: A 147 GLN cc_start: 0.8238 (mt0) cc_final: 0.8029 (mt0) REVERT: A 186 ILE cc_start: 0.9463 (mt) cc_final: 0.9108 (mt) REVERT: A 188 ILE cc_start: 0.8860 (mt) cc_final: 0.8631 (mt) REVERT: A 218 ASN cc_start: 0.7556 (t0) cc_final: 0.7313 (t0) REVERT: A 227 MET cc_start: 0.8028 (mtp) cc_final: 0.7605 (mtp) REVERT: A 284 ILE cc_start: 0.8838 (mt) cc_final: 0.8593 (mt) REVERT: A 345 LYS cc_start: 0.8439 (tttt) cc_final: 0.8018 (tttt) REVERT: A 362 ASP cc_start: 0.6722 (m-30) cc_final: 0.5937 (m-30) REVERT: A 367 VAL cc_start: 0.8979 (m) cc_final: 0.8743 (t) REVERT: A 405 LEU cc_start: 0.8675 (mt) cc_final: 0.8433 (mt) REVERT: A 468 LEU cc_start: 0.9021 (tp) cc_final: 0.8799 (tp) REVERT: A 598 MET cc_start: 0.7516 (mtm) cc_final: 0.7306 (mtp) REVERT: A 624 PHE cc_start: 0.6941 (t80) cc_final: 0.6583 (t80) REVERT: A 645 GLN cc_start: 0.7642 (tp40) cc_final: 0.7292 (tp40) REVERT: B 186 ILE cc_start: 0.9221 (mt) cc_final: 0.8997 (mt) REVERT: B 191 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8476 (mm-40) REVERT: B 232 ASN cc_start: 0.7705 (OUTLIER) cc_final: 0.7242 (m-40) REVERT: B 253 ILE cc_start: 0.8665 (tt) cc_final: 0.8421 (tt) REVERT: B 288 PHE cc_start: 0.8107 (t80) cc_final: 0.7847 (t80) REVERT: B 355 TYR cc_start: 0.8184 (m-80) cc_final: 0.7817 (m-10) REVERT: B 358 ILE cc_start: 0.9180 (mm) cc_final: 0.8900 (mm) REVERT: B 425 ILE cc_start: 0.8694 (mt) cc_final: 0.8367 (mt) REVERT: B 468 LEU cc_start: 0.9158 (tp) cc_final: 0.8853 (tp) REVERT: B 494 MET cc_start: 0.7656 (mtp) cc_final: 0.7443 (mtp) REVERT: B 522 TYR cc_start: 0.8262 (m-80) cc_final: 0.7988 (m-80) REVERT: B 626 TYR cc_start: 0.7100 (m-80) cc_final: 0.6872 (m-80) REVERT: B 658 LEU cc_start: 0.8613 (mt) cc_final: 0.8288 (mt) REVERT: B 686 ARG cc_start: 0.7706 (mtp85) cc_final: 0.7041 (mtp180) REVERT: C 101 HIS cc_start: 0.4240 (m170) cc_final: 0.3777 (m-70) REVERT: C 131 LEU cc_start: 0.5337 (OUTLIER) cc_final: 0.4946 (tp) REVERT: C 163 LEU cc_start: 0.5588 (tt) cc_final: 0.4993 (tt) REVERT: C 213 TYR cc_start: 0.2249 (t80) cc_final: 0.1797 (t80) outliers start: 22 outliers final: 5 residues processed: 823 average time/residue: 0.1280 time to fit residues: 154.4532 Evaluate side-chains 554 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 547 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 126 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 GLN A 232 ASN A 239 GLN A 320 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 GLN A 650 GLN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN B 338 ASN B 390 GLN B 410 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.158435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.113758 restraints weight = 32173.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.117891 restraints weight = 15863.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.120629 restraints weight = 9581.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.121873 restraints weight = 6724.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.123057 restraints weight = 5464.010| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3494 r_free = 0.3494 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3494 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16386 Z= 0.227 Angle : 0.676 9.214 22134 Z= 0.354 Chirality : 0.045 0.185 2360 Planarity : 0.004 0.039 2818 Dihedral : 9.736 130.692 2303 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.20 % Allowed : 18.12 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.19), residues: 1932 helix: 1.43 (0.15), residues: 1133 sheet: 0.36 (0.43), residues: 130 loop : 0.53 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 256 TYR 0.023 0.002 TYR C 169 PHE 0.036 0.002 PHE C 168 TRP 0.015 0.002 TRP D 44 HIS 0.006 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.23 (16386) covalent geometry : angle 0.67557 / 0.35 (22134) hydrogen bonds : bond 0.04712 / 2.97 ( 871) hydrogen bonds : angle 5.10367 / 3.64 ( 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 628 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 556 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASP cc_start: 0.8930 (m-30) cc_final: 0.8517 (m-30) REVERT: A 116 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7789 (mt-10) REVERT: A 138 LYS cc_start: 0.8965 (mtpt) cc_final: 0.8634 (mtpp) REVERT: A 147 GLN cc_start: 0.9321 (mt0) cc_final: 0.8990 (mt0) REVERT: A 218 ASN cc_start: 0.8782 (t0) cc_final: 0.8239 (t0) REVERT: A 221 LYS cc_start: 0.8653 (mmtp) cc_final: 0.8248 (mmtp) REVERT: A 232 ASN cc_start: 0.9374 (OUTLIER) cc_final: 0.9159 (m-40) REVERT: A 259 ASN cc_start: 0.8928 (m-40) cc_final: 0.8661 (m110) REVERT: A 263 ASP cc_start: 0.8305 (m-30) cc_final: 0.8017 (m-30) REVERT: A 362 ASP cc_start: 0.7986 (m-30) cc_final: 0.6935 (m-30) REVERT: A 381 LEU cc_start: 0.8934 (tp) cc_final: 0.8381 (pt) REVERT: A 384 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7649 (pm20) REVERT: A 415 ASN cc_start: 0.8916 (t0) cc_final: 0.8572 (t0) REVERT: A 446 ARG cc_start: 0.7597 (mmm160) cc_final: 0.7309 (mmm160) REVERT: A 468 LEU cc_start: 0.9385 (tp) cc_final: 0.9145 (tp) REVERT: A 493 MET cc_start: 0.9016 (tmm) cc_final: 0.8772 (tmm) REVERT: A 494 MET cc_start: 0.8812 (mtp) cc_final: 0.8539 (mtp) REVERT: A 570 MET cc_start: 0.8900 (mtp) cc_final: 0.8697 (mtp) REVERT: A 586 TYR cc_start: 0.8315 (m-80) cc_final: 0.8075 (m-80) REVERT: A 640 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8204 (tpp) REVERT: B 15 GLU cc_start: 0.8871 (tp30) cc_final: 0.8670 (tp30) REVERT: B 147 GLN cc_start: 0.9216 (mt0) cc_final: 0.8876 (mt0) REVERT: B 184 ARG cc_start: 0.9230 (tpp-160) cc_final: 0.8983 (tpp-160) REVERT: B 232 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8518 (m-40) REVERT: B 252 ASN cc_start: 0.8954 (t0) cc_final: 0.8702 (t0) REVERT: B 267 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8677 (mm) REVERT: B 288 PHE cc_start: 0.9243 (t80) cc_final: 0.8984 (t80) REVERT: B 425 ILE cc_start: 0.9391 (mt) cc_final: 0.9180 (mt) REVERT: B 479 TYR cc_start: 0.8652 (t80) cc_final: 0.8199 (t80) REVERT: B 494 MET cc_start: 0.9064 (mtp) cc_final: 0.8654 (mtp) REVERT: B 550 MET cc_start: 0.7789 (mtm) cc_final: 0.7549 (mtm) REVERT: B 571 TYR cc_start: 0.8488 (t80) cc_final: 0.8227 (t80) REVERT: B 586 TYR cc_start: 0.8376 (m-80) cc_final: 0.7745 (m-80) REVERT: B 598 MET cc_start: 0.7927 (mtm) cc_final: 0.7600 (mtp) REVERT: B 604 ARG cc_start: 0.9011 (tpp80) cc_final: 0.8581 (mmt-90) REVERT: B 626 TYR cc_start: 0.8261 (m-80) cc_final: 0.7914 (m-80) REVERT: B 686 ARG cc_start: 0.8565 (mtp85) cc_final: 0.8355 (mtp-110) REVERT: C 41 LEU cc_start: 0.6807 (pp) cc_final: 0.6391 (mm) REVERT: C 56 MET cc_start: 0.4887 (ptt) cc_final: 0.4640 (ptt) REVERT: C 93 MET cc_start: 0.2047 (mtp) cc_final: 0.1726 (mtp) REVERT: C 141 LEU cc_start: 0.8741 (mt) cc_final: 0.8377 (pp) REVERT: C 154 PHE cc_start: 0.9141 (t80) cc_final: 0.8927 (t80) REVERT: C 162 TYR cc_start: 0.9223 (m-10) cc_final: 0.8736 (m-80) REVERT: C 168 PHE cc_start: 0.8794 (m-80) cc_final: 0.8576 (m-80) REVERT: C 237 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8236 (pp20) REVERT: C 242 TYR cc_start: 0.9241 (t80) cc_final: 0.8609 (t80) REVERT: D 95 MET cc_start: 0.8283 (ptm) cc_final: 0.7985 (ptm) REVERT: D 96 MET cc_start: 0.7245 (mmm) cc_final: 0.7018 (mmm) REVERT: D 138 ILE cc_start: 0.9179 (mm) cc_final: 0.8958 (tp) REVERT: D 234 GLN cc_start: 0.7898 (pt0) cc_final: 0.7659 (tm-30) outliers start: 72 outliers final: 35 residues processed: 591 average time/residue: 0.1221 time to fit residues: 109.8047 Evaluate side-chains 514 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 474 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 6.9990 chunk 131 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 182 optimal weight: 6.9990 chunk 159 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 ASN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 467 ASN B 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN D 28 GLN D 71 ASN D 84 HIS D 201 HIS D 210 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.156078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.112501 restraints weight = 33092.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.116515 restraints weight = 16400.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.119019 restraints weight = 9909.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.120882 restraints weight = 6973.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.122107 restraints weight = 5342.286| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.3509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16386 Z= 0.170 Angle : 0.614 9.211 22134 Z= 0.324 Chirality : 0.044 0.161 2360 Planarity : 0.003 0.042 2818 Dihedral : 9.043 131.455 2295 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.32 % Allowed : 19.99 % Favored : 76.69 % 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: 1.36 (0.19), residues: 1932 helix: 1.39 (0.15), residues: 1137 sheet: 0.10 (0.42), residues: 134 loop : 0.40 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 686 TYR 0.029 0.002 TYR C 55 PHE 0.037 0.002 PHE C 168 TRP 0.022 0.002 TRP D 44 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (16386) covalent geometry : angle 0.61439 / 0.32 (22134) hydrogen bonds : bond 0.04239 / 2.70 ( 871) hydrogen bonds : angle 4.99811 / 3.57 ( 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 597 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 540 time to evaluate : 0.647 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: A 27 ASP cc_start: 0.9006 (p0) cc_final: 0.8628 (p0) REVERT: A 76 ASP cc_start: 0.8970 (m-30) cc_final: 0.8671 (m-30) REVERT: A 147 GLN cc_start: 0.9212 (mt0) cc_final: 0.8969 (mt0) REVERT: A 218 ASN cc_start: 0.8750 (t0) cc_final: 0.8247 (t0) REVERT: A 221 LYS cc_start: 0.8676 (mmtp) cc_final: 0.8466 (mmtp) REVERT: A 263 ASP cc_start: 0.8387 (m-30) cc_final: 0.7989 (m-30) REVERT: A 322 MET cc_start: 0.8405 (tpp) cc_final: 0.7593 (tpp) REVERT: A 362 ASP cc_start: 0.7911 (m-30) cc_final: 0.7405 (m-30) REVERT: A 381 LEU cc_start: 0.8951 (tp) cc_final: 0.8416 (pt) REVERT: A 384 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7340 (pm20) REVERT: A 409 CYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8405 (p) REVERT: A 411 LEU cc_start: 0.8072 (mp) cc_final: 0.7806 (mt) REVERT: A 453 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8260 (ttt-90) REVERT: A 468 LEU cc_start: 0.9374 (tp) cc_final: 0.9152 (tp) REVERT: A 479 TYR cc_start: 0.8831 (t80) cc_final: 0.8416 (t80) REVERT: A 493 MET cc_start: 0.9001 (tmm) cc_final: 0.8702 (tmm) REVERT: A 498 TYR cc_start: 0.9096 (m-80) cc_final: 0.8713 (m-80) REVERT: A 505 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8216 (mt-10) REVERT: A 550 MET cc_start: 0.6866 (mtt) cc_final: 0.6026 (mtt) REVERT: A 570 MET cc_start: 0.8918 (mtp) cc_final: 0.8672 (mtp) REVERT: A 640 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8086 (tpp) REVERT: B 15 GLU cc_start: 0.8876 (tp30) cc_final: 0.8623 (tp30) REVERT: B 108 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8221 (p) REVERT: B 119 GLU cc_start: 0.8906 (mp0) cc_final: 0.8279 (mp0) REVERT: B 147 GLN cc_start: 0.9110 (mt0) cc_final: 0.8857 (mt0) REVERT: B 232 ASN cc_start: 0.8698 (OUTLIER) cc_final: 0.8461 (m-40) REVERT: B 267 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8870 (mm) REVERT: B 321 GLU cc_start: 0.8435 (pp20) cc_final: 0.8207 (pp20) REVERT: B 348 MET cc_start: 0.8843 (ptt) cc_final: 0.8522 (ptt) REVERT: B 350 ARG cc_start: 0.8245 (mtp85) cc_final: 0.7826 (mtp85) REVERT: B 425 ILE cc_start: 0.9401 (mt) cc_final: 0.9143 (mt) REVERT: B 447 ASN cc_start: 0.8520 (m-40) cc_final: 0.8318 (m-40) REVERT: B 494 MET cc_start: 0.8975 (mtp) cc_final: 0.8551 (mtp) REVERT: B 550 MET cc_start: 0.7737 (mtm) cc_final: 0.7503 (mtm) REVERT: B 586 TYR cc_start: 0.8367 (m-80) cc_final: 0.7728 (m-80) REVERT: B 588 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8646 (tp40) REVERT: B 604 ARG cc_start: 0.8929 (tpp80) cc_final: 0.8547 (mmt-90) REVERT: B 627 LYS cc_start: 0.8884 (tttt) cc_final: 0.8536 (tttp) REVERT: B 686 ARG cc_start: 0.8606 (mtp85) cc_final: 0.8389 (mtp-110) REVERT: C 41 LEU cc_start: 0.6953 (pp) cc_final: 0.6500 (mm) REVERT: C 141 LEU cc_start: 0.8918 (mt) cc_final: 0.8648 (pp) REVERT: C 162 TYR cc_start: 0.9173 (m-10) cc_final: 0.8817 (m-80) REVERT: C 168 PHE cc_start: 0.9181 (m-80) cc_final: 0.8545 (m-80) REVERT: C 242 TYR cc_start: 0.9270 (t80) cc_final: 0.8746 (t80) REVERT: D 138 ILE cc_start: 0.9128 (mm) cc_final: 0.8917 (tp) outliers start: 57 outliers final: 36 residues processed: 568 average time/residue: 0.1229 time to fit residues: 106.4507 Evaluate side-chains 503 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 460 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 148 GLU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 242 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 168 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 127 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 chunk 191 optimal weight: 10.0000 chunk 159 optimal weight: 20.0000 chunk 182 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN B 361 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN D 283 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.151081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.108555 restraints weight = 32878.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.112265 restraints weight = 15975.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.114584 restraints weight = 9633.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.116306 restraints weight = 6752.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.117350 restraints weight = 5143.141| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3433 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3433 r_free = 0.3433 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3433 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16386 Z= 0.207 Angle : 0.638 11.557 22134 Z= 0.335 Chirality : 0.045 0.209 2360 Planarity : 0.003 0.033 2818 Dihedral : 8.727 133.924 2295 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.67 % Allowed : 21.33 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.19), residues: 1932 helix: 1.28 (0.15), residues: 1131 sheet: 0.59 (0.46), residues: 100 loop : 0.19 (0.23), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 686 TYR 0.022 0.002 TYR C 55 PHE 0.034 0.002 PHE C 166 TRP 0.021 0.002 TRP D 44 HIS 0.009 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.21 (16386) covalent geometry : angle 0.63822 / 0.34 (22134) hydrogen bonds : bond 0.04099 / 2.62 ( 871) hydrogen bonds : angle 5.01393 / 3.58 ( 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 548 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 485 time to evaluate : 0.647 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 27 ASP cc_start: 0.9000 (p0) cc_final: 0.8526 (p0) REVERT: A 69 LEU cc_start: 0.9391 (mt) cc_final: 0.9057 (pp) REVERT: A 76 ASP cc_start: 0.9007 (m-30) cc_final: 0.8752 (m-30) REVERT: A 116 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7955 (mt-10) REVERT: A 147 GLN cc_start: 0.9223 (mt0) cc_final: 0.8970 (mt0) REVERT: A 218 ASN cc_start: 0.8748 (t0) cc_final: 0.8223 (t0) REVERT: A 221 LYS cc_start: 0.8873 (mmtp) cc_final: 0.8536 (mmtp) REVERT: A 263 ASP cc_start: 0.8364 (m-30) cc_final: 0.7964 (m-30) REVERT: A 286 ASP cc_start: 0.7773 (m-30) cc_final: 0.7547 (m-30) REVERT: A 346 LEU cc_start: 0.9444 (mp) cc_final: 0.9234 (mp) REVERT: A 362 ASP cc_start: 0.7905 (m-30) cc_final: 0.7477 (m-30) REVERT: A 375 LYS cc_start: 0.8856 (mttt) cc_final: 0.8650 (mtmm) REVERT: A 381 LEU cc_start: 0.8954 (tp) cc_final: 0.8402 (pt) REVERT: A 384 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7498 (pm20) REVERT: A 415 ASN cc_start: 0.8937 (t0) cc_final: 0.8199 (t0) REVERT: A 418 ASN cc_start: 0.9150 (m-40) cc_final: 0.8646 (m-40) REVERT: A 453 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8249 (ttt-90) REVERT: A 468 LEU cc_start: 0.9385 (tp) cc_final: 0.9176 (tp) REVERT: A 479 TYR cc_start: 0.8943 (t80) cc_final: 0.8572 (t80) REVERT: A 493 MET cc_start: 0.8954 (tmm) cc_final: 0.8659 (tmm) REVERT: A 494 MET cc_start: 0.8526 (mtp) cc_final: 0.8310 (mtp) REVERT: A 498 TYR cc_start: 0.9096 (m-80) cc_final: 0.8733 (m-80) REVERT: A 505 GLU cc_start: 0.8544 (mt-10) cc_final: 0.8230 (mt-10) REVERT: A 561 LEU cc_start: 0.8747 (tp) cc_final: 0.8379 (tt) REVERT: A 570 MET cc_start: 0.9013 (mtp) cc_final: 0.8717 (mtp) REVERT: A 604 ARG cc_start: 0.8433 (tpp-160) cc_final: 0.8138 (tpp-160) REVERT: A 640 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.8131 (tpp) REVERT: B 15 GLU cc_start: 0.8892 (tp30) cc_final: 0.8609 (tp30) REVERT: B 119 GLU cc_start: 0.8955 (mp0) cc_final: 0.8292 (mp0) REVERT: B 250 TYR cc_start: 0.8926 (m-80) cc_final: 0.8695 (m-80) REVERT: B 267 ILE cc_start: 0.9099 (OUTLIER) cc_final: 0.8767 (mm) REVERT: B 274 ARG cc_start: 0.7429 (ttm170) cc_final: 0.6730 (ttm170) REVERT: B 375 LYS cc_start: 0.8971 (mmtm) cc_final: 0.8500 (mppt) REVERT: B 425 ILE cc_start: 0.9407 (mt) cc_final: 0.9169 (mt) REVERT: B 467 ASN cc_start: 0.9267 (m-40) cc_final: 0.8778 (m-40) REVERT: B 494 MET cc_start: 0.8962 (mtp) cc_final: 0.8549 (mtp) REVERT: B 550 MET cc_start: 0.7846 (mtm) cc_final: 0.7627 (mtm) REVERT: B 571 TYR cc_start: 0.8338 (t80) cc_final: 0.8123 (t80) REVERT: B 594 VAL cc_start: 0.9469 (m) cc_final: 0.9144 (p) REVERT: B 604 ARG cc_start: 0.8965 (tpp80) cc_final: 0.8542 (mmt-90) REVERT: B 686 ARG cc_start: 0.8689 (mtp85) cc_final: 0.8464 (mtp-110) REVERT: C 41 LEU cc_start: 0.7231 (pp) cc_final: 0.6688 (mm) REVERT: C 74 MET cc_start: 0.7255 (mmm) cc_final: 0.6833 (mmm) REVERT: C 141 LEU cc_start: 0.8935 (mt) cc_final: 0.8632 (pp) REVERT: C 163 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8868 (tt) REVERT: C 168 PHE cc_start: 0.8967 (m-80) cc_final: 0.8285 (m-80) REVERT: C 242 TYR cc_start: 0.9259 (t80) cc_final: 0.8414 (t80) REVERT: C 269 MET cc_start: 0.8932 (ptp) cc_final: 0.8689 (ppp) REVERT: C 271 LEU cc_start: 0.7317 (mm) cc_final: 0.7031 (mm) REVERT: D 95 MET cc_start: 0.7517 (ppp) cc_final: 0.7229 (ppp) REVERT: D 138 ILE cc_start: 0.9148 (mm) cc_final: 0.8937 (tp) REVERT: D 191 ILE cc_start: 0.0418 (pt) cc_final: 0.0192 (pt) outliers start: 63 outliers final: 45 residues processed: 516 average time/residue: 0.1275 time to fit residues: 100.2658 Evaluate side-chains 487 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 437 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 242 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 126 optimal weight: 0.0060 chunk 129 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 122 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 168 optimal weight: 9.9990 chunk 157 optimal weight: 3.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 467 ASN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 210 GLN D 98 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.153798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.111268 restraints weight = 32706.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.114930 restraints weight = 16006.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.117157 restraints weight = 9619.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.118865 restraints weight = 6867.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.119859 restraints weight = 5280.426| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.5337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16386 Z= 0.151 Angle : 0.618 13.712 22134 Z= 0.321 Chirality : 0.044 0.240 2360 Planarity : 0.003 0.055 2818 Dihedral : 8.438 136.528 2292 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.90 % Allowed : 21.62 % Favored : 74.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.19), residues: 1932 helix: 1.28 (0.15), residues: 1127 sheet: -0.20 (0.41), residues: 134 loop : 0.21 (0.23), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 350 TYR 0.025 0.001 TYR A 571 PHE 0.023 0.002 PHE C 172 TRP 0.024 0.002 TRP D 44 HIS 0.010 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (16386) covalent geometry : angle 0.61784 / 0.32 (22134) hydrogen bonds : bond 0.03868 / 2.47 ( 871) hydrogen bonds : angle 4.93710 / 3.54 ( 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 555 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 488 time to evaluate : 0.655 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: A 27 ASP cc_start: 0.8991 (p0) cc_final: 0.8345 (p0) REVERT: A 69 LEU cc_start: 0.9359 (mt) cc_final: 0.8962 (pp) REVERT: A 76 ASP cc_start: 0.8997 (m-30) cc_final: 0.8757 (m-30) REVERT: A 77 ILE cc_start: 0.9475 (pt) cc_final: 0.9231 (mp) REVERT: A 116 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7839 (mt-10) REVERT: A 139 GLU cc_start: 0.8608 (mt-10) cc_final: 0.8285 (mt-10) REVERT: A 147 GLN cc_start: 0.9216 (mt0) cc_final: 0.8512 (mt0) REVERT: A 179 LEU cc_start: 0.9204 (tp) cc_final: 0.8978 (tt) REVERT: A 218 ASN cc_start: 0.8677 (t0) cc_final: 0.8179 (t0) REVERT: A 221 LYS cc_start: 0.8872 (mmtp) cc_final: 0.8464 (mmtp) REVERT: A 263 ASP cc_start: 0.8379 (m-30) cc_final: 0.7942 (m-30) REVERT: A 346 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9066 (mp) REVERT: A 375 LYS cc_start: 0.8851 (mttt) cc_final: 0.8623 (mtmm) REVERT: A 381 LEU cc_start: 0.8968 (tp) cc_final: 0.8420 (pt) REVERT: A 384 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7490 (pm20) REVERT: A 415 ASN cc_start: 0.8941 (t0) cc_final: 0.8269 (t0) REVERT: A 418 ASN cc_start: 0.9084 (m-40) cc_final: 0.8525 (m-40) REVERT: A 420 MET cc_start: 0.8937 (mmm) cc_final: 0.8475 (mmm) REVERT: A 453 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8291 (ttt-90) REVERT: A 468 LEU cc_start: 0.9373 (tp) cc_final: 0.9159 (tp) REVERT: A 479 TYR cc_start: 0.8955 (t80) cc_final: 0.8585 (t80) REVERT: A 493 MET cc_start: 0.8954 (tmm) cc_final: 0.8520 (tmm) REVERT: A 494 MET cc_start: 0.8488 (mtp) cc_final: 0.8236 (mtp) REVERT: A 498 TYR cc_start: 0.9076 (m-80) cc_final: 0.8742 (m-80) REVERT: A 505 GLU cc_start: 0.8494 (mt-10) cc_final: 0.8168 (mt-10) REVERT: A 561 LEU cc_start: 0.8721 (tp) cc_final: 0.8305 (tt) REVERT: A 583 SER cc_start: 0.8914 (m) cc_final: 0.8519 (t) REVERT: A 588 GLN cc_start: 0.8889 (mm110) cc_final: 0.8590 (mm110) REVERT: A 604 ARG cc_start: 0.8386 (tpp-160) cc_final: 0.8123 (tpp-160) REVERT: A 640 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8035 (tpp) REVERT: B 15 GLU cc_start: 0.8945 (tp30) cc_final: 0.8656 (tp30) REVERT: B 71 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9040 (mp) REVERT: B 108 THR cc_start: 0.8669 (OUTLIER) cc_final: 0.8339 (p) REVERT: B 119 GLU cc_start: 0.8966 (mp0) cc_final: 0.8356 (mp0) REVERT: B 186 ILE cc_start: 0.9724 (mp) cc_final: 0.9457 (mp) REVERT: B 190 MET cc_start: 0.9199 (mtm) cc_final: 0.8953 (mtm) REVERT: B 191 GLN cc_start: 0.9098 (mm-40) cc_final: 0.8706 (mm-40) REVERT: B 194 LYS cc_start: 0.9386 (ttpt) cc_final: 0.9020 (ttpt) REVERT: B 267 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8747 (mm) REVERT: B 274 ARG cc_start: 0.7413 (ttm170) cc_final: 0.6875 (ttm170) REVERT: B 341 LYS cc_start: 0.9250 (pttm) cc_final: 0.9040 (mtmm) REVERT: B 425 ILE cc_start: 0.9386 (mt) cc_final: 0.9181 (mt) REVERT: B 494 MET cc_start: 0.8939 (mtp) cc_final: 0.8529 (mtp) REVERT: B 515 ASP cc_start: 0.8823 (m-30) cc_final: 0.8611 (m-30) REVERT: B 550 MET cc_start: 0.7930 (mtm) cc_final: 0.7678 (mtm) REVERT: B 604 ARG cc_start: 0.8965 (tpp80) cc_final: 0.8554 (mmt-90) REVERT: C 41 LEU cc_start: 0.7286 (pp) cc_final: 0.6796 (mm) REVERT: C 74 MET cc_start: 0.7228 (mmm) cc_final: 0.7023 (mmm) REVERT: C 124 TRP cc_start: 0.7223 (t60) cc_final: 0.6792 (t60) REVERT: C 141 LEU cc_start: 0.9140 (mt) cc_final: 0.8863 (pp) REVERT: C 157 MET cc_start: 0.9091 (mtt) cc_final: 0.8860 (mtt) REVERT: C 166 PHE cc_start: 0.7789 (m-80) cc_final: 0.7187 (m-80) REVERT: C 168 PHE cc_start: 0.8777 (m-80) cc_final: 0.8201 (m-80) REVERT: C 242 TYR cc_start: 0.9225 (t80) cc_final: 0.8686 (t80) REVERT: C 269 MET cc_start: 0.8972 (ptp) cc_final: 0.8584 (ppp) REVERT: C 270 ASN cc_start: 0.7903 (OUTLIER) cc_final: 0.7584 (t0) REVERT: C 271 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7062 (mm) REVERT: C 281 ASP cc_start: 0.7844 (m-30) cc_final: 0.6936 (t70) REVERT: D 95 MET cc_start: 0.7557 (ppp) cc_final: 0.7325 (ppp) REVERT: D 138 ILE cc_start: 0.9056 (mm) cc_final: 0.8825 (tp) REVERT: D 191 ILE cc_start: 0.0305 (pt) cc_final: 0.0088 (pt) outliers start: 67 outliers final: 39 residues processed: 520 average time/residue: 0.1212 time to fit residues: 96.2545 Evaluate side-chains 489 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 441 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 242 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 172 optimal weight: 0.9980 chunk 52 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 136 optimal weight: 0.0570 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN A 365 ASN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 28 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.154916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.112892 restraints weight = 32083.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.116808 restraints weight = 15856.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.119183 restraints weight = 9566.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.120927 restraints weight = 6752.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.121951 restraints weight = 5186.091| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3504 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3504 r_free = 0.3504 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3504 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.5595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16386 Z= 0.130 Angle : 0.617 12.259 22134 Z= 0.317 Chirality : 0.043 0.192 2360 Planarity : 0.003 0.049 2818 Dihedral : 8.244 137.697 2291 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.26 % Allowed : 23.14 % Favored : 73.60 % 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: 1.09 (0.19), residues: 1932 helix: 1.26 (0.15), residues: 1126 sheet: -0.29 (0.40), residues: 134 loop : 0.20 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 686 TYR 0.019 0.001 TYR C 55 PHE 0.035 0.001 PHE D 109 TRP 0.029 0.002 TRP D 44 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (16386) covalent geometry : angle 0.61749 / 0.32 (22134) hydrogen bonds : bond 0.03763 / 2.40 ( 871) hydrogen bonds : angle 4.86865 / 3.48 ( 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 542 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 486 time to evaluate : 0.503 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: A 27 ASP cc_start: 0.8928 (p0) cc_final: 0.8554 (t0) REVERT: A 116 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7487 (mt-10) REVERT: A 138 LYS cc_start: 0.9126 (mtpt) cc_final: 0.8838 (mtmm) REVERT: A 139 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8256 (mt-10) REVERT: A 147 GLN cc_start: 0.9179 (mt0) cc_final: 0.8459 (mt0) REVERT: A 150 GLN cc_start: 0.9129 (tm-30) cc_final: 0.8686 (tm-30) REVERT: A 178 SER cc_start: 0.8759 (OUTLIER) cc_final: 0.8533 (p) REVERT: A 218 ASN cc_start: 0.8684 (t0) cc_final: 0.8152 (t0) REVERT: A 221 LYS cc_start: 0.8909 (mmtp) cc_final: 0.8562 (mmtp) REVERT: A 250 TYR cc_start: 0.8676 (m-80) cc_final: 0.8319 (m-80) REVERT: A 263 ASP cc_start: 0.8392 (m-30) cc_final: 0.7924 (m-30) REVERT: A 286 ASP cc_start: 0.7585 (m-30) cc_final: 0.7368 (m-30) REVERT: A 346 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9031 (mp) REVERT: A 359 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7605 (ttp) REVERT: A 362 ASP cc_start: 0.7984 (m-30) cc_final: 0.7558 (m-30) REVERT: A 375 LYS cc_start: 0.8775 (mttt) cc_final: 0.8531 (mtmm) REVERT: A 381 LEU cc_start: 0.8916 (tp) cc_final: 0.8359 (pt) REVERT: A 384 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7455 (pm20) REVERT: A 415 ASN cc_start: 0.8974 (t0) cc_final: 0.8221 (t0) REVERT: A 418 ASN cc_start: 0.9090 (m-40) cc_final: 0.8515 (m-40) REVERT: A 420 MET cc_start: 0.8863 (mmm) cc_final: 0.8396 (mmm) REVERT: A 479 TYR cc_start: 0.8999 (t80) cc_final: 0.8595 (t80) REVERT: A 480 GLU cc_start: 0.8447 (mt-10) cc_final: 0.8238 (mt-10) REVERT: A 493 MET cc_start: 0.8917 (tmm) cc_final: 0.8636 (tmm) REVERT: A 494 MET cc_start: 0.8470 (mtp) cc_final: 0.8254 (mtp) REVERT: A 498 TYR cc_start: 0.9065 (m-80) cc_final: 0.8735 (m-80) REVERT: A 505 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8195 (mt-10) REVERT: A 561 LEU cc_start: 0.8665 (tp) cc_final: 0.8254 (tt) REVERT: A 570 MET cc_start: 0.9004 (mtp) cc_final: 0.8756 (mtp) REVERT: A 588 GLN cc_start: 0.8848 (mm110) cc_final: 0.8484 (mm110) REVERT: A 604 ARG cc_start: 0.8291 (tpp-160) cc_final: 0.8049 (tpp-160) REVERT: A 640 MET cc_start: 0.9226 (OUTLIER) cc_final: 0.7926 (tpp) REVERT: A 668 ASN cc_start: 0.8643 (m-40) cc_final: 0.8276 (m-40) REVERT: B 15 GLU cc_start: 0.8971 (tp30) cc_final: 0.8734 (tp30) REVERT: B 108 THR cc_start: 0.8801 (OUTLIER) cc_final: 0.8497 (p) REVERT: B 119 GLU cc_start: 0.8847 (mp0) cc_final: 0.8478 (mp0) REVERT: B 186 ILE cc_start: 0.9709 (mp) cc_final: 0.9464 (mp) REVERT: B 190 MET cc_start: 0.9233 (mtm) cc_final: 0.9018 (mtm) REVERT: B 191 GLN cc_start: 0.8914 (mm-40) cc_final: 0.8628 (mm-40) REVERT: B 194 LYS cc_start: 0.9367 (ttpt) cc_final: 0.8998 (ttpt) REVERT: B 267 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8753 (mm) REVERT: B 274 ARG cc_start: 0.7370 (ttm170) cc_final: 0.6907 (ttm170) REVERT: B 341 LYS cc_start: 0.9175 (pttm) cc_final: 0.8909 (mtmm) REVERT: B 494 MET cc_start: 0.8901 (mtp) cc_final: 0.8481 (mtp) REVERT: B 515 ASP cc_start: 0.8790 (m-30) cc_final: 0.8567 (m-30) REVERT: B 550 MET cc_start: 0.7949 (mtm) cc_final: 0.7705 (mtm) REVERT: B 586 TYR cc_start: 0.8371 (m-80) cc_final: 0.8048 (m-80) REVERT: B 604 ARG cc_start: 0.8866 (tpp80) cc_final: 0.8506 (mmt-90) REVERT: B 627 LYS cc_start: 0.9130 (tttt) cc_final: 0.8528 (ttpp) REVERT: B 632 MET cc_start: 0.8405 (mtp) cc_final: 0.7851 (mtp) REVERT: C 41 LEU cc_start: 0.7229 (pp) cc_final: 0.6727 (mm) REVERT: C 74 MET cc_start: 0.7127 (mmm) cc_final: 0.6904 (mmm) REVERT: C 110 MET cc_start: 0.6416 (mpp) cc_final: 0.6076 (mpp) REVERT: C 124 TRP cc_start: 0.7198 (t60) cc_final: 0.6745 (t60) REVERT: C 141 LEU cc_start: 0.9133 (mt) cc_final: 0.8835 (pp) REVERT: C 163 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8816 (tt) REVERT: C 168 PHE cc_start: 0.8673 (m-80) cc_final: 0.8254 (m-80) REVERT: C 242 TYR cc_start: 0.9206 (t80) cc_final: 0.8920 (t80) REVERT: C 269 MET cc_start: 0.8945 (ptp) cc_final: 0.8733 (ppp) REVERT: C 271 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.7045 (mm) REVERT: D 138 ILE cc_start: 0.9030 (mm) cc_final: 0.8803 (tp) outliers start: 56 outliers final: 33 residues processed: 509 average time/residue: 0.1250 time to fit residues: 97.3793 Evaluate side-chains 499 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 457 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 242 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 0.4980 chunk 51 optimal weight: 5.9990 chunk 74 optimal weight: 0.4980 chunk 105 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 186 optimal weight: 7.9990 chunk 140 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.157450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.114750 restraints weight = 32163.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.118729 restraints weight = 15999.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.121179 restraints weight = 9583.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.123025 restraints weight = 6717.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.124061 restraints weight = 5111.255| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3510 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3510 r_free = 0.3510 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3510 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16386 Z= 0.132 Angle : 0.623 12.080 22134 Z= 0.321 Chirality : 0.043 0.203 2360 Planarity : 0.003 0.036 2818 Dihedral : 8.131 138.946 2291 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.38 % Allowed : 23.54 % Favored : 73.08 % 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: 1.10 (0.19), residues: 1932 helix: 1.27 (0.15), residues: 1125 sheet: -0.20 (0.41), residues: 138 loop : 0.18 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 350 TYR 0.039 0.001 TYR B 36 PHE 0.045 0.002 PHE D 109 TRP 0.032 0.002 TRP D 44 HIS 0.007 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (16386) covalent geometry : angle 0.62321 / 0.32 (22134) hydrogen bonds : bond 0.03757 / 2.41 ( 871) hydrogen bonds : angle 4.83203 / 3.44 ( 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 543 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 485 time to evaluate : 0.681 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: A 27 ASP cc_start: 0.8881 (p0) cc_final: 0.8488 (t0) REVERT: A 77 ILE cc_start: 0.9467 (pt) cc_final: 0.9264 (mp) REVERT: A 116 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7845 (mt-10) REVERT: A 139 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8256 (mt-10) REVERT: A 147 GLN cc_start: 0.9158 (mt0) cc_final: 0.8481 (mt0) REVERT: A 150 GLN cc_start: 0.9137 (tm-30) cc_final: 0.8688 (tm-30) REVERT: A 218 ASN cc_start: 0.8601 (t0) cc_final: 0.8043 (t0) REVERT: A 221 LYS cc_start: 0.8907 (mmtp) cc_final: 0.8550 (mmtp) REVERT: A 228 LYS cc_start: 0.9168 (mttp) cc_final: 0.8968 (mmtt) REVERT: A 250 TYR cc_start: 0.8685 (m-80) cc_final: 0.8353 (m-80) REVERT: A 263 ASP cc_start: 0.8434 (m-30) cc_final: 0.7966 (m-30) REVERT: A 312 GLN cc_start: 0.8062 (tp-100) cc_final: 0.7839 (tp-100) REVERT: A 346 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9016 (mp) REVERT: A 359 MET cc_start: 0.8368 (OUTLIER) cc_final: 0.7753 (ttp) REVERT: A 362 ASP cc_start: 0.8002 (m-30) cc_final: 0.7468 (m-30) REVERT: A 375 LYS cc_start: 0.8759 (mttt) cc_final: 0.8531 (mtmm) REVERT: A 381 LEU cc_start: 0.8950 (tp) cc_final: 0.8399 (pt) REVERT: A 384 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7466 (pm20) REVERT: A 415 ASN cc_start: 0.8828 (t0) cc_final: 0.8490 (t0) REVERT: A 420 MET cc_start: 0.8828 (mmm) cc_final: 0.8287 (mmm) REVERT: A 459 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8506 (mttm) REVERT: A 479 TYR cc_start: 0.9027 (t80) cc_final: 0.8672 (t80) REVERT: A 493 MET cc_start: 0.8905 (tmm) cc_final: 0.8591 (tmm) REVERT: A 494 MET cc_start: 0.8464 (mtp) cc_final: 0.8258 (ttm) REVERT: A 498 TYR cc_start: 0.9049 (m-80) cc_final: 0.8563 (m-80) REVERT: A 505 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8282 (mt-10) REVERT: A 561 LEU cc_start: 0.8654 (tp) cc_final: 0.8272 (tt) REVERT: A 571 TYR cc_start: 0.9037 (t80) cc_final: 0.8106 (t80) REVERT: A 588 GLN cc_start: 0.8884 (mm110) cc_final: 0.8527 (mm110) REVERT: A 640 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8899 (tmm) REVERT: A 668 ASN cc_start: 0.8627 (m-40) cc_final: 0.8259 (m-40) REVERT: B 71 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9132 (mp) REVERT: B 108 THR cc_start: 0.8800 (OUTLIER) cc_final: 0.8507 (p) REVERT: B 186 ILE cc_start: 0.9708 (OUTLIER) cc_final: 0.9471 (mp) REVERT: B 194 LYS cc_start: 0.9364 (ttpt) cc_final: 0.9146 (ttpt) REVERT: B 267 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8716 (mm) REVERT: B 274 ARG cc_start: 0.7360 (ttm170) cc_final: 0.6872 (ttm170) REVERT: B 384 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.6684 (pm20) REVERT: B 467 ASN cc_start: 0.9119 (t0) cc_final: 0.8692 (m-40) REVERT: B 494 MET cc_start: 0.8853 (mtp) cc_final: 0.8462 (mtp) REVERT: B 515 ASP cc_start: 0.8787 (m-30) cc_final: 0.8573 (m-30) REVERT: B 627 LYS cc_start: 0.9155 (tttt) cc_final: 0.8615 (tttt) REVERT: B 632 MET cc_start: 0.8357 (mtp) cc_final: 0.7586 (mtp) REVERT: B 668 ASN cc_start: 0.8746 (OUTLIER) cc_final: 0.8483 (t0) REVERT: C 74 MET cc_start: 0.7212 (mmm) cc_final: 0.6857 (mmm) REVERT: C 110 MET cc_start: 0.6070 (mpp) cc_final: 0.5856 (mpp) REVERT: C 141 LEU cc_start: 0.9198 (mt) cc_final: 0.8817 (pp) REVERT: C 149 ASP cc_start: 0.8301 (t0) cc_final: 0.7729 (m-30) REVERT: C 166 PHE cc_start: 0.7725 (m-80) cc_final: 0.7438 (m-80) REVERT: C 168 PHE cc_start: 0.8662 (m-80) cc_final: 0.8263 (m-80) REVERT: C 242 TYR cc_start: 0.9194 (t80) cc_final: 0.8891 (t80) REVERT: C 270 ASN cc_start: 0.8087 (OUTLIER) cc_final: 0.7752 (t0) outliers start: 58 outliers final: 40 residues processed: 512 average time/residue: 0.1233 time to fit residues: 96.7845 Evaluate side-chains 485 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 433 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 270 ASN Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 242 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 0.9980 chunk 99 optimal weight: 0.4980 chunk 61 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 153 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 97 optimal weight: 7.9990 chunk 151 optimal weight: 10.0000 chunk 81 optimal weight: 4.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 418 ASN ** 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 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.157498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.115555 restraints weight = 32446.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.119512 restraints weight = 15899.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.122005 restraints weight = 9628.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.123582 restraints weight = 6707.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.124699 restraints weight = 5204.615| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16386 Z= 0.135 Angle : 0.655 11.961 22134 Z= 0.337 Chirality : 0.044 0.242 2360 Planarity : 0.003 0.064 2818 Dihedral : 8.030 139.406 2291 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.15 % Allowed : 24.36 % Favored : 72.49 % 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: 1.05 (0.19), residues: 1932 helix: 1.22 (0.15), residues: 1128 sheet: -0.27 (0.41), residues: 134 loop : 0.19 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 350 TYR 0.038 0.001 TYR C 55 PHE 0.055 0.002 PHE D 109 TRP 0.037 0.002 TRP D 44 HIS 0.010 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 (16386) covalent geometry : angle 0.65546 / 0.34 (22134) hydrogen bonds : bond 0.03794 / 2.41 ( 871) hydrogen bonds : angle 4.83592 / 3.45 ( 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 518 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 464 time to evaluate : 0.599 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: A 27 ASP cc_start: 0.8855 (p0) cc_final: 0.8504 (t0) REVERT: A 77 ILE cc_start: 0.9469 (pt) cc_final: 0.9261 (mp) REVERT: A 109 ASN cc_start: 0.8954 (m110) cc_final: 0.8567 (p0) REVERT: A 139 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8286 (mt-10) REVERT: A 147 GLN cc_start: 0.9133 (mt0) cc_final: 0.8530 (mt0) REVERT: A 150 GLN cc_start: 0.9140 (tm-30) cc_final: 0.8679 (tm-30) REVERT: A 218 ASN cc_start: 0.8554 (t0) cc_final: 0.7984 (t0) REVERT: A 250 TYR cc_start: 0.8684 (m-80) cc_final: 0.8344 (m-80) REVERT: A 263 ASP cc_start: 0.8442 (m-30) cc_final: 0.7971 (m-30) REVERT: A 346 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9018 (mp) REVERT: A 359 MET cc_start: 0.8366 (OUTLIER) cc_final: 0.7705 (ttp) REVERT: A 362 ASP cc_start: 0.7844 (m-30) cc_final: 0.7618 (m-30) REVERT: A 375 LYS cc_start: 0.8739 (mttt) cc_final: 0.8522 (mtmm) REVERT: A 381 LEU cc_start: 0.8953 (tp) cc_final: 0.8406 (pt) REVERT: A 384 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7424 (pm20) REVERT: A 415 ASN cc_start: 0.8786 (t0) cc_final: 0.8445 (t0) REVERT: A 420 MET cc_start: 0.8837 (mmm) cc_final: 0.8341 (mmm) REVERT: A 459 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8525 (mttm) REVERT: A 493 MET cc_start: 0.8891 (tmm) cc_final: 0.8639 (tmm) REVERT: A 494 MET cc_start: 0.8498 (mtp) cc_final: 0.8182 (ttm) REVERT: A 498 TYR cc_start: 0.9069 (m-80) cc_final: 0.8559 (m-80) REVERT: A 505 GLU cc_start: 0.8564 (mt-10) cc_final: 0.8266 (mt-10) REVERT: A 561 LEU cc_start: 0.8676 (tp) cc_final: 0.8295 (tt) REVERT: A 588 GLN cc_start: 0.8877 (mm110) cc_final: 0.8433 (mm110) REVERT: A 640 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8923 (tmm) REVERT: A 668 ASN cc_start: 0.8636 (m-40) cc_final: 0.8228 (m-40) REVERT: B 108 THR cc_start: 0.8597 (OUTLIER) cc_final: 0.7659 (p) REVERT: B 190 MET cc_start: 0.8975 (mtm) cc_final: 0.8677 (mtm) REVERT: B 194 LYS cc_start: 0.9343 (ttpt) cc_final: 0.9072 (ttpt) REVERT: B 267 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8795 (mm) REVERT: B 274 ARG cc_start: 0.7428 (ttm170) cc_final: 0.6980 (ttm170) REVERT: B 341 LYS cc_start: 0.9316 (pttp) cc_final: 0.8930 (mtmm) REVERT: B 348 MET cc_start: 0.8868 (ptt) cc_final: 0.8643 (ptt) REVERT: B 384 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7818 (pt0) REVERT: B 467 ASN cc_start: 0.9097 (t0) cc_final: 0.8678 (m-40) REVERT: B 494 MET cc_start: 0.8848 (mtp) cc_final: 0.8446 (mtp) REVERT: B 515 ASP cc_start: 0.8781 (m-30) cc_final: 0.8570 (m-30) REVERT: B 627 LYS cc_start: 0.9156 (tttt) cc_final: 0.8651 (tttt) REVERT: B 632 MET cc_start: 0.8312 (mtp) cc_final: 0.7499 (mtp) REVERT: B 639 ASP cc_start: 0.8714 (m-30) cc_final: 0.8438 (m-30) REVERT: B 640 MET cc_start: 0.9072 (tpp) cc_final: 0.8265 (tpp) REVERT: C 74 MET cc_start: 0.7126 (mmm) cc_final: 0.6644 (mmt) REVERT: C 110 MET cc_start: 0.5755 (mpp) cc_final: 0.5524 (mpp) REVERT: C 141 LEU cc_start: 0.9275 (mt) cc_final: 0.8905 (pp) REVERT: C 149 ASP cc_start: 0.8291 (t0) cc_final: 0.7534 (m-30) REVERT: C 168 PHE cc_start: 0.8712 (m-80) cc_final: 0.8436 (m-80) REVERT: C 242 TYR cc_start: 0.9220 (t80) cc_final: 0.8926 (t80) REVERT: D 154 PHE cc_start: 0.4542 (t80) cc_final: 0.4010 (t80) outliers start: 54 outliers final: 37 residues processed: 491 average time/residue: 0.1202 time to fit residues: 90.8795 Evaluate side-chains 482 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 437 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 242 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 8.9990 chunk 133 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 114 optimal weight: 0.8980 chunk 86 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN B 418 ASN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN B 588 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.155343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.113148 restraints weight = 32682.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.117001 restraints weight = 16079.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.119390 restraints weight = 9735.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.121101 restraints weight = 6823.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.122118 restraints weight = 5312.267| |-----------------------------------------------------------------------------| r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3482 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3482 r_free = 0.3482 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3482 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.6183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16386 Z= 0.162 Angle : 0.683 11.860 22134 Z= 0.352 Chirality : 0.045 0.241 2360 Planarity : 0.003 0.057 2818 Dihedral : 7.937 139.961 2291 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.73 % Allowed : 23.54 % Favored : 72.73 % 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: 1.03 (0.19), residues: 1932 helix: 1.22 (0.15), residues: 1127 sheet: -0.31 (0.41), residues: 138 loop : 0.16 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 350 TYR 0.030 0.001 TYR C 55 PHE 0.058 0.002 PHE D 109 TRP 0.038 0.002 TRP D 44 HIS 0.013 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (16386) covalent geometry : angle 0.68308 / 0.35 (22134) hydrogen bonds : bond 0.03818 / 2.42 ( 871) hydrogen bonds : angle 4.90492 / 3.51 ( 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 513 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 449 time to evaluate : 0.688 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: A 27 ASP cc_start: 0.8830 (p0) cc_final: 0.8490 (t0) REVERT: A 139 GLU cc_start: 0.8581 (mt-10) cc_final: 0.8284 (mt-10) REVERT: A 147 GLN cc_start: 0.9131 (mt0) cc_final: 0.8710 (mt0) REVERT: A 150 GLN cc_start: 0.9157 (tm-30) cc_final: 0.8666 (tm-30) REVERT: A 218 ASN cc_start: 0.8567 (t0) cc_final: 0.8047 (t0) REVERT: A 250 TYR cc_start: 0.8671 (m-80) cc_final: 0.8319 (m-80) REVERT: A 263 ASP cc_start: 0.8441 (m-30) cc_final: 0.7994 (m-30) REVERT: A 346 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9078 (mp) REVERT: A 359 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.7967 (ttp) REVERT: A 381 LEU cc_start: 0.9020 (tp) cc_final: 0.8445 (pt) REVERT: A 384 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.6872 (pm20) REVERT: A 415 ASN cc_start: 0.8822 (t0) cc_final: 0.8478 (t0) REVERT: A 420 MET cc_start: 0.8865 (mmm) cc_final: 0.8301 (mmm) REVERT: A 493 MET cc_start: 0.8942 (tmm) cc_final: 0.8652 (tmm) REVERT: A 498 TYR cc_start: 0.9052 (m-80) cc_final: 0.8851 (m-80) REVERT: A 505 GLU cc_start: 0.8582 (mt-10) cc_final: 0.8024 (mt-10) REVERT: A 561 LEU cc_start: 0.8763 (tp) cc_final: 0.8403 (tt) REVERT: A 571 TYR cc_start: 0.8873 (t80) cc_final: 0.8522 (t80) REVERT: A 640 MET cc_start: 0.9162 (OUTLIER) cc_final: 0.7892 (tpp) REVERT: A 668 ASN cc_start: 0.8571 (m-40) cc_final: 0.8192 (m-40) REVERT: B 71 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9121 (mp) REVERT: B 267 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8725 (mm) REVERT: B 274 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.6977 (ttm170) REVERT: B 341 LYS cc_start: 0.9355 (pttp) cc_final: 0.8974 (mtmm) REVERT: B 348 MET cc_start: 0.8858 (ptt) cc_final: 0.8652 (ptt) REVERT: B 384 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.6737 (pm20) REVERT: B 494 MET cc_start: 0.8839 (mtp) cc_final: 0.8487 (mtp) REVERT: B 515 ASP cc_start: 0.8812 (m-30) cc_final: 0.8586 (m-30) REVERT: B 627 LYS cc_start: 0.9159 (tttt) cc_final: 0.8722 (tttt) REVERT: B 639 ASP cc_start: 0.8714 (m-30) cc_final: 0.8426 (m-30) REVERT: C 110 MET cc_start: 0.5769 (mpp) cc_final: 0.5506 (mpp) REVERT: C 141 LEU cc_start: 0.9354 (mt) cc_final: 0.8986 (pp) REVERT: C 149 ASP cc_start: 0.8342 (t0) cc_final: 0.7672 (m-30) REVERT: C 163 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8714 (tt) REVERT: C 168 PHE cc_start: 0.8683 (m-80) cc_final: 0.8225 (m-80) REVERT: C 242 TYR cc_start: 0.9224 (t80) cc_final: 0.8907 (t80) REVERT: D 96 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.6909 (tpp) outliers start: 64 outliers final: 47 residues processed: 481 average time/residue: 0.1205 time to fit residues: 88.8396 Evaluate side-chains 488 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 431 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 409 CYS Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 242 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 189 optimal weight: 30.0000 chunk 181 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.156341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.114467 restraints weight = 32563.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.118315 restraints weight = 16060.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.120843 restraints weight = 9752.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.122548 restraints weight = 6746.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.123569 restraints weight = 5226.088| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.6329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 16386 Z= 0.154 Angle : 0.703 13.943 22134 Z= 0.363 Chirality : 0.045 0.252 2360 Planarity : 0.003 0.056 2818 Dihedral : 7.899 139.879 2291 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.26 % Allowed : 24.94 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.19), residues: 1932 helix: 1.17 (0.15), residues: 1126 sheet: -0.38 (0.41), residues: 138 loop : 0.11 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 293 TYR 0.032 0.001 TYR C 55 PHE 0.059 0.002 PHE D 109 TRP 0.041 0.002 TRP D 44 HIS 0.017 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (16386) covalent geometry : angle 0.70288 / 0.36 (22134) hydrogen bonds : bond 0.03874 / 2.48 ( 871) hydrogen bonds : angle 4.98375 / 3.57 ( 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 509 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 453 time to evaluate : 0.601 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: A 27 ASP cc_start: 0.8796 (p0) cc_final: 0.8322 (t0) REVERT: A 139 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8265 (mt-10) REVERT: A 150 GLN cc_start: 0.9251 (tm-30) cc_final: 0.8712 (tm-30) REVERT: A 218 ASN cc_start: 0.8549 (t0) cc_final: 0.8033 (t0) REVERT: A 250 TYR cc_start: 0.8646 (m-80) cc_final: 0.8323 (m-80) REVERT: A 263 ASP cc_start: 0.8427 (m-30) cc_final: 0.7955 (m-30) REVERT: A 312 GLN cc_start: 0.7795 (tp-100) cc_final: 0.7520 (tp-100) REVERT: A 346 LEU cc_start: 0.9352 (OUTLIER) cc_final: 0.9081 (mp) REVERT: A 359 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.7923 (ttp) REVERT: A 381 LEU cc_start: 0.9024 (tp) cc_final: 0.8448 (pt) REVERT: A 384 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.6806 (pm20) REVERT: A 415 ASN cc_start: 0.8730 (t0) cc_final: 0.8058 (t0) REVERT: A 418 ASN cc_start: 0.9116 (m-40) cc_final: 0.8598 (m-40) REVERT: A 420 MET cc_start: 0.8868 (mmm) cc_final: 0.8298 (mmm) REVERT: A 446 ARG cc_start: 0.7852 (mmm160) cc_final: 0.7557 (mmm160) REVERT: A 493 MET cc_start: 0.8924 (tmm) cc_final: 0.8449 (tmm) REVERT: A 505 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8024 (mt-10) REVERT: A 561 LEU cc_start: 0.8752 (tp) cc_final: 0.8359 (tt) REVERT: A 571 TYR cc_start: 0.8867 (t80) cc_final: 0.8599 (t80) REVERT: A 640 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8617 (tmm) REVERT: A 668 ASN cc_start: 0.8616 (m-40) cc_final: 0.8231 (m-40) REVERT: B 71 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9061 (mp) REVERT: B 174 GLU cc_start: 0.7908 (tp30) cc_final: 0.7629 (tp30) REVERT: B 227 MET cc_start: 0.9052 (mtp) cc_final: 0.8776 (mtp) REVERT: B 267 ILE cc_start: 0.9108 (OUTLIER) cc_final: 0.8723 (mm) REVERT: B 274 ARG cc_start: 0.7454 (OUTLIER) cc_final: 0.6992 (ttm170) REVERT: B 341 LYS cc_start: 0.9360 (pttp) cc_final: 0.8967 (mtmm) REVERT: B 384 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.6711 (pm20) REVERT: B 494 MET cc_start: 0.8843 (mtp) cc_final: 0.8501 (mtp) REVERT: B 515 ASP cc_start: 0.8816 (m-30) cc_final: 0.8592 (m-30) REVERT: B 550 MET cc_start: 0.7790 (mtt) cc_final: 0.7373 (mtt) REVERT: B 586 TYR cc_start: 0.8678 (m-80) cc_final: 0.8323 (m-80) REVERT: B 627 LYS cc_start: 0.9118 (tttt) cc_final: 0.8718 (tttt) REVERT: B 639 ASP cc_start: 0.8739 (m-30) cc_final: 0.8427 (m-30) REVERT: B 668 ASN cc_start: 0.8762 (m-40) cc_final: 0.8400 (t0) REVERT: C 110 MET cc_start: 0.5891 (mpp) cc_final: 0.5665 (mpp) REVERT: C 141 LEU cc_start: 0.9368 (mt) cc_final: 0.9000 (pp) REVERT: C 149 ASP cc_start: 0.8388 (t0) cc_final: 0.7621 (m-30) REVERT: C 163 LEU cc_start: 0.9246 (OUTLIER) cc_final: 0.8792 (tt) REVERT: C 168 PHE cc_start: 0.8734 (m-80) cc_final: 0.8133 (m-80) REVERT: C 242 TYR cc_start: 0.9214 (t80) cc_final: 0.8919 (t80) REVERT: D 212 ILE cc_start: 0.3978 (OUTLIER) cc_final: 0.3738 (tt) outliers start: 56 outliers final: 42 residues processed: 485 average time/residue: 0.1191 time to fit residues: 89.0893 Evaluate side-chains 489 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 437 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 221 LYS Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 96 MET Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 242 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 chunk 125 optimal weight: 0.0040 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 overall best weight: 0.8794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.154935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.113518 restraints weight = 32051.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.117235 restraints weight = 15891.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.119436 restraints weight = 9638.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.121110 restraints weight = 6917.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.122274 restraints weight = 5384.950| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3506 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3506 r_free = 0.3506 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3506 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.6372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 16386 Z= 0.157 Angle : 0.726 12.002 22134 Z= 0.375 Chirality : 0.046 0.273 2360 Planarity : 0.004 0.056 2818 Dihedral : 7.906 139.818 2291 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.09 % Allowed : 25.76 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 1932 helix: 1.13 (0.15), residues: 1126 sheet: -0.44 (0.41), residues: 138 loop : 0.07 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 350 TYR 0.029 0.001 TYR C 55 PHE 0.061 0.002 PHE D 109 TRP 0.039 0.003 TRP D 44 HIS 0.016 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 (16386) covalent geometry : angle 0.72612 / 0.37 (22134) hydrogen bonds : bond 0.03910 / 2.50 ( 871) hydrogen bonds : angle 4.99229 / 3.57 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3205.18 seconds wall clock time: 56 minutes 24.00 seconds (3384.00 seconds total)