Starting phenix.real_space_refine on Fri Jul 3 19:45:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byx_45047/07_2026/9byx_45047_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byx_45047/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9byx_45047/07_2026/9byx_45047_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byx_45047/07_2026/9byx_45047_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9byx_45047/07_2026/9byx_45047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byx_45047/07_2026/9byx_45047.map" } 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-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.36, 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: 1.11 Conformation dependent library (CDL) restraints added in 641.0 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: 0.34 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: 2.41 Time building geometry restraints manager: 1.53 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 3.060 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 3.060 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 3.060 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: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.380 Find NCS groups from input model: 0.270 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.320 ------------------------------------------------------------------------------- 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 : 0.485 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: 0.1352 time to fit residues: 163.0956 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 : 0.698 ------------------------------------------------------------------------------- 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 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 201 HIS ** 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 201 HIS D 234 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.158106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.112417 restraints weight = 32632.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.116423 restraints weight = 16259.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.118991 restraints weight = 9916.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.120849 restraints weight = 7067.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.122008 restraints weight = 5460.929| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3498 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3498 r_free = 0.3498 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 = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (7 function evaluations) r_final: 0.3497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16386 Z= 0.217 Angle : 0.672 9.213 22134 Z= 0.351 Chirality : 0.045 0.172 2360 Planarity : 0.004 0.037 2818 Dihedral : 9.733 130.845 2303 Min Nonbonded Distance : 1.746 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.08 % Allowed : 18.30 % Favored : 77.62 % 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: 1.44 (0.15), residues: 1132 sheet: 0.37 (0.43), residues: 130 loop : 0.51 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 256 TYR 0.025 0.002 TYR C 169 PHE 0.038 0.002 PHE C 168 TRP 0.016 0.002 TRP D 44 HIS 0.006 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.22 (16386) covalent geometry : angle 0.67231 / 0.35 (22134) hydrogen bonds : bond 0.04821 / 3.04 ( 871) hydrogen bonds : angle 5.10234 / 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 633 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 563 time to evaluate : 0.656 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 76 ASP cc_start: 0.8917 (m-30) cc_final: 0.8506 (m-30) REVERT: A 116 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7819 (mt-10) REVERT: A 138 LYS cc_start: 0.8995 (mtpt) cc_final: 0.8668 (mtpp) REVERT: A 147 GLN cc_start: 0.9323 (mt0) cc_final: 0.9059 (mt0) REVERT: A 218 ASN cc_start: 0.8796 (t0) cc_final: 0.8262 (t0) REVERT: A 221 LYS cc_start: 0.8638 (mmtp) cc_final: 0.8241 (mmtp) REVERT: A 232 ASN cc_start: 0.9413 (m-40) cc_final: 0.9141 (m-40) REVERT: A 259 ASN cc_start: 0.8937 (m-40) cc_final: 0.8653 (m110) REVERT: A 263 ASP cc_start: 0.8301 (m-30) cc_final: 0.8002 (m-30) REVERT: A 362 ASP cc_start: 0.7988 (m-30) cc_final: 0.6955 (m-30) REVERT: A 381 LEU cc_start: 0.8934 (tp) cc_final: 0.8379 (pt) REVERT: A 384 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7656 (pm20) REVERT: A 415 ASN cc_start: 0.8927 (t0) cc_final: 0.8588 (t0) REVERT: A 446 ARG cc_start: 0.7629 (mmm160) cc_final: 0.7325 (mmm160) REVERT: A 468 LEU cc_start: 0.9387 (tp) cc_final: 0.9140 (tp) REVERT: A 494 MET cc_start: 0.8801 (mtp) cc_final: 0.8544 (mtp) REVERT: A 604 ARG cc_start: 0.8277 (tpp-160) cc_final: 0.8047 (tpp-160) REVERT: A 640 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.8245 (tpp) REVERT: A 654 PHE cc_start: 0.9278 (t80) cc_final: 0.9006 (t80) REVERT: B 147 GLN cc_start: 0.9219 (mt0) cc_final: 0.8900 (mt0) REVERT: B 232 ASN cc_start: 0.8830 (OUTLIER) cc_final: 0.8491 (m-40) REVERT: B 252 ASN cc_start: 0.8956 (t0) cc_final: 0.8696 (t0) REVERT: B 267 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8671 (mm) REVERT: B 288 PHE cc_start: 0.9230 (t80) cc_final: 0.8976 (t80) REVERT: B 321 GLU cc_start: 0.8343 (pp20) cc_final: 0.8099 (pp20) REVERT: B 322 MET cc_start: 0.8923 (mmt) cc_final: 0.8642 (mmt) REVERT: B 425 ILE cc_start: 0.9390 (mt) cc_final: 0.9183 (mt) REVERT: B 479 TYR cc_start: 0.8652 (t80) cc_final: 0.8205 (t80) REVERT: B 494 MET cc_start: 0.9056 (mtp) cc_final: 0.8641 (mtp) REVERT: B 550 MET cc_start: 0.7785 (mtm) cc_final: 0.7549 (mtm) REVERT: B 571 TYR cc_start: 0.8474 (t80) cc_final: 0.8224 (t80) REVERT: B 586 TYR cc_start: 0.8415 (m-80) cc_final: 0.7800 (m-80) REVERT: B 598 MET cc_start: 0.7931 (mtm) cc_final: 0.7582 (mtp) REVERT: B 626 TYR cc_start: 0.8242 (m-80) cc_final: 0.7900 (m-80) REVERT: B 686 ARG cc_start: 0.8565 (mtp85) cc_final: 0.8362 (mtp-110) REVERT: C 41 LEU cc_start: 0.6761 (pp) cc_final: 0.6344 (mm) REVERT: C 56 MET cc_start: 0.4968 (ptt) cc_final: 0.4716 (ptt) REVERT: C 96 MET cc_start: 0.8712 (mmm) cc_final: 0.8083 (mmm) REVERT: C 141 LEU cc_start: 0.8708 (mt) cc_final: 0.8331 (pp) REVERT: C 154 PHE cc_start: 0.9146 (t80) cc_final: 0.8943 (t80) REVERT: C 162 TYR cc_start: 0.9209 (m-10) cc_final: 0.8708 (m-80) REVERT: C 168 PHE cc_start: 0.9089 (m-80) cc_final: 0.8816 (m-80) REVERT: C 242 TYR cc_start: 0.9269 (t80) cc_final: 0.8658 (t80) REVERT: D 95 MET cc_start: 0.8271 (ptm) cc_final: 0.8049 (ptm) REVERT: D 138 ILE cc_start: 0.9181 (mm) cc_final: 0.8962 (tp) REVERT: D 234 GLN cc_start: 0.7833 (pt0) cc_final: 0.7620 (tm-30) outliers start: 70 outliers final: 36 residues processed: 599 average time/residue: 0.1205 time to fit residues: 109.0772 Evaluate side-chains 510 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 470 time to evaluate : 0.616 ------------------------------------------------------------------------------- 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 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 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 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: 0.9980 chunk 164 optimal weight: 7.9990 chunk 28 optimal weight: 0.7980 chunk 182 optimal weight: 7.9990 chunk 159 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 150 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 158 optimal weight: 9.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- 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 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** 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 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN D 28 GLN ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN D 210 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.150953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.107767 restraints weight = 33553.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.111588 restraints weight = 16738.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.113949 restraints weight = 10195.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.115687 restraints weight = 7246.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.116829 restraints weight = 5589.563| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3434 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3434 r_free = 0.3434 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (12 function evaluations) r_final: 0.3434 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 16386 Z= 0.250 Angle : 0.659 9.243 22134 Z= 0.350 Chirality : 0.045 0.164 2360 Planarity : 0.004 0.046 2818 Dihedral : 9.105 132.893 2295 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.90 % Allowed : 20.80 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.19), residues: 1932 helix: 1.23 (0.15), residues: 1134 sheet: 0.01 (0.42), residues: 134 loop : 0.35 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 225 TYR 0.031 0.002 TYR C 55 PHE 0.035 0.002 PHE C 172 TRP 0.021 0.002 TRP D 44 HIS 0.012 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00548 / 0.25 (16386) covalent geometry : angle 0.65949 / 0.35 (22134) hydrogen bonds : bond 0.04431 / 2.82 ( 871) hydrogen bonds : angle 5.07857 / 3.62 ( 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 604 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 537 time to evaluate : 0.370 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: 0.9018 (p0) cc_final: 0.8667 (p0) REVERT: A 76 ASP cc_start: 0.9012 (m-30) cc_final: 0.8742 (m-30) REVERT: A 147 GLN cc_start: 0.9269 (mt0) cc_final: 0.9019 (mt0) REVERT: A 157 LEU cc_start: 0.9104 (tp) cc_final: 0.8732 (tp) REVERT: A 218 ASN cc_start: 0.8756 (t0) cc_final: 0.8286 (t0) REVERT: A 221 LYS cc_start: 0.8730 (mmtp) cc_final: 0.8151 (mmtp) REVERT: A 232 ASN cc_start: 0.9369 (m-40) cc_final: 0.8557 (m110) REVERT: A 263 ASP cc_start: 0.8421 (m-30) cc_final: 0.8045 (m-30) REVERT: A 286 ASP cc_start: 0.7712 (m-30) cc_final: 0.7442 (m-30) REVERT: A 362 ASP cc_start: 0.7936 (m-30) cc_final: 0.7246 (m-30) REVERT: A 375 LYS cc_start: 0.8882 (mttt) cc_final: 0.8638 (mtmm) REVERT: A 381 LEU cc_start: 0.9005 (tp) cc_final: 0.8439 (pt) REVERT: A 384 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7228 (pm20) REVERT: A 447 ASN cc_start: 0.8156 (m-40) cc_final: 0.7907 (t0) REVERT: A 453 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8429 (ttt-90) REVERT: A 479 TYR cc_start: 0.8922 (t80) cc_final: 0.8340 (t80) REVERT: A 498 TYR cc_start: 0.9127 (m-80) cc_final: 0.8805 (m-80) REVERT: A 505 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8262 (mt-10) REVERT: A 586 TYR cc_start: 0.8303 (m-80) cc_final: 0.7999 (m-80) REVERT: A 590 SER cc_start: 0.9529 (p) cc_final: 0.9237 (p) REVERT: A 602 GLU cc_start: 0.7579 (pt0) cc_final: 0.6906 (pt0) REVERT: A 640 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8180 (ttp) REVERT: B 190 MET cc_start: 0.9211 (mtm) cc_final: 0.8869 (mtm) REVERT: B 232 ASN cc_start: 0.8817 (OUTLIER) cc_final: 0.8285 (m-40) REVERT: B 252 ASN cc_start: 0.9047 (t0) cc_final: 0.8847 (t0) REVERT: B 267 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8889 (mm) REVERT: B 322 MET cc_start: 0.8995 (mmt) cc_final: 0.8518 (mmt) REVERT: B 348 MET cc_start: 0.8802 (ptt) cc_final: 0.8478 (ptt) REVERT: B 375 LYS cc_start: 0.8958 (mmtm) cc_final: 0.8514 (mppt) REVERT: B 441 GLU cc_start: 0.8707 (pt0) cc_final: 0.8495 (pt0) REVERT: B 447 ASN cc_start: 0.8636 (m-40) cc_final: 0.8429 (m-40) REVERT: B 494 MET cc_start: 0.8991 (mtp) cc_final: 0.8613 (mtp) REVERT: B 571 TYR cc_start: 0.8430 (t80) cc_final: 0.8149 (t80) REVERT: B 586 TYR cc_start: 0.8330 (m-80) cc_final: 0.7681 (m-80) REVERT: B 604 ARG cc_start: 0.9007 (tpp80) cc_final: 0.8515 (mmt-90) REVERT: C 41 LEU cc_start: 0.7105 (pp) cc_final: 0.6560 (mm) REVERT: C 162 TYR cc_start: 0.9221 (m-10) cc_final: 0.8756 (m-80) REVERT: C 168 PHE cc_start: 0.9375 (m-80) cc_final: 0.8807 (m-80) REVERT: C 227 PHE cc_start: 0.7969 (t80) cc_final: 0.7683 (t80) REVERT: C 242 TYR cc_start: 0.9306 (t80) cc_final: 0.8704 (t80) outliers start: 67 outliers final: 44 residues processed: 574 average time/residue: 0.1014 time to fit residues: 88.7283 Evaluate side-chains 510 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 461 time to evaluate : 0.590 ------------------------------------------------------------------------------- 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 231 ASP Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 384 GLU 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 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 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 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 367 VAL Chi-restraints excluded: chain B residue 408 SER 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 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 117 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 185 optimal weight: 20.0000 chunk 191 optimal weight: 0.0570 chunk 159 optimal weight: 5.9990 chunk 182 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 overall best weight: 2.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 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 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 28 GLN ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.150065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.108736 restraints weight = 32968.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.112175 restraints weight = 15878.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.114736 restraints weight = 9619.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.116352 restraints weight = 6753.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.117389 restraints weight = 5120.885| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3398 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3398 r_free = 0.3398 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (12 function evaluations) r_final: 0.3398 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16386 Z= 0.200 Angle : 0.638 11.159 22134 Z= 0.335 Chirality : 0.045 0.201 2360 Planarity : 0.004 0.038 2818 Dihedral : 8.753 133.509 2295 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.02 % Allowed : 21.85 % Favored : 74.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.19), residues: 1932 helix: 1.20 (0.15), residues: 1126 sheet: 0.57 (0.47), residues: 100 loop : 0.15 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 686 TYR 0.026 0.002 TYR A 571 PHE 0.028 0.002 PHE C 172 TRP 0.022 0.002 TRP D 44 HIS 0.006 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.20 (16386) covalent geometry : angle 0.63755 / 0.33 (22134) hydrogen bonds : bond 0.04164 / 2.66 ( 871) hydrogen bonds : angle 4.98572 / 3.57 ( 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 561 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 492 time to evaluate : 0.524 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 27 ASP cc_start: 0.8986 (p0) cc_final: 0.8404 (p0) REVERT: A 31 GLU cc_start: 0.9054 (mp0) cc_final: 0.8659 (mp0) REVERT: A 69 LEU cc_start: 0.9445 (mt) cc_final: 0.9091 (pp) REVERT: A 76 ASP cc_start: 0.9015 (m-30) cc_final: 0.8620 (m-30) REVERT: A 116 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7880 (mt-10) REVERT: A 139 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8326 (mt-10) REVERT: A 147 GLN cc_start: 0.9268 (mt0) cc_final: 0.8383 (mt0) REVERT: A 218 ASN cc_start: 0.8762 (t0) cc_final: 0.8236 (t0) REVERT: A 221 LYS cc_start: 0.8699 (mmtp) cc_final: 0.8329 (mmtp) REVERT: A 232 ASN cc_start: 0.9381 (m-40) cc_final: 0.9035 (m110) REVERT: A 263 ASP cc_start: 0.8354 (m-30) cc_final: 0.7936 (m-30) REVERT: A 346 LEU cc_start: 0.9427 (mp) cc_final: 0.9205 (mp) REVERT: A 381 LEU cc_start: 0.8979 (tp) cc_final: 0.8434 (pt) REVERT: A 384 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7569 (pm20) REVERT: A 411 LEU cc_start: 0.8284 (mp) cc_final: 0.8074 (mt) REVERT: A 415 ASN cc_start: 0.8981 (t0) cc_final: 0.8607 (t0) REVERT: A 420 MET cc_start: 0.8608 (mmm) cc_final: 0.8295 (mmm) REVERT: A 427 LYS cc_start: 0.9054 (mmmm) cc_final: 0.8752 (tppt) REVERT: A 447 ASN cc_start: 0.8163 (m-40) cc_final: 0.7168 (t0) REVERT: A 453 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8307 (ttt-90) REVERT: A 479 TYR cc_start: 0.8969 (t80) cc_final: 0.8567 (t80) REVERT: A 498 TYR cc_start: 0.9148 (m-80) cc_final: 0.8799 (m-80) REVERT: A 505 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8251 (mt-10) REVERT: A 561 LEU cc_start: 0.8740 (tp) cc_final: 0.8364 (tt) REVERT: A 588 GLN cc_start: 0.8977 (mm110) cc_final: 0.8541 (mm110) REVERT: A 602 GLU cc_start: 0.7543 (pt0) cc_final: 0.6712 (pt0) REVERT: A 604 ARG cc_start: 0.8411 (tpp-160) cc_final: 0.8129 (tpp-160) REVERT: A 640 MET cc_start: 0.9254 (OUTLIER) cc_final: 0.8155 (tpp) REVERT: A 684 TYR cc_start: 0.7256 (OUTLIER) cc_final: 0.6906 (m-10) REVERT: B 108 THR cc_start: 0.8756 (OUTLIER) cc_final: 0.8441 (p) REVERT: B 119 GLU cc_start: 0.9005 (mp0) cc_final: 0.8373 (mp0) REVERT: B 190 MET cc_start: 0.9202 (mtm) cc_final: 0.8899 (mtm) REVERT: B 267 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8823 (mm) REVERT: B 274 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6899 (ttm170) REVERT: B 322 MET cc_start: 0.8976 (mmt) cc_final: 0.8639 (mmt) REVERT: B 375 LYS cc_start: 0.9011 (mmtm) cc_final: 0.8511 (mppt) REVERT: B 441 GLU cc_start: 0.8715 (pt0) cc_final: 0.8475 (pt0) REVERT: B 467 ASN cc_start: 0.9295 (m-40) cc_final: 0.8528 (m-40) REVERT: B 494 MET cc_start: 0.8908 (mtp) cc_final: 0.8613 (mtp) REVERT: B 515 ASP cc_start: 0.8896 (m-30) cc_final: 0.8661 (m-30) REVERT: B 571 TYR cc_start: 0.8410 (t80) cc_final: 0.8138 (t80) REVERT: B 595 MET cc_start: 0.8904 (mmm) cc_final: 0.8484 (mmm) REVERT: B 604 ARG cc_start: 0.8974 (tpp80) cc_final: 0.8404 (mmt-90) REVERT: B 667 LEU cc_start: 0.8583 (mt) cc_final: 0.8330 (tt) REVERT: C 41 LEU cc_start: 0.7208 (pp) cc_final: 0.6606 (mm) REVERT: C 162 TYR cc_start: 0.9191 (m-10) cc_final: 0.8792 (m-80) REVERT: C 221 LYS cc_start: 0.6320 (OUTLIER) cc_final: 0.6106 (ptmm) REVERT: C 227 PHE cc_start: 0.8164 (t80) cc_final: 0.7884 (t80) REVERT: C 242 TYR cc_start: 0.9261 (t80) cc_final: 0.8334 (t80) REVERT: D 191 ILE cc_start: 0.0567 (pt) cc_final: 0.0219 (pt) outliers start: 69 outliers final: 48 residues processed: 528 average time/residue: 0.1124 time to fit residues: 89.8881 Evaluate side-chains 518 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 462 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 216 VAL 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 320 ASN Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 442 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 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 653 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR 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 231 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 274 ARG 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 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 141 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 312 VAL 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 237 GLU Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 chunk 120 optimal weight: 0.0970 chunk 37 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 32 optimal weight: 0.3980 chunk 122 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 168 optimal weight: 7.9990 chunk 157 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 320 ASN A 410 ASN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.153131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.111717 restraints weight = 32593.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.115405 restraints weight = 15817.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.117738 restraints weight = 9562.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.119400 restraints weight = 6659.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.120550 restraints weight = 5118.512| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.5507 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= 0.139 Angle : 0.621 13.159 22134 Z= 0.323 Chirality : 0.043 0.230 2360 Planarity : 0.003 0.050 2818 Dihedral : 8.427 135.437 2293 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 3.21 % Allowed : 22.90 % Favored : 73.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.19), residues: 1932 helix: 1.24 (0.15), residues: 1124 sheet: -0.22 (0.42), residues: 134 loop : 0.20 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 686 TYR 0.019 0.001 TYR C 162 PHE 0.038 0.002 PHE C 166 TRP 0.025 0.002 TRP D 44 HIS 0.007 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (16386) covalent geometry : angle 0.62141 / 0.32 (22134) hydrogen bonds : bond 0.03953 / 2.52 ( 871) hydrogen bonds : angle 4.90175 / 3.51 ( 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 554 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 499 time to evaluate : 0.567 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: A 27 ASP cc_start: 0.8946 (p0) cc_final: 0.8527 (p0) REVERT: A 69 LEU cc_start: 0.9417 (mt) cc_final: 0.9093 (pp) REVERT: A 76 ASP cc_start: 0.8764 (m-30) cc_final: 0.8472 (m-30) REVERT: A 116 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7713 (mt-10) REVERT: A 139 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8183 (mt-10) REVERT: A 147 GLN cc_start: 0.9148 (mt0) cc_final: 0.8410 (mt0) REVERT: A 150 GLN cc_start: 0.9141 (tm-30) cc_final: 0.8691 (tm-30) REVERT: A 179 LEU cc_start: 0.9150 (tp) cc_final: 0.8869 (tt) REVERT: A 188 ILE cc_start: 0.9613 (mt) cc_final: 0.9378 (mm) REVERT: A 209 LYS cc_start: 0.8707 (ttmt) cc_final: 0.8245 (ttmm) REVERT: A 218 ASN cc_start: 0.8665 (t0) cc_final: 0.8143 (t0) REVERT: A 228 LYS cc_start: 0.9171 (mttp) cc_final: 0.8931 (mmtt) REVERT: A 263 ASP cc_start: 0.8334 (m-30) cc_final: 0.7889 (m-30) REVERT: A 346 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9060 (mp) REVERT: A 362 ASP cc_start: 0.8013 (m-30) cc_final: 0.7486 (m-30) REVERT: A 381 LEU cc_start: 0.8956 (tp) cc_final: 0.8390 (pt) REVERT: A 384 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7468 (pm20) REVERT: A 411 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7911 (mt) REVERT: A 415 ASN cc_start: 0.8944 (t0) cc_final: 0.8591 (t0) REVERT: A 420 MET cc_start: 0.8587 (mmm) cc_final: 0.8248 (mmm) REVERT: A 453 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8833 (ttt180) REVERT: A 467 ASN cc_start: 0.9074 (t0) cc_final: 0.8832 (t0) REVERT: A 493 MET cc_start: 0.8867 (tmm) cc_final: 0.8573 (tmm) REVERT: A 498 TYR cc_start: 0.9092 (m-80) cc_final: 0.8691 (m-80) REVERT: A 505 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8199 (mt-10) REVERT: A 510 LYS cc_start: 0.9421 (mtmt) cc_final: 0.9102 (mtpt) REVERT: A 561 LEU cc_start: 0.8710 (tp) cc_final: 0.8331 (tt) REVERT: A 583 SER cc_start: 0.8890 (m) cc_final: 0.8576 (t) REVERT: A 588 GLN cc_start: 0.8831 (mm110) cc_final: 0.8560 (mm110) REVERT: A 590 SER cc_start: 0.9269 (p) cc_final: 0.8819 (t) REVERT: A 640 MET cc_start: 0.9228 (OUTLIER) cc_final: 0.8932 (tmm) REVERT: B 71 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9120 (mp) REVERT: B 108 THR cc_start: 0.8688 (OUTLIER) cc_final: 0.8387 (p) REVERT: B 112 LYS cc_start: 0.9507 (OUTLIER) cc_final: 0.9272 (ptmm) REVERT: B 119 GLU cc_start: 0.8941 (mp0) cc_final: 0.8260 (mp0) REVERT: B 191 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8625 (mm-40) REVERT: B 194 LYS cc_start: 0.9389 (ttpt) cc_final: 0.9068 (ttpt) REVERT: B 267 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8852 (mm) REVERT: B 274 ARG cc_start: 0.7401 (OUTLIER) cc_final: 0.6864 (ttm170) REVERT: B 374 SER cc_start: 0.9271 (t) cc_final: 0.9069 (p) REVERT: B 494 MET cc_start: 0.8763 (mtp) cc_final: 0.8503 (mtp) REVERT: B 515 ASP cc_start: 0.8817 (m-30) cc_final: 0.8582 (m-30) REVERT: B 604 ARG cc_start: 0.8779 (tpp80) cc_final: 0.8334 (mmt-90) REVERT: B 627 LYS cc_start: 0.9095 (tttt) cc_final: 0.8648 (tttt) REVERT: B 657 PHE cc_start: 0.9032 (m-80) cc_final: 0.8697 (m-80) REVERT: C 41 LEU cc_start: 0.7204 (pp) cc_final: 0.6636 (mm) REVERT: C 124 TRP cc_start: 0.7196 (t60) cc_final: 0.6774 (t60) REVERT: C 141 LEU cc_start: 0.9175 (mt) cc_final: 0.8854 (pp) REVERT: C 157 MET cc_start: 0.9083 (mtt) cc_final: 0.8861 (mtt) REVERT: C 163 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9113 (tt) REVERT: C 168 PHE cc_start: 0.9157 (m-80) cc_final: 0.8721 (m-80) REVERT: C 242 TYR cc_start: 0.9177 (t80) cc_final: 0.8602 (t80) REVERT: C 271 LEU cc_start: 0.7289 (mm) cc_final: 0.7067 (mm) outliers start: 55 outliers final: 29 residues processed: 529 average time/residue: 0.1159 time to fit residues: 93.2560 Evaluate side-chains 485 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 445 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 321 GLU Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 112 LYS 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 274 ARG Chi-restraints excluded: chain B residue 319 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 467 ASN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 168 PHE 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: 9.9990 chunk 183 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 172 optimal weight: 0.4980 chunk 52 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 136 optimal weight: 0.0980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN A 320 ASN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 232 ASN B 320 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.152901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.110806 restraints weight = 32617.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.114585 restraints weight = 16094.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.116904 restraints weight = 9720.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.118707 restraints weight = 6858.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.119694 restraints weight = 5237.160| |-----------------------------------------------------------------------------| r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3466 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.5718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16386 Z= 0.152 Angle : 0.639 11.243 22134 Z= 0.330 Chirality : 0.043 0.180 2360 Planarity : 0.003 0.050 2818 Dihedral : 8.329 137.323 2291 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.79 % Allowed : 23.83 % Favored : 72.38 % 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: 1.01 (0.19), residues: 1932 helix: 1.21 (0.15), residues: 1123 sheet: -0.33 (0.42), residues: 134 loop : 0.14 (0.24), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 686 TYR 0.035 0.001 TYR B 36 PHE 0.028 0.002 PHE C 168 TRP 0.028 0.002 TRP D 44 HIS 0.007 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (16386) covalent geometry : angle 0.63922 / 0.33 (22134) hydrogen bonds : bond 0.03878 / 2.47 ( 871) hydrogen bonds : angle 4.87670 / 3.49 ( 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 557 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 492 time to evaluate : 0.557 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: 0.8933 (p0) cc_final: 0.8283 (p0) REVERT: A 69 LEU cc_start: 0.9415 (mt) cc_final: 0.9088 (pp) REVERT: A 76 ASP cc_start: 0.8780 (m-30) cc_final: 0.8488 (m-30) REVERT: A 139 GLU cc_start: 0.8526 (mt-10) cc_final: 0.8140 (mt-10) REVERT: A 147 GLN cc_start: 0.9165 (mt0) cc_final: 0.8373 (mt0) REVERT: A 150 GLN cc_start: 0.9155 (tm-30) cc_final: 0.8721 (tm-30) REVERT: A 178 SER cc_start: 0.8789 (OUTLIER) cc_final: 0.8581 (p) REVERT: A 205 LYS cc_start: 0.8565 (mmmm) cc_final: 0.8352 (mmtp) REVERT: A 209 LYS cc_start: 0.8682 (ttmt) cc_final: 0.8329 (ttmm) REVERT: A 218 ASN cc_start: 0.8622 (t0) cc_final: 0.8102 (t0) REVERT: A 221 LYS cc_start: 0.8860 (mmtp) cc_final: 0.8480 (mmtp) REVERT: A 263 ASP cc_start: 0.8368 (m-30) cc_final: 0.7926 (m-30) REVERT: A 286 ASP cc_start: 0.7540 (m-30) cc_final: 0.7262 (m-30) REVERT: A 346 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9087 (mp) REVERT: A 348 MET cc_start: 0.8368 (mmm) cc_final: 0.7884 (mmm) REVERT: A 362 ASP cc_start: 0.7966 (m-30) cc_final: 0.7539 (m-30) REVERT: A 381 LEU cc_start: 0.8968 (tp) cc_final: 0.8381 (pt) REVERT: A 384 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7493 (pm20) REVERT: A 411 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7888 (mt) REVERT: A 415 ASN cc_start: 0.9021 (t0) cc_final: 0.8179 (t0) REVERT: A 418 ASN cc_start: 0.9116 (m-40) cc_final: 0.8532 (m-40) REVERT: A 420 MET cc_start: 0.8659 (mmm) cc_final: 0.8287 (mmm) REVERT: A 479 TYR cc_start: 0.8988 (t80) cc_final: 0.8681 (t80) REVERT: A 493 MET cc_start: 0.8898 (tmm) cc_final: 0.8589 (tmm) REVERT: A 494 MET cc_start: 0.8599 (ttm) cc_final: 0.8387 (ttm) REVERT: A 498 TYR cc_start: 0.9079 (m-80) cc_final: 0.8652 (m-80) REVERT: A 505 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8052 (mt-10) REVERT: A 561 LEU cc_start: 0.8722 (tp) cc_final: 0.8333 (tt) REVERT: A 583 SER cc_start: 0.8884 (m) cc_final: 0.8571 (t) REVERT: A 590 SER cc_start: 0.9251 (p) cc_final: 0.9038 (m) REVERT: A 640 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.7926 (tpp) REVERT: A 684 TYR cc_start: 0.7379 (OUTLIER) cc_final: 0.6674 (m-10) REVERT: B 71 LEU cc_start: 0.9391 (OUTLIER) cc_final: 0.9170 (mp) REVERT: B 108 THR cc_start: 0.8802 (OUTLIER) cc_final: 0.8518 (p) REVERT: B 112 LYS cc_start: 0.9503 (OUTLIER) cc_final: 0.9259 (ptmm) REVERT: B 119 GLU cc_start: 0.8880 (mp0) cc_final: 0.8253 (mp0) REVERT: B 186 ILE cc_start: 0.9699 (mp) cc_final: 0.9435 (mp) REVERT: B 190 MET cc_start: 0.9201 (mtm) cc_final: 0.9000 (mtm) REVERT: B 191 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8714 (mm-40) REVERT: B 194 LYS cc_start: 0.9375 (ttpt) cc_final: 0.9001 (ttpt) REVERT: B 267 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8847 (mm) REVERT: B 274 ARG cc_start: 0.7341 (OUTLIER) cc_final: 0.6834 (ttm170) REVERT: B 322 MET cc_start: 0.8804 (mmm) cc_final: 0.8506 (mmm) REVERT: B 341 LYS cc_start: 0.9296 (pttp) cc_final: 0.8919 (mtmm) REVERT: B 384 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.6777 (pm20) REVERT: B 467 ASN cc_start: 0.9196 (t0) cc_final: 0.8479 (m-40) REVERT: B 494 MET cc_start: 0.8849 (mtp) cc_final: 0.8532 (mtp) REVERT: B 515 ASP cc_start: 0.8818 (m-30) cc_final: 0.8595 (m-30) REVERT: B 578 ILE cc_start: 0.8755 (mt) cc_final: 0.8555 (mt) REVERT: B 602 GLU cc_start: 0.7554 (pt0) cc_final: 0.6434 (pt0) REVERT: B 604 ARG cc_start: 0.8868 (tpp80) cc_final: 0.8373 (mmt-90) REVERT: C 110 MET cc_start: 0.6468 (mpp) cc_final: 0.6191 (mpp) REVERT: C 141 LEU cc_start: 0.9190 (mt) cc_final: 0.8864 (pp) REVERT: C 163 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9074 (tt) REVERT: C 168 PHE cc_start: 0.9151 (m-80) cc_final: 0.8706 (m-80) REVERT: C 242 TYR cc_start: 0.9194 (t80) cc_final: 0.8797 (t80) REVERT: C 271 LEU cc_start: 0.7369 (OUTLIER) cc_final: 0.7125 (mm) outliers start: 65 outliers final: 41 residues processed: 527 average time/residue: 0.1092 time to fit residues: 87.5915 Evaluate side-chains 498 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 443 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 270 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 112 LYS 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 274 ARG 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 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 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 594 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 668 ASN Chi-restraints excluded: chain C residue 97 GLU Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 244 GLU 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 168 PHE 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: 4.9990 chunk 51 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 186 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 115 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN A 320 ASN A 447 ASN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 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 = 0.3921 r_free = 0.3921 target = 0.150177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.108802 restraints weight = 32745.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.112347 restraints weight = 16074.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.114772 restraints weight = 9890.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.116386 restraints weight = 6773.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.117445 restraints weight = 5253.984| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (13 function evaluations) r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.5965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 16386 Z= 0.202 Angle : 0.663 11.111 22134 Z= 0.343 Chirality : 0.045 0.279 2360 Planarity : 0.003 0.034 2818 Dihedral : 8.256 138.463 2291 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.79 % Allowed : 24.18 % Favored : 72.03 % 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: 0.90 (0.19), residues: 1932 helix: 1.10 (0.15), residues: 1123 sheet: -0.39 (0.42), residues: 138 loop : 0.14 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 686 TYR 0.024 0.002 TYR B 36 PHE 0.033 0.002 PHE D 109 TRP 0.030 0.002 TRP D 44 HIS 0.008 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (16386) covalent geometry : angle 0.66291 / 0.34 (22134) hydrogen bonds : bond 0.03986 / 2.54 ( 871) hydrogen bonds : angle 4.96915 / 3.55 ( 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 526 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 461 time to evaluate : 0.667 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 76 ASP cc_start: 0.8764 (m-30) cc_final: 0.8476 (m-30) REVERT: A 150 GLN cc_start: 0.9219 (tm-30) cc_final: 0.8702 (tm-30) REVERT: A 164 ARG cc_start: 0.7429 (ptm-80) cc_final: 0.7180 (ptt90) REVERT: A 179 LEU cc_start: 0.9200 (tp) cc_final: 0.8907 (tt) REVERT: A 205 LYS cc_start: 0.8456 (mmmm) cc_final: 0.8250 (mmtp) REVERT: A 209 LYS cc_start: 0.8815 (ttmt) cc_final: 0.8372 (ttmm) REVERT: A 218 ASN cc_start: 0.8601 (t0) cc_final: 0.8073 (t0) REVERT: A 263 ASP cc_start: 0.8393 (m-30) cc_final: 0.7938 (m-30) REVERT: A 346 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9188 (mp) REVERT: A 350 ARG cc_start: 0.8472 (mtp85) cc_final: 0.8210 (mtp-110) REVERT: A 381 LEU cc_start: 0.8987 (tp) cc_final: 0.8384 (pt) REVERT: A 384 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.6946 (pm20) REVERT: A 415 ASN cc_start: 0.8964 (t0) cc_final: 0.8151 (t0) REVERT: A 418 ASN cc_start: 0.9138 (m-40) cc_final: 0.8567 (m-40) REVERT: A 420 MET cc_start: 0.8742 (mmm) cc_final: 0.8482 (mmm) REVERT: A 453 ARG cc_start: 0.9198 (OUTLIER) cc_final: 0.8492 (ttt-90) REVERT: A 493 MET cc_start: 0.8938 (tmm) cc_final: 0.8671 (tmm) REVERT: A 494 MET cc_start: 0.8634 (ttm) cc_final: 0.8273 (ttm) REVERT: A 498 TYR cc_start: 0.9080 (m-80) cc_final: 0.8481 (m-80) REVERT: A 505 GLU cc_start: 0.8574 (mt-10) cc_final: 0.8062 (mt-10) REVERT: A 570 MET cc_start: 0.9049 (mtp) cc_final: 0.8838 (mtp) REVERT: A 640 MET cc_start: 0.9211 (OUTLIER) cc_final: 0.8940 (tmm) REVERT: A 652 ILE cc_start: 0.7323 (mm) cc_final: 0.6931 (mm) REVERT: A 668 ASN cc_start: 0.8681 (m-40) cc_final: 0.8325 (m-40) REVERT: A 684 TYR cc_start: 0.7291 (OUTLIER) cc_final: 0.6903 (m-10) REVERT: B 71 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9150 (mp) REVERT: B 95 MET cc_start: 0.8462 (tpp) cc_final: 0.8182 (tpp) REVERT: B 108 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8545 (p) REVERT: B 112 LYS cc_start: 0.9523 (OUTLIER) cc_final: 0.9305 (ptmm) REVERT: B 147 GLN cc_start: 0.9368 (mt0) cc_final: 0.9102 (mm-40) REVERT: B 186 ILE cc_start: 0.9694 (mp) cc_final: 0.9469 (mp) REVERT: B 191 GLN cc_start: 0.9058 (mm-40) cc_final: 0.8686 (mm-40) REVERT: B 194 LYS cc_start: 0.9399 (ttpt) cc_final: 0.9052 (ttpt) REVERT: B 267 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8825 (mm) REVERT: B 274 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.7075 (ttm170) REVERT: B 341 LYS cc_start: 0.9321 (pttp) cc_final: 0.9012 (mtmm) REVERT: B 375 LYS cc_start: 0.8929 (mmtm) cc_final: 0.8525 (mppt) REVERT: B 384 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.6877 (pm20) REVERT: B 441 GLU cc_start: 0.8825 (pt0) cc_final: 0.8543 (pt0) REVERT: B 494 MET cc_start: 0.8869 (mtp) cc_final: 0.8564 (mtp) REVERT: B 515 ASP cc_start: 0.8890 (m-30) cc_final: 0.8657 (m-30) REVERT: B 586 TYR cc_start: 0.8551 (m-80) cc_final: 0.8258 (m-80) REVERT: B 602 GLU cc_start: 0.7107 (pt0) cc_final: 0.6616 (pt0) REVERT: B 604 ARG cc_start: 0.8881 (tpp80) cc_final: 0.8434 (mmt-90) REVERT: B 667 LEU cc_start: 0.8425 (mt) cc_final: 0.8146 (tp) REVERT: C 141 LEU cc_start: 0.9295 (mt) cc_final: 0.8937 (pp) REVERT: C 149 ASP cc_start: 0.8341 (t0) cc_final: 0.7667 (m-30) REVERT: C 163 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9158 (tt) REVERT: C 168 PHE cc_start: 0.9122 (m-80) cc_final: 0.8680 (m-80) REVERT: C 242 TYR cc_start: 0.9213 (t80) cc_final: 0.8881 (t80) REVERT: C 271 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7292 (mm) outliers start: 65 outliers final: 40 residues processed: 497 average time/residue: 0.1176 time to fit residues: 87.7137 Evaluate side-chains 489 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 436 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 320 ASN Chi-restraints excluded: chain A residue 346 LEU 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 453 ARG Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 112 LYS 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 224 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 274 ARG Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 384 GLU 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 451 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 594 VAL Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 81 VAL Chi-restraints excluded: chain D residue 168 PHE 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: 4.9990 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 153 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 158 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 365 ASN A 447 ASN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 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 = 0.3966 r_free = 0.3966 target = 0.154042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.112426 restraints weight = 32886.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.116248 restraints weight = 16335.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.118712 restraints weight = 10010.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.120237 restraints weight = 6975.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.121368 restraints weight = 5419.203| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3487 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3487 r_free = 0.3487 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3487 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.6178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16386 Z= 0.144 Angle : 0.658 11.168 22134 Z= 0.341 Chirality : 0.044 0.179 2360 Planarity : 0.003 0.036 2818 Dihedral : 8.080 139.228 2291 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.21 % Allowed : 23.83 % Favored : 72.96 % 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: 0.87 (0.19), residues: 1932 helix: 1.15 (0.15), residues: 1120 sheet: -0.53 (0.42), residues: 138 loop : 0.02 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 686 TYR 0.021 0.001 TYR C 204 PHE 0.047 0.002 PHE D 109 TRP 0.035 0.002 TRP D 44 HIS 0.009 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (16386) covalent geometry : angle 0.65776 / 0.34 (22134) hydrogen bonds : bond 0.03873 / 2.46 ( 871) hydrogen bonds : angle 4.90325 / 3.51 ( 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 521 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 466 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8824 (p0) cc_final: 0.8481 (t0) REVERT: A 76 ASP cc_start: 0.8765 (m-30) cc_final: 0.8508 (m-30) REVERT: A 112 LYS cc_start: 0.8618 (ptpp) cc_final: 0.8343 (ptpp) REVERT: A 150 GLN cc_start: 0.9238 (tm-30) cc_final: 0.8679 (tm-30) REVERT: A 191 GLN cc_start: 0.7698 (mm-40) cc_final: 0.7492 (mm-40) REVERT: A 205 LYS cc_start: 0.8395 (mmmm) cc_final: 0.8122 (mmtp) REVERT: A 209 LYS cc_start: 0.8826 (ttmt) cc_final: 0.8338 (ttmm) REVERT: A 218 ASN cc_start: 0.8628 (t0) cc_final: 0.8083 (t0) REVERT: A 263 ASP cc_start: 0.8392 (m-30) cc_final: 0.7925 (m-30) REVERT: A 346 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9061 (mp) REVERT: A 359 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.7941 (ttp) REVERT: A 362 ASP cc_start: 0.7716 (m-30) cc_final: 0.7298 (m-30) REVERT: A 381 LEU cc_start: 0.8948 (tp) cc_final: 0.8370 (pt) REVERT: A 384 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.6954 (pm20) REVERT: A 415 ASN cc_start: 0.8887 (t0) cc_final: 0.8181 (t0) REVERT: A 418 ASN cc_start: 0.9103 (m-40) cc_final: 0.8554 (m-40) REVERT: A 427 LYS cc_start: 0.9089 (tppt) cc_final: 0.8885 (mmmt) REVERT: A 479 TYR cc_start: 0.8974 (t80) cc_final: 0.8719 (t80) REVERT: A 493 MET cc_start: 0.8960 (tmm) cc_final: 0.8701 (tmm) REVERT: A 505 GLU cc_start: 0.8585 (mt-10) cc_final: 0.8065 (mt-10) REVERT: A 561 LEU cc_start: 0.8740 (tp) cc_final: 0.8325 (tt) REVERT: A 570 MET cc_start: 0.9036 (mtp) cc_final: 0.8815 (mtp) REVERT: A 626 TYR cc_start: 0.8563 (m-80) cc_final: 0.8315 (m-80) REVERT: A 640 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8058 (tpp) REVERT: A 646 GLN cc_start: 0.8603 (pt0) cc_final: 0.8356 (pt0) REVERT: A 652 ILE cc_start: 0.7343 (mm) cc_final: 0.7014 (mm) REVERT: A 668 ASN cc_start: 0.8643 (m-40) cc_final: 0.8252 (m-40) REVERT: B 71 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9060 (mp) REVERT: B 95 MET cc_start: 0.8406 (tpp) cc_final: 0.8137 (tpp) REVERT: B 108 THR cc_start: 0.8803 (OUTLIER) cc_final: 0.8557 (p) REVERT: B 190 MET cc_start: 0.8971 (mtm) cc_final: 0.8763 (mtm) REVERT: B 194 LYS cc_start: 0.9387 (ttpt) cc_final: 0.9035 (ttpt) REVERT: B 267 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8827 (mm) REVERT: B 274 ARG cc_start: 0.7390 (OUTLIER) cc_final: 0.6972 (ttm170) REVERT: B 341 LYS cc_start: 0.9297 (pttp) cc_final: 0.8959 (mtmm) REVERT: B 348 MET cc_start: 0.8841 (ptt) cc_final: 0.8618 (ptt) REVERT: B 375 LYS cc_start: 0.8926 (mmtm) cc_final: 0.8505 (mppt) REVERT: B 384 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.6709 (pm20) REVERT: B 441 GLU cc_start: 0.8848 (pt0) cc_final: 0.8604 (pt0) REVERT: B 494 MET cc_start: 0.8815 (mtp) cc_final: 0.8495 (mtp) REVERT: B 515 ASP cc_start: 0.8816 (m-30) cc_final: 0.8574 (m-30) REVERT: B 586 TYR cc_start: 0.8471 (m-80) cc_final: 0.8115 (m-80) REVERT: B 602 GLU cc_start: 0.7085 (pt0) cc_final: 0.6490 (pt0) REVERT: B 604 ARG cc_start: 0.8776 (tpp80) cc_final: 0.8353 (mmt-90) REVERT: C 141 LEU cc_start: 0.9322 (mt) cc_final: 0.8965 (pp) REVERT: C 149 ASP cc_start: 0.8257 (t0) cc_final: 0.7674 (m-30) REVERT: C 163 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9152 (tt) REVERT: C 168 PHE cc_start: 0.9111 (m-80) cc_final: 0.8761 (m-80) REVERT: C 242 TYR cc_start: 0.9289 (t80) cc_final: 0.8943 (t80) REVERT: D 154 PHE cc_start: 0.4506 (t80) cc_final: 0.3923 (t80) outliers start: 55 outliers final: 34 residues processed: 493 average time/residue: 0.1230 time to fit residues: 92.2331 Evaluate side-chains 493 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 449 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 321 GLU 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 447 ASN Chi-restraints excluded: chain A residue 565 VAL 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 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 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 343 LEU 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 460 SER 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 594 VAL Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 131 LEU 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 81 VAL 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: 6.9990 chunk 133 optimal weight: 6.9990 chunk 149 optimal weight: 0.0000 chunk 16 optimal weight: 0.7980 chunk 114 optimal weight: 0.9990 chunk 86 optimal weight: 0.0070 chunk 49 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 88 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 overall best weight: 0.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 447 ASN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 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 = 0.3994 r_free = 0.3994 target = 0.157302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.115586 restraints weight = 32693.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.119424 restraints weight = 16191.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.121752 restraints weight = 9767.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.123490 restraints weight = 6894.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.124618 restraints weight = 5318.515| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3523 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3523 r_free = 0.3523 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 = 0.3523 r_free = 0.3523 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 (7 function evaluations) r_final: 0.3523 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.6416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 16386 Z= 0.135 Angle : 0.679 11.055 22134 Z= 0.349 Chirality : 0.044 0.251 2360 Planarity : 0.004 0.064 2818 Dihedral : 7.951 139.454 2291 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.68 % Allowed : 24.83 % 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: 0.87 (0.19), residues: 1932 helix: 1.13 (0.15), residues: 1122 sheet: -0.43 (0.42), residues: 134 loop : 0.04 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 235 TYR 0.022 0.001 TYR C 204 PHE 0.053 0.002 PHE D 109 TRP 0.040 0.002 TRP D 44 HIS 0.014 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (16386) covalent geometry : angle 0.67853 / 0.35 (22134) hydrogen bonds : bond 0.03825 / 2.44 ( 871) hydrogen bonds : angle 4.90313 / 3.52 ( 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 512 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 466 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8779 (p0) cc_final: 0.8475 (t0) REVERT: A 112 LYS cc_start: 0.8552 (ptpp) cc_final: 0.8261 (ptpp) REVERT: A 139 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8229 (mt-10) REVERT: A 147 GLN cc_start: 0.8500 (mt0) cc_final: 0.7688 (mm-40) REVERT: A 150 GLN cc_start: 0.9214 (tm-30) cc_final: 0.8717 (tm-30) REVERT: A 218 ASN cc_start: 0.8526 (t0) cc_final: 0.7936 (t0) REVERT: A 232 ASN cc_start: 0.8932 (m110) cc_final: 0.8411 (m110) REVERT: A 263 ASP cc_start: 0.8394 (m-30) cc_final: 0.7909 (m-30) REVERT: A 346 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.9004 (mp) REVERT: A 359 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7621 (ttp) REVERT: A 362 ASP cc_start: 0.7569 (m-30) cc_final: 0.7258 (m-30) REVERT: A 381 LEU cc_start: 0.8954 (tp) cc_final: 0.8370 (pt) REVERT: A 384 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.6979 (pm20) REVERT: A 415 ASN cc_start: 0.8781 (t0) cc_final: 0.8030 (t0) REVERT: A 418 ASN cc_start: 0.9069 (m-40) cc_final: 0.8512 (m-40) REVERT: A 447 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.7279 (t0) REVERT: A 493 MET cc_start: 0.8967 (tmm) cc_final: 0.8681 (tmm) REVERT: A 505 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8072 (mt-10) REVERT: A 561 LEU cc_start: 0.8709 (tp) cc_final: 0.8304 (tt) REVERT: A 590 SER cc_start: 0.9134 (t) cc_final: 0.8791 (p) REVERT: A 626 TYR cc_start: 0.8530 (m-80) cc_final: 0.8275 (m-80) REVERT: A 640 MET cc_start: 0.9145 (OUTLIER) cc_final: 0.7925 (tpp) REVERT: A 646 GLN cc_start: 0.8574 (pt0) cc_final: 0.8287 (pt0) REVERT: A 668 ASN cc_start: 0.8572 (m-40) cc_final: 0.8228 (m-40) REVERT: A 686 ARG cc_start: 0.7927 (mtp-110) cc_final: 0.7582 (mtp-110) REVERT: B 71 LEU cc_start: 0.9392 (OUTLIER) cc_final: 0.9114 (mp) REVERT: B 87 LYS cc_start: 0.8763 (tppt) cc_final: 0.8471 (mmmt) REVERT: B 88 LYS cc_start: 0.8655 (mmmm) cc_final: 0.8365 (mppt) REVERT: B 95 MET cc_start: 0.8454 (tpp) cc_final: 0.8184 (tpp) REVERT: B 108 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.7548 (p) REVERT: B 227 MET cc_start: 0.9076 (mtp) cc_final: 0.8789 (mtp) REVERT: B 267 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8887 (mm) REVERT: B 274 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7242 (ttm170) REVERT: B 348 MET cc_start: 0.8848 (ptt) cc_final: 0.8630 (ptt) REVERT: B 441 GLU cc_start: 0.8848 (pt0) cc_final: 0.8576 (pt0) REVERT: B 471 TYR cc_start: 0.8768 (t80) cc_final: 0.7967 (t80) REVERT: B 494 MET cc_start: 0.8740 (mtp) cc_final: 0.8363 (mtp) REVERT: B 515 ASP cc_start: 0.8782 (m-30) cc_final: 0.8565 (m-30) REVERT: B 586 TYR cc_start: 0.8446 (m-80) cc_final: 0.8179 (m-80) REVERT: B 602 GLU cc_start: 0.7005 (pt0) cc_final: 0.6492 (pt0) REVERT: B 604 ARG cc_start: 0.8737 (tpp80) cc_final: 0.8397 (mmt-90) REVERT: B 639 ASP cc_start: 0.8710 (m-30) cc_final: 0.8437 (m-30) REVERT: B 640 MET cc_start: 0.8988 (tpp) cc_final: 0.8222 (tpp) REVERT: C 141 LEU cc_start: 0.9376 (mt) cc_final: 0.8976 (pp) REVERT: C 149 ASP cc_start: 0.8260 (t0) cc_final: 0.7679 (m-30) REVERT: C 163 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9174 (tt) REVERT: C 168 PHE cc_start: 0.9062 (m-80) cc_final: 0.8724 (m-80) REVERT: C 242 TYR cc_start: 0.9294 (t80) cc_final: 0.8973 (t80) outliers start: 46 outliers final: 30 residues processed: 489 average time/residue: 0.1197 time to fit residues: 88.9435 Evaluate side-chains 481 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 441 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 321 GLU 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 421 GLU Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR 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 193 SER Chi-restraints excluded: chain B residue 216 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 343 LEU 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 451 VAL 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 594 VAL Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 174 TYR 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: 5.9990 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 189 optimal weight: 30.0000 chunk 181 optimal weight: 5.9990 chunk 165 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 191 GLN A 232 ASN A 320 ASN ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 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 = 0.3965 r_free = 0.3965 target = 0.153515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.112794 restraints weight = 33109.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.116570 restraints weight = 16359.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.119009 restraints weight = 9986.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.120531 restraints weight = 6900.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.121316 restraints weight = 5341.643| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3484 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3484 r_free = 0.3484 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3484 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.6477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 16386 Z= 0.169 Angle : 0.706 11.321 22134 Z= 0.364 Chirality : 0.045 0.283 2360 Planarity : 0.004 0.060 2818 Dihedral : 7.897 140.060 2291 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.68 % Allowed : 25.00 % Favored : 72.32 % 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: 0.79 (0.19), residues: 1932 helix: 1.09 (0.15), residues: 1118 sheet: -0.46 (0.43), residues: 134 loop : -0.05 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 235 TYR 0.021 0.001 TYR C 204 PHE 0.056 0.002 PHE D 109 TRP 0.038 0.002 TRP D 44 HIS 0.015 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.17 (16386) covalent geometry : angle 0.70587 / 0.36 (22134) hydrogen bonds : bond 0.03862 / 2.47 ( 871) hydrogen bonds : angle 4.95707 / 3.56 ( 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 498 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 452 time to evaluate : 0.580 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 8 LYS cc_start: 0.9001 (ptmt) cc_final: 0.8792 (ptmm) REVERT: A 27 ASP cc_start: 0.8766 (p0) cc_final: 0.8441 (t0) REVERT: A 147 GLN cc_start: 0.8743 (mt0) cc_final: 0.7593 (mm-40) REVERT: A 150 GLN cc_start: 0.9229 (tm-30) cc_final: 0.8691 (tm-30) REVERT: A 179 LEU cc_start: 0.9077 (tp) cc_final: 0.8853 (tt) REVERT: A 218 ASN cc_start: 0.8595 (t0) cc_final: 0.8031 (t0) REVERT: A 263 ASP cc_start: 0.8399 (m-30) cc_final: 0.7905 (m-30) REVERT: A 346 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9072 (mp) REVERT: A 359 MET cc_start: 0.8458 (OUTLIER) cc_final: 0.8029 (ttp) REVERT: A 381 LEU cc_start: 0.8997 (tp) cc_final: 0.8432 (pt) REVERT: A 384 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.6897 (pm20) REVERT: A 415 ASN cc_start: 0.8798 (t0) cc_final: 0.8084 (t0) REVERT: A 418 ASN cc_start: 0.9118 (m-40) cc_final: 0.8545 (m-40) REVERT: A 493 MET cc_start: 0.8942 (tmm) cc_final: 0.8673 (tmm) REVERT: A 505 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8078 (mt-10) REVERT: A 626 TYR cc_start: 0.8750 (m-80) cc_final: 0.8373 (m-80) REVERT: A 640 MET cc_start: 0.9137 (OUTLIER) cc_final: 0.7859 (tpp) REVERT: A 646 GLN cc_start: 0.8565 (pt0) cc_final: 0.8259 (pt0) REVERT: A 668 ASN cc_start: 0.8612 (m-40) cc_final: 0.8246 (m-40) REVERT: A 686 ARG cc_start: 0.7845 (mtp-110) cc_final: 0.7531 (mtp-110) REVERT: B 88 LYS cc_start: 0.8701 (mmmm) cc_final: 0.8440 (mppt) REVERT: B 95 MET cc_start: 0.8493 (tpp) cc_final: 0.8183 (tpp) REVERT: B 232 ASN cc_start: 0.8764 (OUTLIER) cc_final: 0.8542 (m110) REVERT: B 267 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8730 (mm) REVERT: B 341 LYS cc_start: 0.9313 (pttp) cc_final: 0.8909 (mtmm) REVERT: B 348 MET cc_start: 0.8851 (ptt) cc_final: 0.8636 (ptt) REVERT: B 375 LYS cc_start: 0.8916 (mmtm) cc_final: 0.8505 (mppt) REVERT: B 384 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.6723 (pm20) REVERT: B 441 GLU cc_start: 0.8841 (pt0) cc_final: 0.8586 (pt0) REVERT: B 494 MET cc_start: 0.8837 (mtp) cc_final: 0.8500 (mtp) REVERT: B 515 ASP cc_start: 0.8800 (m-30) cc_final: 0.8559 (m-30) REVERT: B 586 TYR cc_start: 0.8447 (m-80) cc_final: 0.7973 (m-80) REVERT: B 602 GLU cc_start: 0.6900 (pt0) cc_final: 0.6127 (pt0) REVERT: B 604 ARG cc_start: 0.8786 (tpp80) cc_final: 0.8434 (mmt-90) REVERT: B 639 ASP cc_start: 0.8708 (m-30) cc_final: 0.8432 (m-30) REVERT: C 141 LEU cc_start: 0.9476 (mt) cc_final: 0.9122 (pp) REVERT: C 149 ASP cc_start: 0.8318 (t0) cc_final: 0.7660 (m-30) REVERT: C 163 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9099 (tt) REVERT: C 168 PHE cc_start: 0.9039 (m-80) cc_final: 0.8681 (m-80) REVERT: C 242 TYR cc_start: 0.9266 (t80) cc_final: 0.8963 (t80) outliers start: 46 outliers final: 31 residues processed: 474 average time/residue: 0.1162 time to fit residues: 83.5907 Evaluate side-chains 472 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 433 time to evaluate : 0.725 ------------------------------------------------------------------------------- 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 321 GLU 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 583 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 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 232 ASN 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 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 425 ILE Chi-restraints excluded: chain B residue 435 SER 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 587 VAL Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 174 TYR 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: 0.9980 chunk 1 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 39 optimal weight: 0.0000 chunk 25 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 125 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.156387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.116009 restraints weight = 32908.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.119806 restraints weight = 16014.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.122118 restraints weight = 9604.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.123793 restraints weight = 6735.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.124954 restraints weight = 5195.723| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.122 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.6633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 16386 Z= 0.140 Angle : 0.717 13.768 22134 Z= 0.367 Chirality : 0.045 0.269 2360 Planarity : 0.004 0.056 2818 Dihedral : 7.806 139.749 2291 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.56 % Allowed : 24.94 % 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: 0.75 (0.19), residues: 1932 helix: 1.06 (0.15), residues: 1124 sheet: -0.43 (0.42), residues: 144 loop : -0.08 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 235 TYR 0.022 0.001 TYR C 204 PHE 0.058 0.002 PHE D 109 TRP 0.041 0.002 TRP D 44 HIS 0.012 0.001 HIS D 80 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (16386) covalent geometry : angle 0.71710 / 0.37 (22134) hydrogen bonds : bond 0.03839 / 2.46 ( 871) hydrogen bonds : angle 4.95870 / 3.56 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3086.59 seconds wall clock time: 54 minutes 22.32 seconds (3262.32 seconds total)