Starting phenix.real_space_refine on Sun Aug 24 01:08:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byx_45047/08_2025/9byx_45047_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byx_45047/08_2025/9byx_45047.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9byx_45047/08_2025/9byx_45047.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byx_45047/08_2025/9byx_45047.map" model { file = "/net/cci-nas-00/data/ceres_data/9byx_45047/08_2025/9byx_45047_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byx_45047/08_2025/9byx_45047_neut.cif" } resolution = 3.94 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.02, per 1000 atoms: 0.19 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: 1.35 Conformation dependent library (CDL) restraints added in 626.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.35 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: 2.65 Time building geometry restraints manager: 1.79 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=" 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=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.039 1.20e-02 6.94e+03 1.04e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.033 1.08e-02 8.57e+03 9.06e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.569 -0.032 1.17e-02 7.31e+03 7.33e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.572 -0.032 1.25e-02 6.40e+03 6.67e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21570 2.09 - 4.18: 521 4.18 - 6.27: 38 6.27 - 8.37: 1 8.37 - 10.46: 4 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 - 35.79: 9470 35.79 - 71.58: 337 71.58 - 107.37: 37 107.37 - 143.16: 3 143.16 - 178.94: 3 Dihedral angle restraints: 9850 sinusoidal: 4092 harmonic: 5758 Sorted by residual: dihedral pdb=" C2 TTP A 803 " pdb=" C1' TTP A 803 " pdb=" N1 TTP A 803 " pdb=" O4' TTP A 803 " ideal model delta sinusoidal sigma weight residual -58.32 120.63 -178.94 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual 301.68 151.17 150.52 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" C5' TTP A 803 " pdb=" O5' TTP A 803 " pdb=" PA TTP A 803 " pdb=" O3A TTP A 803 " ideal model delta sinusoidal sigma weight residual 179.97 31.91 148.06 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 9847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2143 0.093 - 0.186: 182 0.186 - 0.279: 30 0.279 - 0.372: 3 0.372 - 0.464: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.39e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.64e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO D 75 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " 0.017 2.00e-02 2.50e+03 1.11e-02 2.16e+00 pdb=" CG PHE D 92 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 169 " 0.017 2.00e-02 2.50e+03 9.81e-03 1.93e+00 pdb=" CG TYR C 169 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 169 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 169 " 0.008 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 129 2.51 - 3.11: 11558 3.11 - 3.70: 27040 3.70 - 4.30: 41539 4.30 - 4.90: 65436 Nonbonded interactions: 145702 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 145697 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.800 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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: 15.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 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 0.061 16386 Z= 0.315 Angle : 0.740 10.457 22134 Z= 0.463 Chirality : 0.057 0.464 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.930 178.944 6154 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 aren 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 covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.73993 (22134) hydrogen bonds : bond 0.15421 ( 871) hydrogen bonds : angle 6.51788 ( 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 : 0.390 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: 0.7984 (m-30) cc_final: 0.7597 (m-30) REVERT: A 106 LEU cc_start: 0.8439 (tp) cc_final: 0.8030 (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: 0.5938 (m-30) REVERT: A 367 VAL cc_start: 0.8979 (m) cc_final: 0.8744 (t) REVERT: A 405 LEU cc_start: 0.8674 (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: 0.6582 (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: 0.7243 (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: 0.8183 (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: 0.7099 (m-80) cc_final: 0.6871 (m-80) REVERT: B 658 LEU cc_start: 0.8613 (mt) cc_final: 0.8287 (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: 0.5589 (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: 0.1323 time to fit residues: 158.5832 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 : 0.552 ------------------------------------------------------------------------------- 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: 9.9990 chunk 149 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 361 GLN 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 25 ASN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.156712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.112264 restraints weight = 32392.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.116243 restraints weight = 16117.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.118706 restraints weight = 9769.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.120508 restraints weight = 6931.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.121532 restraints weight = 5374.267| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.3784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 16386 Z= 0.241 Angle : 0.691 9.151 22134 Z= 0.360 Chirality : 0.045 0.181 2360 Planarity : 0.004 0.037 2818 Dihedral : 11.495 174.114 2255 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.25 % Allowed : 18.07 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.19), residues: 1932 helix: 1.37 (0.15), residues: 1133 sheet: 0.38 (0.43), residues: 130 loop : 0.57 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 256 TYR 0.024 0.002 TYR C 169 PHE 0.026 0.002 PHE C 227 TRP 0.015 0.002 TRP A 623 HIS 0.006 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00533 (16386) covalent geometry : angle 0.69069 (22134) hydrogen bonds : bond 0.04688 ( 871) hydrogen bonds : angle 5.12097 ( 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 637 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 564 time to evaluate : 0.662 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: 0.8946 (m-30) cc_final: 0.8550 (m-30) REVERT: A 116 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7860 (mt-10) REVERT: A 138 LYS cc_start: 0.8995 (mtpt) cc_final: 0.8683 (mtpp) REVERT: A 147 GLN cc_start: 0.9332 (mt0) cc_final: 0.8707 (mt0) REVERT: A 218 ASN cc_start: 0.8777 (t0) cc_final: 0.8276 (t0) REVERT: A 221 LYS cc_start: 0.8695 (mmtp) cc_final: 0.8333 (mmtp) REVERT: A 232 ASN cc_start: 0.9428 (m-40) cc_final: 0.9107 (m-40) REVERT: A 259 ASN cc_start: 0.8981 (m-40) cc_final: 0.8699 (m110) REVERT: A 263 ASP cc_start: 0.8333 (m-30) cc_final: 0.8059 (m-30) REVERT: A 381 LEU cc_start: 0.8908 (tp) cc_final: 0.8369 (pt) REVERT: A 384 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7531 (pm20) REVERT: A 415 ASN cc_start: 0.8941 (t0) cc_final: 0.8584 (t0) REVERT: A 446 ARG cc_start: 0.7673 (mmm160) cc_final: 0.7321 (mmm160) REVERT: A 468 LEU cc_start: 0.9389 (tp) cc_final: 0.9139 (tp) REVERT: A 494 MET cc_start: 0.8805 (mtp) cc_final: 0.8539 (mtp) REVERT: A 586 TYR cc_start: 0.8322 (m-80) cc_final: 0.8074 (m-80) REVERT: A 588 GLN cc_start: 0.9031 (mm-40) cc_final: 0.8781 (mm-40) REVERT: A 604 ARG cc_start: 0.8276 (tpp-160) cc_final: 0.8069 (tpp-160) REVERT: A 640 MET cc_start: 0.9183 (OUTLIER) cc_final: 0.8224 (tpp) REVERT: B 15 GLU cc_start: 0.8873 (tp30) cc_final: 0.8672 (tp30) REVERT: B 119 GLU cc_start: 0.8914 (mp0) cc_final: 0.8284 (mp0) REVERT: B 147 GLN cc_start: 0.9259 (mt0) cc_final: 0.8980 (mt0) REVERT: B 184 ARG cc_start: 0.9249 (tpp-160) cc_final: 0.8798 (tpp-160) REVERT: B 252 ASN cc_start: 0.8973 (t0) cc_final: 0.8737 (t0) REVERT: B 267 ILE cc_start: 0.9126 (OUTLIER) cc_final: 0.8720 (mm) REVERT: B 274 ARG cc_start: 0.7280 (OUTLIER) cc_final: 0.6973 (ttm170) REVERT: B 288 PHE cc_start: 0.9244 (t80) cc_final: 0.9007 (t80) REVERT: B 322 MET cc_start: 0.8928 (mmt) cc_final: 0.8596 (mmt) REVERT: B 415 ASN cc_start: 0.9532 (t0) cc_final: 0.9331 (t0) REVERT: B 479 TYR cc_start: 0.8747 (t80) cc_final: 0.8395 (t80) REVERT: B 494 MET cc_start: 0.9061 (mtp) cc_final: 0.8650 (mtp) REVERT: B 550 MET cc_start: 0.7846 (mtm) cc_final: 0.7634 (mtm) REVERT: B 571 TYR cc_start: 0.8513 (t80) cc_final: 0.8261 (t80) REVERT: B 586 TYR cc_start: 0.8487 (m-80) cc_final: 0.7937 (m-80) REVERT: B 598 MET cc_start: 0.7943 (mtm) cc_final: 0.7575 (mtp) REVERT: B 615 MET cc_start: 0.9369 (mmp) cc_final: 0.9152 (mmp) REVERT: B 626 TYR cc_start: 0.8291 (m-80) cc_final: 0.7929 (m-80) REVERT: B 686 ARG cc_start: 0.8643 (mtp85) cc_final: 0.8433 (mtp-110) REVERT: C 41 LEU cc_start: 0.6792 (pp) cc_final: 0.6367 (mm) REVERT: C 56 MET cc_start: 0.5016 (ptt) cc_final: 0.4765 (ptt) REVERT: C 93 MET cc_start: 0.2096 (mtp) cc_final: 0.1747 (mtp) REVERT: C 96 MET cc_start: 0.8815 (mmm) cc_final: 0.8614 (mmm) REVERT: C 141 LEU cc_start: 0.8770 (mt) cc_final: 0.8418 (pp) REVERT: C 162 TYR cc_start: 0.9223 (m-10) cc_final: 0.8729 (m-80) REVERT: C 237 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8218 (pp20) REVERT: C 242 TYR cc_start: 0.9285 (t80) cc_final: 0.8656 (t80) REVERT: D 138 ILE cc_start: 0.9181 (mm) cc_final: 0.8966 (tp) REVERT: D 234 GLN cc_start: 0.7906 (pt0) cc_final: 0.7689 (tm-30) outliers start: 73 outliers final: 39 residues processed: 600 average time/residue: 0.1297 time to fit residues: 117.1354 Evaluate side-chains 509 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 466 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 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 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 232 ASN 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 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 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 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: 7.9990 chunk 131 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 182 optimal weight: 10.0000 chunk 159 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 150 optimal weight: 0.8980 chunk 63 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 158 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 ASN A 410 ASN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 GLN ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 467 ASN B 645 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN D 28 GLN ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS D 210 GLN D 238 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.156675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.113196 restraints weight = 33003.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.117261 restraints weight = 16377.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.119817 restraints weight = 9795.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.121646 restraints weight = 6862.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.122812 restraints weight = 5264.798| |-----------------------------------------------------------------------------| r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3524 r_free = 0.3524 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16386 Z= 0.153 Angle : 0.628 9.243 22134 Z= 0.328 Chirality : 0.044 0.198 2360 Planarity : 0.003 0.042 2818 Dihedral : 11.042 165.783 2247 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.68 % Allowed : 21.33 % Favored : 75.99 % 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 aren not related in a simple way. whole: 1.32 (0.19), residues: 1932 helix: 1.37 (0.15), residues: 1135 sheet: 0.15 (0.42), residues: 134 loop : 0.36 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 686 TYR 0.028 0.001 TYR C 55 PHE 0.054 0.002 PHE C 168 TRP 0.022 0.002 TRP D 44 HIS 0.009 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00337 (16386) covalent geometry : angle 0.62772 (22134) hydrogen bonds : bond 0.04267 ( 871) hydrogen bonds : angle 4.97365 ( 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 576 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 530 time to evaluate : 0.663 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: 0.9012 (p0) cc_final: 0.8629 (p0) REVERT: A 76 ASP cc_start: 0.8957 (m-30) cc_final: 0.8722 (m-30) REVERT: A 157 LEU cc_start: 0.9059 (tp) cc_final: 0.8681 (tp) REVERT: A 218 ASN cc_start: 0.8710 (t0) cc_final: 0.8220 (t0) REVERT: A 221 LYS cc_start: 0.8638 (mmtp) cc_final: 0.8044 (mmtp) REVERT: A 232 ASN cc_start: 0.9409 (m-40) cc_final: 0.9054 (m-40) REVERT: A 263 ASP cc_start: 0.8386 (m-30) cc_final: 0.7997 (m-30) REVERT: A 348 MET cc_start: 0.8075 (tpp) cc_final: 0.7870 (tpt) REVERT: A 362 ASP cc_start: 0.7901 (m-30) cc_final: 0.7400 (m-30) REVERT: A 381 LEU cc_start: 0.8902 (tp) cc_final: 0.8384 (pt) REVERT: A 384 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7644 (pm20) REVERT: A 411 LEU cc_start: 0.8071 (mp) cc_final: 0.7790 (mt) REVERT: A 453 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8222 (ttt-90) REVERT: A 479 TYR cc_start: 0.8801 (t80) cc_final: 0.8403 (t80) REVERT: A 498 TYR cc_start: 0.9110 (m-80) cc_final: 0.8832 (m-80) REVERT: A 505 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8193 (mt-10) REVERT: A 550 MET cc_start: 0.6802 (mtt) cc_final: 0.6182 (mtt) REVERT: A 634 MET cc_start: 0.8466 (mmt) cc_final: 0.8253 (mmp) REVERT: A 640 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.8068 (tpp) REVERT: B 15 GLU cc_start: 0.8888 (tp30) cc_final: 0.8627 (tp30) REVERT: B 125 VAL cc_start: 0.9599 (t) cc_final: 0.9384 (m) REVERT: B 147 GLN cc_start: 0.9046 (mt0) cc_final: 0.8697 (mt0) REVERT: B 267 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8828 (mm) REVERT: B 274 ARG cc_start: 0.7284 (OUTLIER) cc_final: 0.6978 (ttm170) REVERT: B 322 MET cc_start: 0.8955 (mmt) cc_final: 0.8651 (mmt) REVERT: B 348 MET cc_start: 0.8852 (ptt) cc_final: 0.8544 (ptt) REVERT: B 350 ARG cc_start: 0.8216 (mtp85) cc_final: 0.7862 (mtp85) REVERT: B 494 MET cc_start: 0.8931 (mtp) cc_final: 0.8531 (mtp) REVERT: B 586 TYR cc_start: 0.8324 (m-80) cc_final: 0.7696 (m-80) REVERT: B 604 ARG cc_start: 0.8926 (tpp80) cc_final: 0.8400 (mmt-90) REVERT: B 615 MET cc_start: 0.9343 (mmp) cc_final: 0.9134 (mmp) REVERT: B 627 LYS cc_start: 0.8961 (tttt) cc_final: 0.8566 (ttpp) REVERT: B 640 MET cc_start: 0.9151 (tpp) cc_final: 0.8561 (tpp) REVERT: B 686 ARG cc_start: 0.8604 (mtp85) cc_final: 0.8395 (mtp-110) REVERT: C 41 LEU cc_start: 0.6928 (pp) cc_final: 0.6519 (mm) REVERT: C 124 TRP cc_start: 0.6923 (t60) cc_final: 0.6638 (t60) REVERT: C 141 LEU cc_start: 0.8781 (mt) cc_final: 0.8469 (pp) REVERT: C 162 TYR cc_start: 0.9144 (m-10) cc_final: 0.8692 (m-80) REVERT: C 242 TYR cc_start: 0.9282 (t80) cc_final: 0.8881 (t80) REVERT: C 269 MET cc_start: 0.8634 (ptp) cc_final: 0.8257 (ptp) REVERT: D 138 ILE cc_start: 0.9129 (mm) cc_final: 0.8918 (tp) REVERT: D 191 ILE cc_start: 0.0366 (pt) cc_final: 0.0037 (pt) outliers start: 46 outliers final: 30 residues processed: 553 average time/residue: 0.1247 time to fit residues: 104.8597 Evaluate side-chains 494 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 459 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 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 453 ARG Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 306 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 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 467 ASN Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 238 ASN Chi-restraints excluded: chain D residue 242 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 168 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 127 optimal weight: 5.9990 chunk 60 optimal weight: 0.6980 chunk 185 optimal weight: 20.0000 chunk 191 optimal weight: 0.0470 chunk 159 optimal weight: 4.9990 chunk 182 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 overall best weight: 2.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 320 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.151656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.108848 restraints weight = 32936.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.112609 restraints weight = 16185.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.114934 restraints weight = 9813.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.116598 restraints weight = 6895.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.117581 restraints weight = 5315.000| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- 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: 2 | |-----------------------------------------------------------------------------| |-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 | |-----------------------------------------------------------------------------| r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16386 Z= 0.197 Angle : 0.641 11.408 22134 Z= 0.334 Chirality : 0.045 0.209 2360 Planarity : 0.003 0.033 2818 Dihedral : 10.865 167.584 2247 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 14.57 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 aren not related in a simple way. whole: 1.20 (0.19), residues: 1932 helix: 1.26 (0.15), residues: 1138 sheet: 0.70 (0.48), residues: 100 loop : 0.18 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 686 TYR 0.021 0.002 TYR C 169 PHE 0.043 0.002 PHE C 168 TRP 0.023 0.002 TRP D 44 HIS 0.011 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00439 (16386) covalent geometry : angle 0.64057 (22134) hydrogen bonds : bond 0.04125 ( 871) hydrogen bonds : angle 4.97667 ( 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 553 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 484 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: A 27 ASP cc_start: 0.8997 (p0) cc_final: 0.8261 (p0) REVERT: A 31 GLU cc_start: 0.9022 (mp0) cc_final: 0.8557 (mp0) REVERT: A 69 LEU cc_start: 0.9395 (mt) cc_final: 0.9057 (pp) REVERT: A 76 ASP cc_start: 0.9003 (m-30) cc_final: 0.8623 (m-30) REVERT: A 116 GLU cc_start: 0.8171 (mt-10) cc_final: 0.7882 (mt-10) REVERT: A 188 ILE cc_start: 0.9605 (mt) cc_final: 0.9354 (mm) REVERT: A 209 LYS cc_start: 0.8630 (ttmm) cc_final: 0.8130 (ttmm) REVERT: A 218 ASN cc_start: 0.8754 (t0) cc_final: 0.8232 (t0) REVERT: A 232 ASN cc_start: 0.9369 (m-40) cc_final: 0.9049 (m110) REVERT: A 263 ASP cc_start: 0.8366 (m-30) cc_final: 0.7955 (m-30) REVERT: A 346 LEU cc_start: 0.9469 (mp) cc_final: 0.9262 (mp) REVERT: A 348 MET cc_start: 0.7997 (tpp) cc_final: 0.7711 (tpt) REVERT: A 352 GLU cc_start: 0.7869 (mm-30) cc_final: 0.7405 (mm-30) REVERT: A 362 ASP cc_start: 0.7927 (m-30) cc_final: 0.7484 (m-30) REVERT: A 381 LEU cc_start: 0.8977 (tp) cc_final: 0.8438 (pt) REVERT: A 384 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7545 (pm20) REVERT: A 411 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8026 (mt) REVERT: A 415 ASN cc_start: 0.8941 (t0) cc_final: 0.8731 (t0) REVERT: A 427 LYS cc_start: 0.9020 (mmmm) cc_final: 0.8767 (mmmm) REVERT: A 453 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8248 (ttt-90) REVERT: A 479 TYR cc_start: 0.8960 (t80) cc_final: 0.8614 (t80) REVERT: A 494 MET cc_start: 0.8511 (mtp) cc_final: 0.8247 (mtp) REVERT: A 498 TYR cc_start: 0.9114 (m-80) cc_final: 0.8829 (m-80) REVERT: A 505 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8194 (mt-10) REVERT: A 586 TYR cc_start: 0.8336 (m-80) cc_final: 0.8067 (m-80) REVERT: A 602 GLU cc_start: 0.7538 (pt0) cc_final: 0.6552 (pt0) REVERT: A 604 ARG cc_start: 0.8429 (tpp-160) cc_final: 0.8129 (tpp-160) REVERT: A 640 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8137 (tpp) REVERT: B 15 GLU cc_start: 0.8921 (tp30) cc_final: 0.8629 (tp30) REVERT: B 108 THR cc_start: 0.8721 (OUTLIER) cc_final: 0.8419 (p) REVERT: B 119 GLU cc_start: 0.8938 (mp0) cc_final: 0.8281 (mp0) REVERT: B 232 ASN cc_start: 0.8920 (OUTLIER) cc_final: 0.8690 (t0) REVERT: B 267 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8604 (mm) REVERT: B 274 ARG cc_start: 0.7338 (ttm170) cc_final: 0.6782 (ttm170) REVERT: B 322 MET cc_start: 0.8993 (mmt) cc_final: 0.8764 (mmm) REVERT: B 375 LYS cc_start: 0.8963 (mmtm) cc_final: 0.8498 (mppt) REVERT: B 467 ASN cc_start: 0.9362 (t0) cc_final: 0.8880 (m-40) REVERT: B 494 MET cc_start: 0.8922 (mtp) cc_final: 0.8585 (mtp) REVERT: B 571 TYR cc_start: 0.8324 (t80) cc_final: 0.8088 (t80) REVERT: B 586 TYR cc_start: 0.8411 (m-80) cc_final: 0.7740 (m-80) REVERT: B 604 ARG cc_start: 0.8994 (tpp80) cc_final: 0.8420 (mmt-90) REVERT: B 686 ARG cc_start: 0.8652 (mtp85) cc_final: 0.8400 (mtp-110) REVERT: C 41 LEU cc_start: 0.7176 (pp) cc_final: 0.6638 (mm) REVERT: C 124 TRP cc_start: 0.7048 (t60) cc_final: 0.6828 (t60) REVERT: C 141 LEU cc_start: 0.9008 (mt) cc_final: 0.8747 (pp) REVERT: C 162 TYR cc_start: 0.9137 (m-10) cc_final: 0.8688 (m-80) REVERT: C 242 TYR cc_start: 0.9264 (t80) cc_final: 0.8506 (t80) REVERT: C 269 MET cc_start: 0.8760 (ptp) cc_final: 0.8559 (ppp) REVERT: D 138 ILE cc_start: 0.9140 (mm) cc_final: 0.8921 (tp) REVERT: D 191 ILE cc_start: 0.0696 (pt) cc_final: 0.0450 (pt) outliers start: 69 outliers final: 46 residues processed: 515 average time/residue: 0.1211 time to fit residues: 95.2798 Evaluate side-chains 498 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 445 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 321 GLU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 200 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 319 MET Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 584 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 131 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: 7.9990 chunk 46 optimal weight: 6.9990 chunk 120 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 126 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 122 optimal weight: 0.5980 chunk 115 optimal weight: 6.9990 chunk 168 optimal weight: 9.9990 chunk 157 optimal weight: 6.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 467 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN D 71 ASN D 283 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.151261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.108533 restraints weight = 33061.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.112306 restraints weight = 16625.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.114738 restraints weight = 9956.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.116480 restraints weight = 7013.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.117714 restraints weight = 5396.639| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3437 r_free = 0.3437 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 = 0.3436 r_free = 0.3436 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3436 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16386 Z= 0.183 Angle : 0.635 13.426 22134 Z= 0.327 Chirality : 0.044 0.252 2360 Planarity : 0.003 0.062 2818 Dihedral : 10.703 174.244 2247 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.25 % Allowed : 22.09 % Favored : 73.66 % 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 aren not related in a simple way. whole: 1.11 (0.19), residues: 1932 helix: 1.28 (0.15), residues: 1128 sheet: -0.20 (0.41), residues: 134 loop : 0.18 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 350 TYR 0.027 0.001 TYR A 571 PHE 0.042 0.002 PHE C 168 TRP 0.025 0.002 TRP D 44 HIS 0.009 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00412 (16386) covalent geometry : angle 0.63538 (22134) hydrogen bonds : bond 0.03955 ( 871) hydrogen bonds : angle 4.92194 ( 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 545 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 472 time to evaluate : 0.459 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8964 (p0) cc_final: 0.8184 (p0) REVERT: A 31 GLU cc_start: 0.9035 (mp0) cc_final: 0.8788 (mp0) REVERT: A 69 LEU cc_start: 0.9384 (mt) cc_final: 0.9024 (pp) REVERT: A 76 ASP cc_start: 0.8793 (m-30) cc_final: 0.8490 (m-30) REVERT: A 116 GLU cc_start: 0.8113 (mt-10) cc_final: 0.7853 (mt-10) REVERT: A 139 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8182 (mt-10) REVERT: A 178 SER cc_start: 0.8821 (OUTLIER) cc_final: 0.8594 (p) REVERT: A 179 LEU cc_start: 0.9151 (tp) cc_final: 0.8849 (tt) REVERT: A 218 ASN cc_start: 0.8685 (t0) cc_final: 0.8222 (t0) REVERT: A 232 ASN cc_start: 0.9399 (m-40) cc_final: 0.9089 (m110) REVERT: A 263 ASP cc_start: 0.8386 (m-30) cc_final: 0.7935 (m-30) REVERT: A 286 ASP cc_start: 0.7764 (m-30) cc_final: 0.7543 (m-30) REVERT: A 346 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9137 (mp) REVERT: A 348 MET cc_start: 0.8033 (tpp) cc_final: 0.7738 (tpt) REVERT: A 352 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7225 (mm-30) REVERT: A 362 ASP cc_start: 0.8023 (m-30) cc_final: 0.7497 (m-30) REVERT: A 381 LEU cc_start: 0.8982 (tp) cc_final: 0.8433 (pt) REVERT: A 384 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7464 (pm20) REVERT: A 411 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.8046 (mt) REVERT: A 415 ASN cc_start: 0.8947 (t0) cc_final: 0.8324 (t0) REVERT: A 418 ASN cc_start: 0.9153 (m-40) cc_final: 0.8524 (m-40) REVERT: A 420 MET cc_start: 0.8946 (mmm) cc_final: 0.8538 (mmm) REVERT: A 447 ASN cc_start: 0.7920 (m-40) cc_final: 0.7697 (t0) REVERT: A 453 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8282 (ttt-90) REVERT: A 493 MET cc_start: 0.8859 (tmm) cc_final: 0.8597 (tmm) REVERT: A 494 MET cc_start: 0.8474 (mtp) cc_final: 0.8236 (mtp) REVERT: A 498 TYR cc_start: 0.9116 (m-80) cc_final: 0.8914 (m-80) REVERT: A 505 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8181 (mt-10) REVERT: A 561 LEU cc_start: 0.8747 (tp) cc_final: 0.8401 (tt) REVERT: A 604 ARG cc_start: 0.8345 (tpp-160) cc_final: 0.8132 (tpp-160) REVERT: A 640 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8896 (tmm) REVERT: B 15 GLU cc_start: 0.8942 (tp30) cc_final: 0.8628 (tp30) REVERT: B 71 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9072 (mp) REVERT: B 108 THR cc_start: 0.8670 (OUTLIER) cc_final: 0.8329 (p) REVERT: B 119 GLU cc_start: 0.8943 (mp0) cc_final: 0.8251 (mp0) REVERT: B 186 ILE cc_start: 0.9704 (mp) cc_final: 0.9453 (mp) REVERT: B 190 MET cc_start: 0.9209 (mtm) cc_final: 0.8944 (mtm) REVERT: B 191 GLN cc_start: 0.9099 (mm-40) cc_final: 0.8717 (mm-40) REVERT: B 194 LYS cc_start: 0.9385 (ttpt) cc_final: 0.9041 (ttpt) REVERT: B 267 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8763 (mm) REVERT: B 274 ARG cc_start: 0.7314 (OUTLIER) cc_final: 0.7111 (ttm170) REVERT: B 322 MET cc_start: 0.9028 (mmt) cc_final: 0.8755 (mmm) REVERT: B 375 LYS cc_start: 0.9002 (mmtm) cc_final: 0.8531 (mppt) REVERT: B 494 MET cc_start: 0.8915 (mtp) cc_final: 0.8572 (mtp) REVERT: B 604 ARG cc_start: 0.8961 (tpp80) cc_final: 0.8383 (mmt-90) REVERT: C 41 LEU cc_start: 0.7249 (pp) cc_final: 0.6722 (mm) REVERT: C 74 MET cc_start: 0.6896 (mmm) cc_final: 0.6428 (mmm) REVERT: C 124 TRP cc_start: 0.7128 (t60) cc_final: 0.6921 (t60) REVERT: C 141 LEU cc_start: 0.9140 (mt) cc_final: 0.8875 (pp) REVERT: C 162 TYR cc_start: 0.9163 (m-10) cc_final: 0.8683 (m-80) REVERT: C 242 TYR cc_start: 0.9310 (t80) cc_final: 0.8720 (t80) REVERT: D 138 ILE cc_start: 0.9076 (mm) cc_final: 0.8850 (tp) REVERT: D 191 ILE cc_start: 0.0682 (pt) cc_final: 0.0426 (pt) outliers start: 73 outliers final: 45 residues processed: 506 average time/residue: 0.1198 time to fit residues: 91.1579 Evaluate side-chains 507 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 452 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 LYS 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 413 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 583 SER 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 653 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 200 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 317 MET Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 336 LYS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 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 246 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 242 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 4.9990 chunk 183 optimal weight: 0.8980 chunk 72 optimal weight: 7.9990 chunk 172 optimal weight: 8.9990 chunk 52 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 136 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 28 GLN ** C 238 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 = 0.3967 r_free = 0.3967 target = 0.155337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.113432 restraints weight = 32558.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.117272 restraints weight = 16268.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.119715 restraints weight = 9762.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.121388 restraints weight = 6807.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.122389 restraints weight = 5245.857| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3483 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3483 r_free = 0.3483 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 = 0.3483 r_free = 0.3483 target_work(ls_wunit_k1) = 0.118 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3483 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.5555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16386 Z= 0.133 Angle : 0.630 11.616 22134 Z= 0.322 Chirality : 0.044 0.265 2360 Planarity : 0.003 0.045 2818 Dihedral : 10.324 158.021 2243 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 4.02 % Allowed : 22.14 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.19), residues: 1932 helix: 1.30 (0.15), residues: 1132 sheet: -0.20 (0.41), residues: 134 loop : 0.18 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 686 TYR 0.020 0.001 TYR C 55 PHE 0.045 0.002 PHE C 168 TRP 0.030 0.002 TRP D 44 HIS 0.007 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00296 (16386) covalent geometry : angle 0.63003 (22134) hydrogen bonds : bond 0.03829 ( 871) hydrogen bonds : angle 4.84504 ( 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 550 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 481 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8923 (p0) cc_final: 0.8279 (p0) REVERT: A 76 ASP cc_start: 0.8744 (m-30) cc_final: 0.8424 (m-30) REVERT: A 116 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7734 (mt-10) REVERT: A 139 GLU cc_start: 0.8520 (mt-10) cc_final: 0.8126 (mt-10) REVERT: A 150 GLN cc_start: 0.9269 (tm-30) cc_final: 0.8684 (tm-30) REVERT: A 178 SER cc_start: 0.8822 (OUTLIER) cc_final: 0.8569 (p) REVERT: A 218 ASN cc_start: 0.8637 (t0) cc_final: 0.8092 (t0) REVERT: A 221 LYS cc_start: 0.8790 (mmtp) cc_final: 0.8433 (mmtp) REVERT: A 232 ASN cc_start: 0.9432 (m-40) cc_final: 0.8961 (m110) REVERT: A 250 TYR cc_start: 0.8680 (m-80) cc_final: 0.8328 (m-80) REVERT: A 263 ASP cc_start: 0.8386 (m-30) cc_final: 0.7930 (m-30) REVERT: A 346 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9103 (mp) REVERT: A 348 MET cc_start: 0.8046 (tpp) cc_final: 0.7594 (tpt) REVERT: A 352 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7224 (mm-30) REVERT: A 359 MET cc_start: 0.8400 (OUTLIER) cc_final: 0.7795 (ttp) REVERT: A 362 ASP cc_start: 0.8073 (m-30) cc_final: 0.7468 (m-30) REVERT: A 381 LEU cc_start: 0.8975 (tp) cc_final: 0.8406 (pt) REVERT: A 384 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7499 (pm20) REVERT: A 411 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7899 (mt) REVERT: A 420 MET cc_start: 0.8873 (mmm) cc_final: 0.8424 (mmm) REVERT: A 453 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8219 (ttt-90) REVERT: A 479 TYR cc_start: 0.8890 (t80) cc_final: 0.8664 (t80) REVERT: A 493 MET cc_start: 0.8827 (tmm) cc_final: 0.8500 (tmm) REVERT: A 498 TYR cc_start: 0.9063 (m-80) cc_final: 0.8557 (m-80) REVERT: A 505 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8201 (mt-10) REVERT: A 561 LEU cc_start: 0.8646 (tp) cc_final: 0.8295 (tt) REVERT: A 570 MET cc_start: 0.8988 (mtp) cc_final: 0.8754 (mtp) REVERT: A 583 SER cc_start: 0.8929 (OUTLIER) cc_final: 0.8461 (t) REVERT: A 590 SER cc_start: 0.9303 (p) cc_final: 0.8789 (m) REVERT: A 604 ARG cc_start: 0.8274 (tpp-160) cc_final: 0.8068 (tpp-160) REVERT: A 626 TYR cc_start: 0.8578 (m-80) cc_final: 0.8370 (m-80) REVERT: A 640 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.7976 (tpp) REVERT: A 684 TYR cc_start: 0.7100 (OUTLIER) cc_final: 0.6764 (m-10) REVERT: B 15 GLU cc_start: 0.8940 (tp30) cc_final: 0.8652 (tp30) REVERT: B 71 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9160 (mp) REVERT: B 108 THR cc_start: 0.8759 (OUTLIER) cc_final: 0.8059 (p) REVERT: B 119 GLU cc_start: 0.8843 (mp0) cc_final: 0.8221 (mp0) REVERT: B 184 ARG cc_start: 0.9238 (tpp-160) cc_final: 0.8824 (tpp-160) REVERT: B 186 ILE cc_start: 0.9703 (mp) cc_final: 0.9494 (mp) REVERT: B 190 MET cc_start: 0.9211 (mtm) cc_final: 0.8976 (mtm) REVERT: B 191 GLN cc_start: 0.8934 (mm-40) cc_final: 0.8653 (mm-40) REVERT: B 194 LYS cc_start: 0.9352 (ttpt) cc_final: 0.9002 (ttpt) REVERT: B 267 ILE cc_start: 0.9084 (OUTLIER) cc_final: 0.8584 (mm) REVERT: B 274 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6787 (ttm170) REVERT: B 322 MET cc_start: 0.9007 (mmt) cc_final: 0.8783 (mmm) REVERT: B 341 LYS cc_start: 0.9292 (pttp) cc_final: 0.8928 (mtmm) REVERT: B 384 GLU cc_start: 0.8744 (OUTLIER) cc_final: 0.6758 (pm20) REVERT: B 494 MET cc_start: 0.8859 (mtp) cc_final: 0.8459 (mtp) REVERT: B 515 ASP cc_start: 0.8779 (m-30) cc_final: 0.8566 (m-30) REVERT: B 604 ARG cc_start: 0.8855 (tpp80) cc_final: 0.8358 (mmt-90) REVERT: C 74 MET cc_start: 0.7095 (mmm) cc_final: 0.6671 (mmm) REVERT: C 124 TRP cc_start: 0.7204 (t60) cc_final: 0.6526 (t60) REVERT: C 141 LEU cc_start: 0.9169 (mt) cc_final: 0.8853 (pp) REVERT: C 242 TYR cc_start: 0.9217 (t80) cc_final: 0.8934 (t80) REVERT: D 96 MET cc_start: 0.7585 (mmp) cc_final: 0.7189 (tpp) REVERT: D 138 ILE cc_start: 0.9047 (mm) cc_final: 0.8814 (tp) REVERT: D 191 ILE cc_start: 0.0629 (pt) cc_final: 0.0398 (pt) outliers start: 69 outliers final: 35 residues processed: 515 average time/residue: 0.1203 time to fit residues: 93.1159 Evaluate side-chains 500 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 451 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 453 ARG 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 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 33 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 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 342 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 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 584 ILE Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 242 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 0.0470 chunk 51 optimal weight: 6.9990 chunk 74 optimal weight: 0.4980 chunk 105 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 186 optimal weight: 10.0000 chunk 140 optimal weight: 0.9980 chunk 115 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 overall best weight: 1.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.153661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111563 restraints weight = 32708.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.115201 restraints weight = 16020.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.117544 restraints weight = 9765.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.119193 restraints weight = 6892.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.120223 restraints weight = 5364.241| |-----------------------------------------------------------------------------| r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3457 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3457 r_free = 0.3457 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3457 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.5775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16386 Z= 0.175 Angle : 0.663 11.678 22134 Z= 0.339 Chirality : 0.044 0.196 2360 Planarity : 0.003 0.068 2818 Dihedral : 10.168 154.653 2243 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.96 % Allowed : 22.49 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.19), residues: 1932 helix: 1.29 (0.15), residues: 1124 sheet: -0.43 (0.40), residues: 152 loop : 0.22 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 350 TYR 0.019 0.001 TYR C 55 PHE 0.051 0.002 PHE D 109 TRP 0.032 0.002 TRP D 44 HIS 0.009 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00396 (16386) covalent geometry : angle 0.66270 (22134) hydrogen bonds : bond 0.03849 ( 871) hydrogen bonds : angle 4.88114 ( 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 533 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 465 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8879 (p0) cc_final: 0.8410 (t0) REVERT: A 31 GLU cc_start: 0.8953 (mp0) cc_final: 0.8575 (mp0) REVERT: A 69 LEU cc_start: 0.9356 (mt) cc_final: 0.9002 (pp) REVERT: A 76 ASP cc_start: 0.8715 (m-30) cc_final: 0.8402 (m-30) REVERT: A 116 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7709 (mt-10) REVERT: A 218 ASN cc_start: 0.8643 (t0) cc_final: 0.8129 (t0) REVERT: A 221 LYS cc_start: 0.8841 (mmtp) cc_final: 0.8466 (mmtp) REVERT: A 232 ASN cc_start: 0.9432 (m-40) cc_final: 0.8924 (m-40) REVERT: A 250 TYR cc_start: 0.8664 (m-80) cc_final: 0.8325 (m-80) REVERT: A 263 ASP cc_start: 0.8400 (m-30) cc_final: 0.7959 (m-30) REVERT: A 346 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9124 (mp) REVERT: A 348 MET cc_start: 0.8044 (tpp) cc_final: 0.7636 (tpt) REVERT: A 352 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7174 (mm-30) REVERT: A 359 MET cc_start: 0.8506 (OUTLIER) cc_final: 0.8029 (ttp) REVERT: A 362 ASP cc_start: 0.7954 (m-30) cc_final: 0.7564 (m-30) REVERT: A 381 LEU cc_start: 0.8992 (tp) cc_final: 0.8413 (pt) REVERT: A 384 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7500 (pm20) REVERT: A 411 LEU cc_start: 0.8172 (OUTLIER) cc_final: 0.7901 (mt) REVERT: A 418 ASN cc_start: 0.9092 (m-40) cc_final: 0.8362 (m110) REVERT: A 420 MET cc_start: 0.8933 (mmm) cc_final: 0.8473 (mmm) REVERT: A 453 ARG cc_start: 0.9139 (OUTLIER) cc_final: 0.8321 (ttt-90) REVERT: A 493 MET cc_start: 0.8848 (tmm) cc_final: 0.8535 (tmm) REVERT: A 498 TYR cc_start: 0.8949 (m-80) cc_final: 0.8599 (m-80) REVERT: A 505 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8052 (mt-10) REVERT: A 640 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8845 (tmm) REVERT: A 684 TYR cc_start: 0.7333 (OUTLIER) cc_final: 0.6593 (m-10) REVERT: B 71 LEU cc_start: 0.9418 (OUTLIER) cc_final: 0.9174 (mm) REVERT: B 108 THR cc_start: 0.8653 (OUTLIER) cc_final: 0.8375 (p) REVERT: B 119 GLU cc_start: 0.8869 (mp0) cc_final: 0.8286 (mp0) REVERT: B 186 ILE cc_start: 0.9699 (OUTLIER) cc_final: 0.9472 (mp) REVERT: B 194 LYS cc_start: 0.9382 (ttpt) cc_final: 0.9031 (ttpt) REVERT: B 267 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8569 (mm) REVERT: B 274 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.6858 (ttm170) REVERT: B 322 MET cc_start: 0.8976 (mmt) cc_final: 0.8739 (mmm) REVERT: B 341 LYS cc_start: 0.9299 (pttp) cc_final: 0.8961 (mtmm) REVERT: B 355 TYR cc_start: 0.8597 (m-10) cc_final: 0.8384 (m-10) REVERT: B 375 LYS cc_start: 0.8768 (mmtm) cc_final: 0.8336 (mppt) REVERT: B 384 GLU cc_start: 0.8807 (OUTLIER) cc_final: 0.6812 (pm20) REVERT: B 494 MET cc_start: 0.8829 (mtp) cc_final: 0.8494 (mtp) REVERT: B 515 ASP cc_start: 0.8807 (m-30) cc_final: 0.8583 (m-30) REVERT: B 586 TYR cc_start: 0.8318 (m-80) cc_final: 0.8103 (m-80) REVERT: B 604 ARG cc_start: 0.8858 (tpp80) cc_final: 0.8381 (mmt-90) REVERT: C 74 MET cc_start: 0.7126 (mmm) cc_final: 0.6753 (mmm) REVERT: C 141 LEU cc_start: 0.9277 (mt) cc_final: 0.8912 (pp) REVERT: C 149 ASP cc_start: 0.8395 (t0) cc_final: 0.7741 (m-30) REVERT: C 242 TYR cc_start: 0.9305 (t80) cc_final: 0.8899 (t80) REVERT: D 96 MET cc_start: 0.7648 (mmp) cc_final: 0.7268 (tpp) REVERT: D 138 ILE cc_start: 0.9091 (mm) cc_final: 0.8887 (tp) REVERT: D 191 ILE cc_start: 0.0571 (pt) cc_final: 0.0307 (pt) outliers start: 68 outliers final: 45 residues processed: 496 average time/residue: 0.1171 time to fit residues: 88.0335 Evaluate side-chains 500 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 442 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 194 LYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 499 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 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 33 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 186 ILE Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 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 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 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 B residue 668 ASN Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 242 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 4.9990 chunk 99 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 153 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 158 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 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 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.155556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.113158 restraints weight = 33062.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.117071 restraints weight = 16340.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.119464 restraints weight = 9873.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.121198 restraints weight = 6993.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.122215 restraints weight = 5439.773| |-----------------------------------------------------------------------------| r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.119 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.5964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16386 Z= 0.140 Angle : 0.672 12.465 22134 Z= 0.339 Chirality : 0.044 0.212 2360 Planarity : 0.003 0.038 2818 Dihedral : 9.683 146.902 2243 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.44 % Allowed : 23.72 % Favored : 72.84 % 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 aren not related in a simple way. whole: 1.03 (0.19), residues: 1932 helix: 1.26 (0.15), residues: 1125 sheet: -0.56 (0.40), residues: 148 loop : 0.17 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 350 TYR 0.017 0.001 TYR C 55 PHE 0.058 0.002 PHE D 109 TRP 0.036 0.002 TRP D 44 HIS 0.009 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00322 (16386) covalent geometry : angle 0.67197 (22134) hydrogen bonds : bond 0.03830 ( 871) hydrogen bonds : angle 4.85784 ( 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 539 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 480 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8981 (p0) cc_final: 0.8570 (p0) REVERT: A 69 LEU cc_start: 0.9347 (mt) cc_final: 0.8946 (pp) REVERT: A 76 ASP cc_start: 0.8676 (m-30) cc_final: 0.8343 (m-30) REVERT: A 116 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7738 (mt-10) REVERT: A 150 GLN cc_start: 0.9246 (tm-30) cc_final: 0.8654 (tm-30) REVERT: A 178 SER cc_start: 0.8817 (OUTLIER) cc_final: 0.8567 (p) REVERT: A 205 LYS cc_start: 0.8591 (mmmm) cc_final: 0.8372 (mmtp) REVERT: A 218 ASN cc_start: 0.8572 (t0) cc_final: 0.8058 (t0) REVERT: A 221 LYS cc_start: 0.8871 (mmtp) cc_final: 0.8394 (mmtp) REVERT: A 250 TYR cc_start: 0.8646 (m-80) cc_final: 0.8305 (m-80) REVERT: A 263 ASP cc_start: 0.8423 (m-30) cc_final: 0.7972 (m-30) REVERT: A 312 GLN cc_start: 0.7991 (tp-100) cc_final: 0.7756 (tp-100) REVERT: A 346 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9093 (mp) REVERT: A 348 MET cc_start: 0.8072 (tpp) cc_final: 0.7578 (tpt) REVERT: A 352 GLU cc_start: 0.7850 (mm-30) cc_final: 0.7237 (mm-30) REVERT: A 359 MET cc_start: 0.8401 (OUTLIER) cc_final: 0.7817 (ttp) REVERT: A 362 ASP cc_start: 0.7851 (m-30) cc_final: 0.7557 (m-30) REVERT: A 366 LYS cc_start: 0.9180 (mtpt) cc_final: 0.8920 (ptpt) REVERT: A 381 LEU cc_start: 0.8954 (tp) cc_final: 0.8393 (pt) REVERT: A 384 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7490 (pm20) REVERT: A 411 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7887 (mt) REVERT: A 420 MET cc_start: 0.8905 (mmm) cc_final: 0.8385 (mmm) REVERT: A 479 TYR cc_start: 0.8946 (t80) cc_final: 0.8689 (t80) REVERT: A 493 MET cc_start: 0.8969 (tmm) cc_final: 0.8701 (tmm) REVERT: A 505 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8045 (mt-10) REVERT: A 561 LEU cc_start: 0.8657 (tp) cc_final: 0.8338 (tt) REVERT: A 640 MET cc_start: 0.9198 (OUTLIER) cc_final: 0.7966 (tpp) REVERT: A 668 ASN cc_start: 0.8486 (m110) cc_final: 0.8242 (m110) REVERT: A 684 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.6715 (m-10) REVERT: B 108 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8200 (p) REVERT: B 119 GLU cc_start: 0.8851 (mp0) cc_final: 0.8490 (mp0) REVERT: B 267 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8571 (mm) REVERT: B 274 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6838 (ttm170) REVERT: B 341 LYS cc_start: 0.9323 (pttp) cc_final: 0.8981 (mtmm) REVERT: B 348 MET cc_start: 0.8885 (ptt) cc_final: 0.8660 (ptt) REVERT: B 384 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.6748 (pm20) REVERT: B 494 MET cc_start: 0.8785 (mtp) cc_final: 0.8413 (mtp) REVERT: B 515 ASP cc_start: 0.8799 (m-30) cc_final: 0.8574 (m-30) REVERT: B 586 TYR cc_start: 0.8312 (m-80) cc_final: 0.7924 (m-80) REVERT: B 599 GLU cc_start: 0.8201 (pm20) cc_final: 0.7719 (pm20) REVERT: B 604 ARG cc_start: 0.8761 (tpp80) cc_final: 0.8374 (mmt-90) REVERT: B 668 ASN cc_start: 0.8765 (OUTLIER) cc_final: 0.8537 (t0) REVERT: C 74 MET cc_start: 0.7025 (mmm) cc_final: 0.6671 (mmm) REVERT: C 141 LEU cc_start: 0.9282 (mt) cc_final: 0.8934 (pp) REVERT: C 149 ASP cc_start: 0.8340 (t0) cc_final: 0.7743 (m-30) REVERT: C 242 TYR cc_start: 0.9326 (t80) cc_final: 0.8935 (t80) REVERT: D 138 ILE cc_start: 0.9050 (mm) cc_final: 0.8839 (tp) outliers start: 59 outliers final: 42 residues processed: 507 average time/residue: 0.1082 time to fit residues: 84.3665 Evaluate side-chains 503 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 449 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 194 LYS Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 270 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 421 GLU Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 499 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 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 33 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 200 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 314 MET Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 384 GLU 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 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 B residue 668 ASN Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 242 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 0.8980 chunk 133 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 86 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 71 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 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 = 0.3981 r_free = 0.3981 target = 0.156114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.114555 restraints weight = 32778.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.118384 restraints weight = 16066.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.120641 restraints weight = 9692.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.122377 restraints weight = 6930.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.123392 restraints weight = 5338.047| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3509 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3509 r_free = 0.3509 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3509 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16386 Z= 0.139 Angle : 0.685 12.008 22134 Z= 0.348 Chirality : 0.045 0.211 2360 Planarity : 0.003 0.058 2818 Dihedral : 9.380 139.224 2243 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.03 % Allowed : 24.65 % 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 aren not related in a simple way. whole: 1.03 (0.19), residues: 1932 helix: 1.25 (0.15), residues: 1120 sheet: -0.58 (0.40), residues: 148 loop : 0.20 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 350 TYR 0.052 0.001 TYR B 36 PHE 0.059 0.002 PHE D 109 TRP 0.039 0.002 TRP D 44 HIS 0.012 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00320 (16386) covalent geometry : angle 0.68457 (22134) hydrogen bonds : bond 0.03814 ( 871) hydrogen bonds : angle 4.88038 ( 2571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 468 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8982 (p0) cc_final: 0.8660 (p0) REVERT: A 109 ASN cc_start: 0.8978 (m-40) cc_final: 0.8481 (p0) REVERT: A 116 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7686 (mt-10) REVERT: A 150 GLN cc_start: 0.9243 (tm-30) cc_final: 0.8606 (tm-30) REVERT: A 178 SER cc_start: 0.8838 (OUTLIER) cc_final: 0.8618 (p) REVERT: A 218 ASN cc_start: 0.8558 (t0) cc_final: 0.7995 (t0) REVERT: A 221 LYS cc_start: 0.8801 (mmtp) cc_final: 0.8317 (mmtp) REVERT: A 250 TYR cc_start: 0.8646 (m-80) cc_final: 0.8314 (m-80) REVERT: A 263 ASP cc_start: 0.8410 (m-30) cc_final: 0.7937 (m-30) REVERT: A 346 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9044 (mp) REVERT: A 348 MET cc_start: 0.8070 (tpp) cc_final: 0.7485 (tpt) REVERT: A 352 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7263 (mm-30) REVERT: A 359 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7818 (ttp) REVERT: A 362 ASP cc_start: 0.7695 (m-30) cc_final: 0.7325 (m-30) REVERT: A 381 LEU cc_start: 0.8987 (tp) cc_final: 0.8446 (pt) REVERT: A 384 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7486 (pm20) REVERT: A 411 LEU cc_start: 0.8218 (mp) cc_final: 0.7956 (mt) REVERT: A 418 ASN cc_start: 0.9147 (m-40) cc_final: 0.8627 (m110) REVERT: A 420 MET cc_start: 0.8824 (mmm) cc_final: 0.8317 (mmm) REVERT: A 447 ASN cc_start: 0.7717 (OUTLIER) cc_final: 0.7003 (t0) REVERT: A 493 MET cc_start: 0.8938 (tmm) cc_final: 0.8686 (tmm) REVERT: A 505 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8053 (mt-10) REVERT: A 561 LEU cc_start: 0.8622 (tp) cc_final: 0.8301 (tt) REVERT: A 571 TYR cc_start: 0.8768 (t80) cc_final: 0.8539 (t80) REVERT: A 640 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8016 (tpp) REVERT: A 646 GLN cc_start: 0.8567 (pt0) cc_final: 0.8349 (pt0) REVERT: A 654 PHE cc_start: 0.9459 (t80) cc_final: 0.9250 (t80) REVERT: A 668 ASN cc_start: 0.8422 (m110) cc_final: 0.8173 (m110) REVERT: B 108 THR cc_start: 0.8229 (OUTLIER) cc_final: 0.7950 (p) REVERT: B 188 ILE cc_start: 0.9597 (mt) cc_final: 0.9349 (mm) REVERT: B 267 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8763 (mm) REVERT: B 321 GLU cc_start: 0.8362 (pp20) cc_final: 0.7955 (pp20) REVERT: B 322 MET cc_start: 0.9079 (mmm) cc_final: 0.8527 (mmm) REVERT: B 341 LYS cc_start: 0.9282 (pttp) cc_final: 0.8958 (mtmm) REVERT: B 494 MET cc_start: 0.8741 (mtp) cc_final: 0.8316 (mtp) REVERT: B 515 ASP cc_start: 0.8803 (m-30) cc_final: 0.8568 (m-30) REVERT: B 586 TYR cc_start: 0.8373 (m-80) cc_final: 0.7842 (m-80) REVERT: B 599 GLU cc_start: 0.8220 (pm20) cc_final: 0.7731 (pm20) REVERT: B 604 ARG cc_start: 0.8730 (tpp80) cc_final: 0.8381 (mmt-90) REVERT: B 639 ASP cc_start: 0.8709 (m-30) cc_final: 0.8419 (m-30) REVERT: B 662 MET cc_start: 0.7715 (ptp) cc_final: 0.7028 (ptp) REVERT: C 74 MET cc_start: 0.7033 (mmm) cc_final: 0.6711 (mmm) REVERT: C 141 LEU cc_start: 0.9334 (mt) cc_final: 0.8983 (pp) REVERT: C 145 ILE cc_start: 0.5108 (tp) cc_final: 0.4349 (tp) REVERT: C 149 ASP cc_start: 0.8463 (t0) cc_final: 0.7818 (p0) REVERT: C 208 LEU cc_start: 0.8432 (mt) cc_final: 0.8227 (mt) REVERT: C 242 TYR cc_start: 0.9305 (t80) cc_final: 0.8922 (t80) REVERT: D 96 MET cc_start: 0.7528 (mmp) cc_final: 0.7323 (tpp) outliers start: 52 outliers final: 37 residues processed: 493 average time/residue: 0.1058 time to fit residues: 80.0124 Evaluate side-chains 491 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 446 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 499 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 638 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 200 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 343 LEU Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 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 76 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 276 TYR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 242 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 3.9990 chunk 62 optimal weight: 0.0070 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 189 optimal weight: 30.0000 chunk 181 optimal weight: 7.9990 chunk 165 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 132 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 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 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 467 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.155080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.114086 restraints weight = 32589.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.117849 restraints weight = 16107.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.120318 restraints weight = 9724.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.121961 restraints weight = 6764.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.123061 restraints weight = 5212.213| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3520 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3520 r_free = 0.3520 target_work(ls_wunit_k1) = 0.120 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3520 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.6299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 16386 Z= 0.143 Angle : 0.711 13.008 22134 Z= 0.361 Chirality : 0.045 0.267 2360 Planarity : 0.003 0.057 2818 Dihedral : 9.306 139.537 2243 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.97 % Allowed : 25.06 % Favored : 71.97 % 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 aren not related in a simple way. whole: 0.96 (0.19), residues: 1932 helix: 1.20 (0.15), residues: 1123 sheet: -0.62 (0.40), residues: 148 loop : 0.14 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 293 TYR 0.039 0.001 TYR B 36 PHE 0.061 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 covalent geometry : bond 0.00330 (16386) covalent geometry : angle 0.71077 (22134) hydrogen bonds : bond 0.03823 ( 871) hydrogen bonds : angle 4.92637 ( 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 506 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 455 time to evaluate : 0.408 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.8939 (p0) cc_final: 0.8624 (p0) REVERT: A 150 GLN cc_start: 0.9218 (tm-30) cc_final: 0.8645 (tm-30) REVERT: A 178 SER cc_start: 0.8829 (OUTLIER) cc_final: 0.8570 (p) REVERT: A 179 LEU cc_start: 0.9111 (tp) cc_final: 0.8780 (tt) REVERT: A 218 ASN cc_start: 0.8545 (t0) cc_final: 0.7938 (t0) REVERT: A 221 LYS cc_start: 0.8788 (mmtp) cc_final: 0.8316 (mmtp) REVERT: A 250 TYR cc_start: 0.8622 (m-80) cc_final: 0.8316 (m-80) REVERT: A 263 ASP cc_start: 0.8405 (m-30) cc_final: 0.7931 (m-30) REVERT: A 312 GLN cc_start: 0.7900 (tp-100) cc_final: 0.7615 (tp-100) REVERT: A 346 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9041 (mp) REVERT: A 348 MET cc_start: 0.8073 (tpp) cc_final: 0.7536 (tpt) REVERT: A 352 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7213 (mm-30) REVERT: A 359 MET cc_start: 0.8389 (OUTLIER) cc_final: 0.7821 (ttp) REVERT: A 362 ASP cc_start: 0.7599 (m-30) cc_final: 0.7390 (t0) REVERT: A 381 LEU cc_start: 0.8984 (tp) cc_final: 0.8444 (pt) REVERT: A 384 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7473 (pm20) REVERT: A 411 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7958 (mt) REVERT: A 420 MET cc_start: 0.8820 (mmm) cc_final: 0.8300 (mmm) REVERT: A 446 ARG cc_start: 0.7373 (mmm160) cc_final: 0.7025 (mmm160) REVERT: A 447 ASN cc_start: 0.7496 (OUTLIER) cc_final: 0.7097 (t0) REVERT: A 479 TYR cc_start: 0.8982 (t80) cc_final: 0.8733 (t80) REVERT: A 493 MET cc_start: 0.8919 (tmm) cc_final: 0.8629 (tmm) REVERT: A 505 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8156 (mt-10) REVERT: A 561 LEU cc_start: 0.8597 (tp) cc_final: 0.8279 (tt) REVERT: A 640 MET cc_start: 0.9150 (OUTLIER) cc_final: 0.8043 (tpp) REVERT: A 646 GLN cc_start: 0.8569 (pt0) cc_final: 0.8308 (pt0) REVERT: A 668 ASN cc_start: 0.8393 (m110) cc_final: 0.8122 (m110) REVERT: B 108 THR cc_start: 0.8215 (OUTLIER) cc_final: 0.7937 (p) REVERT: B 184 ARG cc_start: 0.9243 (tpp-160) cc_final: 0.8873 (tpp-160) REVERT: B 267 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8765 (mm) REVERT: B 274 ARG cc_start: 0.7540 (ttm170) cc_final: 0.6968 (ttm170) REVERT: B 321 GLU cc_start: 0.8366 (pp20) cc_final: 0.7990 (pp20) REVERT: B 322 MET cc_start: 0.9028 (mmm) cc_final: 0.8560 (mmm) REVERT: B 341 LYS cc_start: 0.9310 (pttp) cc_final: 0.8961 (mtmm) REVERT: B 384 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.6658 (pm20) REVERT: B 494 MET cc_start: 0.8713 (mtp) cc_final: 0.8295 (mtp) REVERT: B 515 ASP cc_start: 0.8806 (m-30) cc_final: 0.8569 (m-30) REVERT: B 586 TYR cc_start: 0.8321 (m-80) cc_final: 0.7771 (m-80) REVERT: B 599 GLU cc_start: 0.8290 (pm20) cc_final: 0.7714 (pm20) REVERT: B 604 ARG cc_start: 0.8711 (tpp80) cc_final: 0.8360 (mmt-90) REVERT: B 639 ASP cc_start: 0.8704 (m-30) cc_final: 0.8400 (m-30) REVERT: C 74 MET cc_start: 0.7008 (mmm) cc_final: 0.6680 (mmm) REVERT: C 141 LEU cc_start: 0.9385 (mt) cc_final: 0.9051 (pp) REVERT: C 145 ILE cc_start: 0.5200 (tp) cc_final: 0.4502 (tp) REVERT: C 149 ASP cc_start: 0.8376 (t0) cc_final: 0.7944 (p0) REVERT: C 242 TYR cc_start: 0.9320 (t80) cc_final: 0.8937 (t80) REVERT: D 212 ILE cc_start: 0.4001 (OUTLIER) cc_final: 0.3727 (tt) outliers start: 51 outliers final: 33 residues processed: 480 average time/residue: 0.1144 time to fit residues: 84.1395 Evaluate side-chains 483 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 439 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 499 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 638 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 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 343 LEU Chi-restraints excluded: chain B residue 384 GLU 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 587 VAL Chi-restraints excluded: chain B residue 594 VAL Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 276 TYR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 168 PHE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 242 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 0.9990 chunk 1 optimal weight: 0.0980 chunk 48 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 125 optimal weight: 0.9990 chunk 28 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** 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 234 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 283 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.154219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.112921 restraints weight = 32874.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.116529 restraints weight = 16245.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.118829 restraints weight = 9852.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.120459 restraints weight = 6998.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.120981 restraints weight = 5465.868| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3465 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.6392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 16386 Z= 0.174 Angle : 0.725 12.025 22134 Z= 0.368 Chirality : 0.046 0.263 2360 Planarity : 0.004 0.060 2818 Dihedral : 9.241 140.074 2243 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.74 % Allowed : 25.52 % Favored : 71.74 % 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 aren not related in a simple way. whole: 0.92 (0.19), residues: 1932 helix: 1.17 (0.16), residues: 1119 sheet: -0.74 (0.40), residues: 148 loop : 0.16 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 350 TYR 0.038 0.001 TYR C 55 PHE 0.059 0.002 PHE D 109 TRP 0.039 0.002 TRP D 44 HIS 0.011 0.001 HIS D 80 Details of bonding type rmsd covalent geometry : bond 0.00401 (16386) covalent geometry : angle 0.72526 (22134) hydrogen bonds : bond 0.03842 ( 871) hydrogen bonds : angle 4.96025 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3005.56 seconds wall clock time: 52 minutes 53.95 seconds (3173.95 seconds total)