Starting phenix.real_space_refine on Thu Sep 18 09:57:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bze_45065/09_2025/9bze_45065_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bze_45065/09_2025/9bze_45065.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bze_45065/09_2025/9bze_45065_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bze_45065/09_2025/9bze_45065_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bze_45065/09_2025/9bze_45065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bze_45065/09_2025/9bze_45065.map" } resolution = 4.19 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-2.0-5805/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: 3.93, per 1000 atoms: 0.25 Number of scatterers: 16038 At special positions: 0 Unit cell: (96.33, 142.974, 129.792, 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: 1.53 Conformation dependent library (CDL) restraints added in 702.3 milliseconds Enol-peptide restraints added in 476.8 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: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.104A 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: 3.516A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.985A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.954A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.665A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.949A 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: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.628A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.118A 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: 3.677A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.872A 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: 3.644A 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: 5.118A 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: 3.632A 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: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.668A 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: 6.359A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.427A 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: 6.477A 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: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A 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: 6.477A 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: 5.661A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.049A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.806A 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: 3.02 Time building geometry restraints manager: 1.89 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: 4876 1.34 - 1.46: 3021 1.46 - 1.58: 8308 1.58 - 1.70: 25 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 2.35e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.577 -0.038 1.20e-02 6.94e+03 9.96e+00 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.032 1.08e-02 8.57e+03 8.85e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.568 -0.031 1.17e-02 7.31e+03 7.17e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.574 -0.033 1.25e-02 6.40e+03 7.14e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21578 2.09 - 4.17: 513 4.17 - 6.26: 38 6.26 - 8.35: 1 8.35 - 10.44: 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 110.54 116.66 -6.12 1.36e+00 5.41e-01 2.03e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.11 -4.40 1.15e+00 7.56e-01 1.46e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.89 -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 111.71 115.69 -3.98 1.15e+00 7.56e-01 1.20e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.53 3.66 1.06e+00 8.90e-01 1.19e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 9471 35.80 - 71.60: 336 71.60 - 107.41: 37 107.41 - 143.21: 3 143.21 - 179.01: 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 -58.32 120.69 -179.01 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 301.68 151.16 150.52 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 31.89 148.08 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: 2142 0.093 - 0.187: 187 0.187 - 0.280: 26 0.280 - 0.373: 3 0.373 - 0.466: 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 2.04 0.47 2.00e-01 2.50e+01 5.43e+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 4.59e+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 2.97e+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 4.13e-02 2.73e+00 pdb=" N PRO D 75 " 0.071 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 " 0.018 2.00e-02 2.50e+03 1.12e-02 2.21e+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 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 179 " -0.017 2.00e-02 2.50e+03 9.87e-03 1.95e+00 pdb=" CG TYR D 179 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR D 179 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 179 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR D 179 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 179 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 179 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 179 " -0.005 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 128 2.51 - 3.11: 11548 3.11 - 3.70: 27036 3.70 - 4.30: 41567 4.30 - 4.90: 65484 Nonbonded interactions: 145763 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.911 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 1.991 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 145758 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 16.140 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6719 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 10.436 22134 Z= 0.463 Chirality : 0.057 0.466 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.907 179.011 6154 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.34 % Allowed : 15.27 % Favored : 83.39 % 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: 0.56 (0.18), residues: 1932 helix: 0.59 (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 0.021 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.009 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 0.74007 (22134) hydrogen bonds : bond 0.15421 ( 871) hydrogen bonds : angle 6.51768 ( 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 1038 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 1015 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8698 (mm) cc_final: 0.8401 (mm) REVERT: A 51 LEU cc_start: 0.8139 (tp) cc_final: 0.7860 (tp) REVERT: A 81 PHE cc_start: 0.8260 (m-80) cc_final: 0.8002 (m-10) REVERT: A 123 SER cc_start: 0.9320 (m) cc_final: 0.8887 (m) REVERT: A 157 LEU cc_start: 0.8978 (tp) cc_final: 0.8774 (tp) REVERT: A 172 LEU cc_start: 0.9490 (mp) cc_final: 0.9147 (mp) REVERT: A 181 ASP cc_start: 0.8241 (m-30) cc_final: 0.7581 (m-30) REVERT: A 211 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6381 (tp30) REVERT: A 258 ILE cc_start: 0.9219 (tp) cc_final: 0.8843 (tp) REVERT: A 265 LYS cc_start: 0.9075 (mmtt) cc_final: 0.8696 (mmmt) REVERT: A 267 ILE cc_start: 0.8833 (mp) cc_final: 0.8078 (pt) REVERT: A 315 ASP cc_start: 0.8472 (p0) cc_final: 0.7912 (p0) REVERT: A 344 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7248 (mt-10) REVERT: A 345 LYS cc_start: 0.8888 (tttt) cc_final: 0.8388 (ttmt) REVERT: A 362 ASP cc_start: 0.6076 (m-30) cc_final: 0.5768 (m-30) REVERT: A 365 ASN cc_start: 0.8288 (m-40) cc_final: 0.8044 (m-40) REVERT: A 377 LYS cc_start: 0.8818 (mttt) cc_final: 0.8462 (mttp) REVERT: A 378 PHE cc_start: 0.8896 (p90) cc_final: 0.8646 (p90) REVERT: A 387 GLN cc_start: 0.7497 (mt0) cc_final: 0.7156 (mt0) REVERT: A 408 SER cc_start: 0.8599 (p) cc_final: 0.8396 (p) REVERT: A 420 MET cc_start: 0.7468 (mmm) cc_final: 0.7259 (mmm) REVERT: A 435 SER cc_start: 0.9408 (p) cc_final: 0.8804 (p) REVERT: A 501 GLN cc_start: 0.8285 (tt0) cc_final: 0.8072 (tt0) REVERT: A 576 LEU cc_start: 0.8683 (mt) cc_final: 0.8130 (mt) REVERT: A 583 SER cc_start: 0.8180 (m) cc_final: 0.7860 (t) REVERT: A 590 SER cc_start: 0.9100 (p) cc_final: 0.8361 (p) REVERT: A 595 MET cc_start: 0.8050 (mmp) cc_final: 0.7671 (mmp) REVERT: A 670 ILE cc_start: 0.8913 (mt) cc_final: 0.8460 (mt) REVERT: A 687 THR cc_start: 0.7729 (m) cc_final: 0.7469 (m) REVERT: B 11 GLN cc_start: 0.7654 (mt0) cc_final: 0.6754 (mt0) REVERT: B 41 ILE cc_start: 0.8792 (mm) cc_final: 0.8338 (mm) REVERT: B 99 LYS cc_start: 0.9064 (mmtt) cc_final: 0.8421 (tppt) REVERT: B 127 LEU cc_start: 0.8999 (mt) cc_final: 0.8785 (mt) REVERT: B 147 GLN cc_start: 0.8314 (mt0) cc_final: 0.8002 (mt0) REVERT: B 172 LEU cc_start: 0.9342 (mp) cc_final: 0.8954 (mp) REVERT: B 175 VAL cc_start: 0.9207 (t) cc_final: 0.9007 (t) REVERT: B 177 ASP cc_start: 0.8671 (t0) cc_final: 0.8058 (t70) REVERT: B 181 ASP cc_start: 0.8122 (m-30) cc_final: 0.7640 (m-30) REVERT: B 192 LEU cc_start: 0.9272 (mt) cc_final: 0.8960 (mt) REVERT: B 204 SER cc_start: 0.9054 (m) cc_final: 0.8209 (t) REVERT: B 226 VAL cc_start: 0.9079 (t) cc_final: 0.8711 (t) REVERT: B 256 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7213 (tpt90) REVERT: B 288 PHE cc_start: 0.7689 (t80) cc_final: 0.7287 (t80) REVERT: B 315 ASP cc_start: 0.8777 (p0) cc_final: 0.8394 (p0) REVERT: B 322 MET cc_start: 0.7584 (mmm) cc_final: 0.6977 (mmm) REVERT: B 345 LYS cc_start: 0.8290 (tttt) cc_final: 0.7970 (ttpt) REVERT: B 346 LEU cc_start: 0.8863 (mt) cc_final: 0.8478 (mt) REVERT: B 359 MET cc_start: 0.8061 (ttt) cc_final: 0.7720 (ttt) REVERT: B 374 SER cc_start: 0.8716 (t) cc_final: 0.8477 (p) REVERT: B 381 LEU cc_start: 0.8730 (tp) cc_final: 0.8511 (tp) REVERT: B 387 GLN cc_start: 0.7301 (mt0) cc_final: 0.6892 (mt0) REVERT: B 417 LEU cc_start: 0.8819 (tp) cc_final: 0.8487 (tt) REVERT: B 418 ASN cc_start: 0.8302 (m-40) cc_final: 0.7799 (m-40) REVERT: B 425 ILE cc_start: 0.8953 (mt) cc_final: 0.8666 (mt) REVERT: B 474 GLN cc_start: 0.7992 (mt0) cc_final: 0.7702 (mt0) REVERT: B 494 MET cc_start: 0.7983 (mtp) cc_final: 0.7781 (mtp) REVERT: B 500 ILE cc_start: 0.9441 (mt) cc_final: 0.8999 (mt) REVERT: B 550 MET cc_start: 0.7876 (mtm) cc_final: 0.6885 (mtm) REVERT: B 587 VAL cc_start: 0.8690 (t) cc_final: 0.8460 (t) REVERT: B 597 ILE cc_start: 0.9427 (pt) cc_final: 0.9221 (pt) REVERT: B 644 ILE cc_start: 0.8904 (mt) cc_final: 0.8659 (mt) REVERT: B 655 THR cc_start: 0.9501 (m) cc_final: 0.9289 (t) REVERT: C 27 LYS cc_start: 0.8055 (ptmm) cc_final: 0.7833 (tmtt) REVERT: C 37 LEU cc_start: 0.5102 (mt) cc_final: 0.4489 (tp) REVERT: C 114 PRO cc_start: 0.5223 (Cg_endo) cc_final: 0.4846 (Cg_exo) REVERT: C 163 LEU cc_start: 0.6465 (tt) cc_final: 0.6189 (tt) REVERT: C 178 PHE cc_start: 0.4924 (m-80) cc_final: 0.4646 (m-80) REVERT: D 47 LEU cc_start: 0.5071 (mt) cc_final: 0.3954 (mp) REVERT: D 96 MET cc_start: 0.5835 (mmm) cc_final: 0.5523 (mmm) REVERT: D 141 LEU cc_start: 0.6273 (mt) cc_final: 0.5960 (mp) REVERT: D 186 GLN cc_start: 0.4627 (mm-40) cc_final: 0.3829 (mm-40) outliers start: 23 outliers final: 6 residues processed: 1020 average time/residue: 0.1545 time to fit residues: 224.8582 Evaluate side-chains 688 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 682 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.0060 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.0170 overall best weight: 0.5434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN A 312 GLN A 320 ASN A 361 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN B 19 GLN B 43 GLN B 61 ASN B 102 ASN B 191 GLN B 304 HIS B 320 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 HIS ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN C 263 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 186 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.131105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.095245 restraints weight = 39087.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.098786 restraints weight = 20341.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.101092 restraints weight = 12818.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.102699 restraints weight = 9089.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.103739 restraints weight = 6957.000| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16386 Z= 0.150 Angle : 0.614 7.200 22134 Z= 0.328 Chirality : 0.043 0.235 2360 Planarity : 0.004 0.033 2818 Dihedral : 11.374 178.940 2242 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.17 % Allowed : 2.80 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.18), residues: 1932 helix: 1.28 (0.15), residues: 1110 sheet: -0.09 (0.39), residues: 138 loop : 0.37 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 331 TYR 0.020 0.002 TYR D 142 PHE 0.027 0.002 PHE C 168 TRP 0.027 0.002 TRP D 124 HIS 0.010 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00320 (16386) covalent geometry : angle 0.61446 (22134) hydrogen bonds : bond 0.04667 ( 871) hydrogen bonds : angle 5.06379 ( 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 824 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 821 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9237 (tptp) cc_final: 0.8857 (tppt) REVERT: A 41 ILE cc_start: 0.9247 (mm) cc_final: 0.8864 (mm) REVERT: A 118 TYR cc_start: 0.9268 (t80) cc_final: 0.8952 (t80) REVERT: A 147 GLN cc_start: 0.9402 (mt0) cc_final: 0.8411 (mt0) REVERT: A 158 ASN cc_start: 0.9358 (m110) cc_final: 0.8980 (m-40) REVERT: A 162 LYS cc_start: 0.8813 (ttmm) cc_final: 0.8574 (ttmm) REVERT: A 181 ASP cc_start: 0.8857 (m-30) cc_final: 0.8647 (m-30) REVERT: A 195 LEU cc_start: 0.9601 (mt) cc_final: 0.9326 (mt) REVERT: A 227 MET cc_start: 0.9326 (mtm) cc_final: 0.9048 (mtm) REVERT: A 238 ASP cc_start: 0.8590 (p0) cc_final: 0.7998 (p0) REVERT: A 255 HIS cc_start: 0.8966 (t-90) cc_final: 0.8167 (t-90) REVERT: A 257 ASP cc_start: 0.9162 (m-30) cc_final: 0.8718 (m-30) REVERT: A 262 LEU cc_start: 0.9825 (mt) cc_final: 0.9561 (mt) REVERT: A 286 ASP cc_start: 0.8586 (m-30) cc_final: 0.8215 (m-30) REVERT: A 333 LYS cc_start: 0.9452 (tppt) cc_final: 0.9242 (tppp) REVERT: A 335 GLU cc_start: 0.7928 (mm-30) cc_final: 0.7597 (mm-30) REVERT: A 359 MET cc_start: 0.8855 (ttp) cc_final: 0.8641 (ttp) REVERT: A 362 ASP cc_start: 0.7971 (m-30) cc_final: 0.7612 (m-30) REVERT: A 366 LYS cc_start: 0.9294 (mtmm) cc_final: 0.8823 (mtmm) REVERT: A 375 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8458 (mmtm) REVERT: A 415 ASN cc_start: 0.9236 (t0) cc_final: 0.8654 (t0) REVERT: A 418 ASN cc_start: 0.9302 (OUTLIER) cc_final: 0.8817 (m110) REVERT: A 447 ASN cc_start: 0.8013 (m-40) cc_final: 0.7631 (t0) REVERT: A 466 MET cc_start: 0.9015 (ptt) cc_final: 0.8614 (ptt) REVERT: A 493 MET cc_start: 0.9081 (tmm) cc_final: 0.8667 (tmm) REVERT: A 494 MET cc_start: 0.9373 (mtp) cc_final: 0.9151 (mtp) REVERT: A 510 LYS cc_start: 0.8994 (mtpt) cc_final: 0.8620 (mtpt) REVERT: A 527 TYR cc_start: 0.8714 (t80) cc_final: 0.8387 (t80) REVERT: A 528 PHE cc_start: 0.9241 (m-80) cc_final: 0.8767 (m-80) REVERT: A 553 PRO cc_start: 0.9546 (Cg_exo) cc_final: 0.9053 (Cg_endo) REVERT: A 602 GLU cc_start: 0.7711 (pt0) cc_final: 0.7164 (pt0) REVERT: A 604 ARG cc_start: 0.9009 (mmm160) cc_final: 0.8703 (mmm-85) REVERT: A 645 GLN cc_start: 0.8670 (tp40) cc_final: 0.7808 (tp40) REVERT: A 657 PHE cc_start: 0.9059 (m-80) cc_final: 0.8674 (m-80) REVERT: A 669 ARG cc_start: 0.9161 (tpp-160) cc_final: 0.8808 (tpp-160) REVERT: A 680 LYS cc_start: 0.9163 (mttt) cc_final: 0.8470 (mttt) REVERT: B 8 LYS cc_start: 0.9450 (tptt) cc_final: 0.9032 (tppt) REVERT: B 12 LEU cc_start: 0.9569 (mt) cc_final: 0.9139 (mt) REVERT: B 15 GLU cc_start: 0.9271 (mt-10) cc_final: 0.9015 (mt-10) REVERT: B 51 LEU cc_start: 0.9431 (tp) cc_final: 0.9215 (tp) REVERT: B 147 GLN cc_start: 0.8636 (mt0) cc_final: 0.8182 (mt0) REVERT: B 184 ARG cc_start: 0.9396 (tpp80) cc_final: 0.9082 (tpp80) REVERT: B 191 GLN cc_start: 0.9209 (mm-40) cc_final: 0.8742 (mt0) REVERT: B 211 GLU cc_start: 0.8657 (mm-30) cc_final: 0.8378 (mm-30) REVERT: B 236 TYR cc_start: 0.9261 (t80) cc_final: 0.8923 (t80) REVERT: B 279 SER cc_start: 0.7921 (m) cc_final: 0.7630 (t) REVERT: B 288 PHE cc_start: 0.9305 (t80) cc_final: 0.8810 (t80) REVERT: B 315 ASP cc_start: 0.8724 (p0) cc_final: 0.8150 (p0) REVERT: B 321 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8219 (tm-30) REVERT: B 322 MET cc_start: 0.8636 (mmm) cc_final: 0.8381 (mmm) REVERT: B 335 GLU cc_start: 0.8262 (mm-30) cc_final: 0.8047 (mm-30) REVERT: B 348 MET cc_start: 0.9470 (ptm) cc_final: 0.9153 (ptm) REVERT: B 374 SER cc_start: 0.8913 (t) cc_final: 0.7922 (p) REVERT: B 375 LYS cc_start: 0.9108 (mttm) cc_final: 0.8617 (mtpp) REVERT: B 390 GLN cc_start: 0.9199 (mt0) cc_final: 0.8991 (mm110) REVERT: B 393 SER cc_start: 0.9375 (m) cc_final: 0.9066 (p) REVERT: B 398 ASP cc_start: 0.7887 (t0) cc_final: 0.7626 (t0) REVERT: B 410 ASN cc_start: 0.8598 (m110) cc_final: 0.8030 (m110) REVERT: B 423 LYS cc_start: 0.9574 (mttt) cc_final: 0.9242 (mppt) REVERT: B 427 LYS cc_start: 0.9340 (mmmm) cc_final: 0.9057 (tppt) REVERT: B 474 GLN cc_start: 0.8673 (mt0) cc_final: 0.8398 (mt0) REVERT: B 493 MET cc_start: 0.9671 (tmm) cc_final: 0.9341 (tmm) REVERT: B 516 GLN cc_start: 0.8822 (tp-100) cc_final: 0.8121 (tp40) REVERT: B 558 TRP cc_start: 0.9224 (m100) cc_final: 0.8569 (m100) REVERT: B 575 ARG cc_start: 0.8657 (mtm-85) cc_final: 0.8365 (mtm-85) REVERT: B 576 LEU cc_start: 0.9073 (mt) cc_final: 0.8828 (mt) REVERT: B 612 TYR cc_start: 0.9073 (m-80) cc_final: 0.8528 (m-10) REVERT: B 639 ASP cc_start: 0.9206 (m-30) cc_final: 0.8813 (m-30) REVERT: B 640 MET cc_start: 0.9421 (tpp) cc_final: 0.9064 (tpp) REVERT: B 677 ARG cc_start: 0.9356 (mmm-85) cc_final: 0.9038 (mmm-85) REVERT: C 35 ILE cc_start: 0.7000 (tt) cc_final: 0.6776 (tt) REVERT: C 93 MET cc_start: 0.8636 (ttm) cc_final: 0.8377 (ttp) REVERT: C 101 HIS cc_start: 0.7837 (m90) cc_final: 0.6049 (m90) REVERT: C 123 GLU cc_start: 0.9541 (mm-30) cc_final: 0.9293 (mm-30) REVERT: C 162 TYR cc_start: 0.9245 (m-10) cc_final: 0.8494 (m-10) REVERT: C 163 LEU cc_start: 0.9601 (tt) cc_final: 0.9188 (tt) REVERT: C 173 TYR cc_start: 0.7403 (t80) cc_final: 0.6398 (t80) REVERT: C 179 TYR cc_start: 0.8215 (t80) cc_final: 0.7865 (t80) REVERT: C 201 HIS cc_start: 0.9081 (m170) cc_final: 0.8765 (m170) REVERT: C 212 ILE cc_start: 0.8362 (mt) cc_final: 0.7892 (mt) REVERT: C 233 ASN cc_start: 0.9299 (m110) cc_final: 0.8663 (m110) REVERT: C 278 GLU cc_start: 0.8406 (mm-30) cc_final: 0.7644 (pm20) REVERT: D 20 MET cc_start: 0.8912 (mtm) cc_final: 0.8675 (mpp) REVERT: D 96 MET cc_start: 0.8990 (mmm) cc_final: 0.8753 (mmt) REVERT: D 148 ASP cc_start: 0.7308 (m-30) cc_final: 0.6967 (m-30) REVERT: D 186 GLN cc_start: 0.7670 (mm110) cc_final: 0.7123 (mm110) REVERT: D 230 ASP cc_start: 0.8916 (t70) cc_final: 0.8644 (t0) outliers start: 3 outliers final: 0 residues processed: 822 average time/residue: 0.1338 time to fit residues: 163.2489 Evaluate side-chains 673 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 672 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 9.9990 chunk 131 optimal weight: 0.8980 chunk 164 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 182 optimal weight: 1.9990 chunk 159 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 150 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 158 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN B 19 GLN B 44 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN C 84 HIS ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN D 28 GLN D 71 ASN D 238 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.125566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.090495 restraints weight = 40306.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.093823 restraints weight = 20888.743| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.096115 restraints weight = 12979.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.097672 restraints weight = 9132.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.098740 restraints weight = 6993.379| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7596 moved from start: 0.4918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16386 Z= 0.156 Angle : 0.578 7.416 22134 Z= 0.308 Chirality : 0.042 0.196 2360 Planarity : 0.003 0.036 2818 Dihedral : 11.083 173.830 2242 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.23 % Allowed : 2.86 % Favored : 96.91 % 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: 1.33 (0.19), residues: 1932 helix: 1.32 (0.15), residues: 1135 sheet: 0.30 (0.43), residues: 114 loop : 0.43 (0.24), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 243 TYR 0.025 0.002 TYR B 683 PHE 0.030 0.002 PHE A 654 TRP 0.020 0.002 TRP D 124 HIS 0.006 0.001 HIS A 255 Details of bonding type rmsd covalent geometry : bond 0.00351 (16386) covalent geometry : angle 0.57811 (22134) hydrogen bonds : bond 0.04137 ( 871) hydrogen bonds : angle 4.87178 ( 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 752 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 748 time to evaluate : 0.605 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 8 LYS cc_start: 0.9242 (tptp) cc_final: 0.8851 (tppt) REVERT: A 12 LEU cc_start: 0.9624 (mt) cc_final: 0.9364 (mt) REVERT: A 41 ILE cc_start: 0.9233 (mm) cc_final: 0.8983 (mm) REVERT: A 118 TYR cc_start: 0.9347 (t80) cc_final: 0.9091 (t80) REVERT: A 147 GLN cc_start: 0.9442 (mt0) cc_final: 0.8588 (mt0) REVERT: A 157 LEU cc_start: 0.9376 (tp) cc_final: 0.9035 (tp) REVERT: A 158 ASN cc_start: 0.9411 (m110) cc_final: 0.9054 (m-40) REVERT: A 181 ASP cc_start: 0.8867 (m-30) cc_final: 0.8614 (m-30) REVERT: A 195 LEU cc_start: 0.9694 (mt) cc_final: 0.9375 (mt) REVERT: A 218 ASN cc_start: 0.9278 (t0) cc_final: 0.8925 (t0) REVERT: A 223 VAL cc_start: 0.9717 (m) cc_final: 0.9205 (p) REVERT: A 227 MET cc_start: 0.9300 (mtm) cc_final: 0.8870 (mtm) REVERT: A 238 ASP cc_start: 0.8489 (p0) cc_final: 0.8136 (p0) REVERT: A 252 ASN cc_start: 0.9426 (t0) cc_final: 0.9160 (t0) REVERT: A 255 HIS cc_start: 0.8767 (t-90) cc_final: 0.7931 (t-90) REVERT: A 257 ASP cc_start: 0.9034 (m-30) cc_final: 0.8674 (m-30) REVERT: A 262 LEU cc_start: 0.9829 (mt) cc_final: 0.9594 (mt) REVERT: A 270 ASP cc_start: 0.8868 (t0) cc_final: 0.8553 (t0) REVERT: A 276 LYS cc_start: 0.9232 (ttpp) cc_final: 0.9028 (tmtt) REVERT: A 322 MET cc_start: 0.8784 (tpt) cc_final: 0.8043 (tpp) REVERT: A 333 LYS cc_start: 0.9537 (tppt) cc_final: 0.9265 (tppp) REVERT: A 335 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7659 (mm-30) REVERT: A 344 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8838 (mt-10) REVERT: A 366 LYS cc_start: 0.9270 (mtmm) cc_final: 0.8721 (mtmm) REVERT: A 375 LYS cc_start: 0.8717 (mmtt) cc_final: 0.8125 (mmtm) REVERT: A 390 GLN cc_start: 0.8523 (mt0) cc_final: 0.8308 (mt0) REVERT: A 405 LEU cc_start: 0.9173 (mt) cc_final: 0.8923 (mt) REVERT: A 415 ASN cc_start: 0.9449 (t0) cc_final: 0.8933 (t0) REVERT: A 447 ASN cc_start: 0.8119 (m-40) cc_final: 0.7719 (t0) REVERT: A 459 LYS cc_start: 0.8920 (mttp) cc_final: 0.8475 (mtmt) REVERT: A 466 MET cc_start: 0.9118 (ptt) cc_final: 0.8724 (ptt) REVERT: A 468 LEU cc_start: 0.9678 (tp) cc_final: 0.9430 (tp) REVERT: A 474 GLN cc_start: 0.9116 (mt0) cc_final: 0.8845 (mm-40) REVERT: A 491 PHE cc_start: 0.9653 (t80) cc_final: 0.9442 (t80) REVERT: A 493 MET cc_start: 0.9112 (tmm) cc_final: 0.8663 (tmm) REVERT: A 494 MET cc_start: 0.9389 (mtp) cc_final: 0.9042 (mtp) REVERT: A 527 TYR cc_start: 0.8831 (t80) cc_final: 0.8562 (t80) REVERT: A 528 PHE cc_start: 0.9293 (m-80) cc_final: 0.8898 (m-80) REVERT: A 552 ILE cc_start: 0.9339 (mp) cc_final: 0.9139 (mp) REVERT: A 553 PRO cc_start: 0.9549 (Cg_exo) cc_final: 0.9091 (Cg_endo) REVERT: A 601 ILE cc_start: 0.9539 (mm) cc_final: 0.9101 (mm) REVERT: A 602 GLU cc_start: 0.7582 (pt0) cc_final: 0.7121 (pt0) REVERT: A 640 MET cc_start: 0.9108 (tpp) cc_final: 0.8901 (tpp) REVERT: A 645 GLN cc_start: 0.8960 (tp40) cc_final: 0.8171 (tp40) REVERT: A 669 ARG cc_start: 0.9106 (tpp-160) cc_final: 0.8506 (tpp-160) REVERT: A 680 LYS cc_start: 0.9027 (mttt) cc_final: 0.8434 (mttt) REVERT: B 8 LYS cc_start: 0.9448 (tptt) cc_final: 0.9014 (tppt) REVERT: B 12 LEU cc_start: 0.9595 (mt) cc_final: 0.9289 (mt) REVERT: B 30 LYS cc_start: 0.9541 (tmtt) cc_final: 0.9337 (tmtt) REVERT: B 41 ILE cc_start: 0.9365 (mm) cc_final: 0.9027 (mm) REVERT: B 111 LYS cc_start: 0.9689 (mptt) cc_final: 0.9467 (mmtt) REVERT: B 117 ARG cc_start: 0.9352 (mmm-85) cc_final: 0.8985 (mmm-85) REVERT: B 150 GLN cc_start: 0.9420 (tp40) cc_final: 0.9054 (tp-100) REVERT: B 176 ASN cc_start: 0.8600 (t0) cc_final: 0.8368 (t0) REVERT: B 184 ARG cc_start: 0.9470 (tpp80) cc_final: 0.8927 (tpp80) REVERT: B 191 GLN cc_start: 0.9207 (mm-40) cc_final: 0.8761 (mt0) REVERT: B 202 ASN cc_start: 0.9279 (t0) cc_final: 0.9076 (t0) REVERT: B 211 GLU cc_start: 0.8748 (mm-30) cc_final: 0.8533 (mm-30) REVERT: B 232 ASN cc_start: 0.9505 (m110) cc_final: 0.9245 (m110) REVERT: B 235 ARG cc_start: 0.9416 (ttm110) cc_final: 0.8915 (ttm110) REVERT: B 236 TYR cc_start: 0.9294 (t80) cc_final: 0.8932 (t80) REVERT: B 239 GLN cc_start: 0.8716 (tm-30) cc_final: 0.8025 (tm-30) REVERT: B 288 PHE cc_start: 0.9334 (t80) cc_final: 0.9127 (t80) REVERT: B 322 MET cc_start: 0.8856 (mmm) cc_final: 0.8400 (mmm) REVERT: B 335 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8040 (mm-30) REVERT: B 350 ARG cc_start: 0.9154 (mmm-85) cc_final: 0.8924 (mmm-85) REVERT: B 358 ILE cc_start: 0.9693 (mm) cc_final: 0.9436 (mm) REVERT: B 375 LYS cc_start: 0.9069 (mttm) cc_final: 0.8563 (mtpp) REVERT: B 386 LEU cc_start: 0.9428 (mt) cc_final: 0.9045 (mt) REVERT: B 387 GLN cc_start: 0.9078 (mt0) cc_final: 0.8449 (mp10) REVERT: B 390 GLN cc_start: 0.9211 (mt0) cc_final: 0.9000 (mm110) REVERT: B 393 SER cc_start: 0.9403 (m) cc_final: 0.9081 (p) REVERT: B 398 ASP cc_start: 0.8049 (t0) cc_final: 0.7742 (t0) REVERT: B 407 ILE cc_start: 0.9009 (mp) cc_final: 0.8711 (mp) REVERT: B 410 ASN cc_start: 0.8820 (m110) cc_final: 0.8350 (m110) REVERT: B 423 LYS cc_start: 0.9585 (mttt) cc_final: 0.9376 (mtpt) REVERT: B 436 LEU cc_start: 0.9586 (mt) cc_final: 0.9377 (mt) REVERT: B 493 MET cc_start: 0.9635 (tmm) cc_final: 0.9408 (tmm) REVERT: B 522 TYR cc_start: 0.9097 (m-10) cc_final: 0.8642 (m-10) REVERT: B 550 MET cc_start: 0.8177 (mtp) cc_final: 0.7892 (mtm) REVERT: B 576 LEU cc_start: 0.9326 (mt) cc_final: 0.8911 (mt) REVERT: B 588 GLN cc_start: 0.9322 (mm-40) cc_final: 0.8917 (mm-40) REVERT: B 612 TYR cc_start: 0.9146 (m-80) cc_final: 0.8711 (m-80) REVERT: B 639 ASP cc_start: 0.9156 (m-30) cc_final: 0.8777 (m-30) REVERT: B 640 MET cc_start: 0.9452 (tpp) cc_final: 0.9019 (tpp) REVERT: B 658 LEU cc_start: 0.9322 (mm) cc_final: 0.9106 (mp) REVERT: B 677 ARG cc_start: 0.9383 (mmm-85) cc_final: 0.9179 (mmm-85) REVERT: B 686 ARG cc_start: 0.8498 (ttm110) cc_final: 0.8253 (ttm110) REVERT: C 20 MET cc_start: 0.9462 (tmm) cc_final: 0.9079 (ptp) REVERT: C 21 PHE cc_start: 0.9177 (m-80) cc_final: 0.8776 (m-80) REVERT: C 58 VAL cc_start: 0.8691 (t) cc_final: 0.8461 (p) REVERT: C 101 HIS cc_start: 0.8036 (m90) cc_final: 0.6355 (m90) REVERT: C 107 ASN cc_start: 0.8840 (m110) cc_final: 0.8520 (t0) REVERT: C 108 ILE cc_start: 0.8795 (mt) cc_final: 0.8522 (mt) REVERT: C 162 TYR cc_start: 0.9362 (m-10) cc_final: 0.8628 (m-10) REVERT: C 163 LEU cc_start: 0.9653 (tt) cc_final: 0.9405 (pp) REVERT: C 173 TYR cc_start: 0.7495 (t80) cc_final: 0.6477 (t80) REVERT: C 179 TYR cc_start: 0.8195 (t80) cc_final: 0.7788 (t80) REVERT: C 185 MET cc_start: 0.5079 (mmm) cc_final: 0.3663 (mpp) REVERT: C 201 HIS cc_start: 0.9120 (m170) cc_final: 0.8788 (m170) REVERT: C 208 LEU cc_start: 0.8780 (mm) cc_final: 0.8560 (mm) REVERT: C 212 ILE cc_start: 0.8267 (mt) cc_final: 0.7638 (mt) REVERT: C 233 ASN cc_start: 0.9335 (m110) cc_final: 0.8757 (m110) REVERT: C 252 LEU cc_start: 0.7621 (mt) cc_final: 0.7374 (mt) REVERT: C 278 GLU cc_start: 0.8515 (mm-30) cc_final: 0.7950 (pm20) REVERT: D 20 MET cc_start: 0.8917 (mtm) cc_final: 0.8678 (mpp) REVERT: D 148 ASP cc_start: 0.7252 (m-30) cc_final: 0.6918 (m-30) REVERT: D 176 LEU cc_start: 0.9586 (mt) cc_final: 0.9143 (tp) REVERT: D 186 GLN cc_start: 0.7750 (mm110) cc_final: 0.7464 (mm110) REVERT: D 201 HIS cc_start: 0.9292 (m170) cc_final: 0.8987 (m170) REVERT: D 219 GLU cc_start: 0.9155 (tp30) cc_final: 0.8872 (tp30) REVERT: D 266 LYS cc_start: 0.8788 (mmtp) cc_final: 0.8559 (mmmm) outliers start: 4 outliers final: 0 residues processed: 748 average time/residue: 0.1302 time to fit residues: 145.1580 Evaluate side-chains 642 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 642 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 6.9990 chunk 157 optimal weight: 5.9990 chunk 168 optimal weight: 0.8980 chunk 89 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 185 optimal weight: 7.9990 chunk 191 optimal weight: 9.9990 chunk 159 optimal weight: 8.9990 chunk 182 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS A 545 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN D 107 ASN D 127 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.111502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.077923 restraints weight = 42351.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.080874 restraints weight = 22010.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.082908 restraints weight = 13839.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.084298 restraints weight = 9760.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.085240 restraints weight = 7483.428| |-----------------------------------------------------------------------------| r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.5940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 16386 Z= 0.328 Angle : 0.714 10.358 22134 Z= 0.379 Chirality : 0.045 0.271 2360 Planarity : 0.004 0.063 2818 Dihedral : 11.408 179.263 2242 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.23 % Allowed : 2.86 % Favored : 96.91 % 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: 0.88 (0.18), residues: 1932 helix: 1.06 (0.15), residues: 1120 sheet: -0.16 (0.40), residues: 128 loop : 0.12 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 243 TYR 0.025 0.002 TYR C 174 PHE 0.026 0.003 PHE D 109 TRP 0.035 0.003 TRP D 124 HIS 0.008 0.002 HIS B 675 Details of bonding type rmsd covalent geometry : bond 0.00686 (16386) covalent geometry : angle 0.71428 (22134) hydrogen bonds : bond 0.04386 ( 871) hydrogen bonds : angle 5.03069 ( 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 715 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 711 time to evaluate : 0.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9231 (tptp) cc_final: 0.8910 (tppt) REVERT: A 12 LEU cc_start: 0.9603 (mt) cc_final: 0.9379 (mt) REVERT: A 91 PHE cc_start: 0.9536 (m-80) cc_final: 0.9276 (m-80) REVERT: A 95 MET cc_start: 0.9178 (mmm) cc_final: 0.8897 (tpp) REVERT: A 107 LYS cc_start: 0.9164 (mttm) cc_final: 0.8796 (mtpp) REVERT: A 123 SER cc_start: 0.9669 (m) cc_final: 0.9456 (p) REVERT: A 143 LEU cc_start: 0.9380 (tp) cc_final: 0.9178 (tp) REVERT: A 147 GLN cc_start: 0.9402 (mt0) cc_final: 0.8743 (mt0) REVERT: A 149 TYR cc_start: 0.9143 (t80) cc_final: 0.8416 (t80) REVERT: A 161 ARG cc_start: 0.8414 (ttm110) cc_final: 0.8058 (mmm-85) REVERT: A 181 ASP cc_start: 0.8949 (m-30) cc_final: 0.8640 (m-30) REVERT: A 195 LEU cc_start: 0.9707 (mt) cc_final: 0.9400 (mt) REVERT: A 214 LYS cc_start: 0.9126 (mmpt) cc_final: 0.8871 (mmtt) REVERT: A 218 ASN cc_start: 0.9574 (t0) cc_final: 0.9345 (t0) REVERT: A 223 VAL cc_start: 0.9788 (m) cc_final: 0.9248 (p) REVERT: A 227 MET cc_start: 0.9323 (mtm) cc_final: 0.8944 (mtm) REVERT: A 232 ASN cc_start: 0.9045 (m-40) cc_final: 0.8825 (m-40) REVERT: A 238 ASP cc_start: 0.8304 (p0) cc_final: 0.7955 (p0) REVERT: A 255 HIS cc_start: 0.8923 (t-90) cc_final: 0.7857 (t-90) REVERT: A 257 ASP cc_start: 0.9011 (m-30) cc_final: 0.8639 (m-30) REVERT: A 262 LEU cc_start: 0.9872 (mt) cc_final: 0.9642 (mt) REVERT: A 270 ASP cc_start: 0.9053 (t0) cc_final: 0.8694 (t0) REVERT: A 314 MET cc_start: 0.9036 (tmm) cc_final: 0.8718 (ppp) REVERT: A 316 GLU cc_start: 0.9003 (tp30) cc_final: 0.8480 (tp30) REVERT: A 322 MET cc_start: 0.8528 (tpt) cc_final: 0.8280 (tpt) REVERT: A 333 LYS cc_start: 0.9559 (tppt) cc_final: 0.9251 (tppp) REVERT: A 335 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7552 (mm-30) REVERT: A 344 GLU cc_start: 0.9349 (mt-10) cc_final: 0.8743 (mt-10) REVERT: A 359 MET cc_start: 0.8985 (ttp) cc_final: 0.8754 (ttp) REVERT: A 366 LYS cc_start: 0.9235 (mtmm) cc_final: 0.9020 (mtmm) REVERT: A 375 LYS cc_start: 0.8839 (mmtt) cc_final: 0.8391 (mmtm) REVERT: A 393 SER cc_start: 0.9339 (m) cc_final: 0.8983 (t) REVERT: A 399 GLU cc_start: 0.9272 (tp30) cc_final: 0.8930 (tp30) REVERT: A 415 ASN cc_start: 0.9383 (t0) cc_final: 0.8799 (t0) REVERT: A 459 LYS cc_start: 0.8943 (mttp) cc_final: 0.8486 (mtmt) REVERT: A 493 MET cc_start: 0.8989 (tmm) cc_final: 0.8510 (tmm) REVERT: A 501 GLN cc_start: 0.9349 (tt0) cc_final: 0.8564 (tm-30) REVERT: A 515 ASP cc_start: 0.9016 (m-30) cc_final: 0.8753 (m-30) REVERT: A 561 LEU cc_start: 0.9416 (tp) cc_final: 0.8976 (tp) REVERT: A 583 SER cc_start: 0.9164 (m) cc_final: 0.8938 (t) REVERT: A 601 ILE cc_start: 0.9472 (mm) cc_final: 0.9058 (tp) REVERT: A 640 MET cc_start: 0.9327 (tpp) cc_final: 0.8897 (tpp) REVERT: A 645 GLN cc_start: 0.9186 (tp40) cc_final: 0.8836 (tp-100) REVERT: A 669 ARG cc_start: 0.9103 (tpp-160) cc_final: 0.8589 (tpp-160) REVERT: B 8 LYS cc_start: 0.9425 (tptt) cc_final: 0.8990 (tppt) REVERT: B 55 LEU cc_start: 0.9747 (mt) cc_final: 0.9529 (mt) REVERT: B 58 LEU cc_start: 0.9769 (mt) cc_final: 0.9523 (mt) REVERT: B 119 GLU cc_start: 0.9415 (mp0) cc_final: 0.9107 (mp0) REVERT: B 143 LEU cc_start: 0.9381 (tp) cc_final: 0.8448 (tp) REVERT: B 148 GLU cc_start: 0.8966 (mp0) cc_final: 0.7980 (mp0) REVERT: B 149 TYR cc_start: 0.9338 (t80) cc_final: 0.8535 (t80) REVERT: B 176 ASN cc_start: 0.8868 (t0) cc_final: 0.8632 (t0) REVERT: B 181 ASP cc_start: 0.8651 (m-30) cc_final: 0.8271 (m-30) REVERT: B 184 ARG cc_start: 0.9435 (tpp80) cc_final: 0.9012 (tpp80) REVERT: B 211 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8305 (mm-30) REVERT: B 252 ASN cc_start: 0.9403 (t0) cc_final: 0.9124 (t0) REVERT: B 288 PHE cc_start: 0.9625 (t80) cc_final: 0.9371 (t80) REVERT: B 321 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8331 (tm-30) REVERT: B 322 MET cc_start: 0.9119 (mmm) cc_final: 0.8201 (mmm) REVERT: B 335 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8259 (mm-30) REVERT: B 350 ARG cc_start: 0.9331 (mmm-85) cc_final: 0.9125 (mmm-85) REVERT: B 390 GLN cc_start: 0.9220 (mt0) cc_final: 0.8905 (mm-40) REVERT: B 393 SER cc_start: 0.9383 (m) cc_final: 0.9094 (p) REVERT: B 415 ASN cc_start: 0.9178 (t0) cc_final: 0.8899 (t0) REVERT: B 423 LYS cc_start: 0.9566 (mttt) cc_final: 0.9360 (mtpt) REVERT: B 437 THR cc_start: 0.9723 (m) cc_final: 0.9507 (m) REVERT: B 492 PHE cc_start: 0.9663 (m-80) cc_final: 0.9413 (m-10) REVERT: B 505 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8425 (mt-10) REVERT: B 522 TYR cc_start: 0.9023 (m-10) cc_final: 0.8809 (m-10) REVERT: B 550 MET cc_start: 0.8207 (mtp) cc_final: 0.7947 (mtm) REVERT: B 570 MET cc_start: 0.8266 (mtm) cc_final: 0.7753 (mtm) REVERT: B 612 TYR cc_start: 0.8973 (m-80) cc_final: 0.8143 (m-10) REVERT: B 615 MET cc_start: 0.9525 (mmp) cc_final: 0.9209 (mmp) REVERT: B 639 ASP cc_start: 0.9109 (m-30) cc_final: 0.8792 (m-30) REVERT: B 640 MET cc_start: 0.9271 (tpp) cc_final: 0.8800 (tpp) REVERT: B 677 ARG cc_start: 0.9481 (mmm-85) cc_final: 0.9242 (mmm-85) REVERT: C 20 MET cc_start: 0.9499 (tmm) cc_final: 0.9035 (ptp) REVERT: C 90 LEU cc_start: 0.9690 (mt) cc_final: 0.9283 (mt) REVERT: C 93 MET cc_start: 0.8936 (ttp) cc_final: 0.8644 (tmm) REVERT: C 101 HIS cc_start: 0.7970 (m90) cc_final: 0.6864 (m90) REVERT: C 107 ASN cc_start: 0.8929 (m110) cc_final: 0.8666 (t0) REVERT: C 108 ILE cc_start: 0.8788 (mt) cc_final: 0.8554 (mt) REVERT: C 158 VAL cc_start: 0.9695 (t) cc_final: 0.9209 (t) REVERT: C 162 TYR cc_start: 0.9374 (m-10) cc_final: 0.8644 (m-10) REVERT: C 163 LEU cc_start: 0.9729 (tt) cc_final: 0.9376 (tt) REVERT: C 168 PHE cc_start: 0.9248 (m-80) cc_final: 0.8776 (m-80) REVERT: C 174 TYR cc_start: 0.8341 (t80) cc_final: 0.7930 (t80) REVERT: C 179 TYR cc_start: 0.8672 (t80) cc_final: 0.8148 (t80) REVERT: C 185 MET cc_start: 0.5572 (mmm) cc_final: 0.5334 (mmp) REVERT: C 201 HIS cc_start: 0.9036 (m170) cc_final: 0.8406 (m170) REVERT: C 208 LEU cc_start: 0.9046 (mm) cc_final: 0.8799 (mm) REVERT: C 278 GLU cc_start: 0.8856 (mm-30) cc_final: 0.8380 (pm20) REVERT: D 20 MET cc_start: 0.8990 (mtm) cc_final: 0.8732 (mpp) REVERT: D 138 ILE cc_start: 0.9804 (mm) cc_final: 0.9507 (mm) REVERT: D 139 VAL cc_start: 0.8620 (t) cc_final: 0.8061 (t) REVERT: D 148 ASP cc_start: 0.7121 (m-30) cc_final: 0.6809 (m-30) REVERT: D 176 LEU cc_start: 0.9651 (mt) cc_final: 0.9319 (tp) REVERT: D 219 GLU cc_start: 0.9152 (tp30) cc_final: 0.8922 (tp30) REVERT: D 240 LEU cc_start: 0.7565 (mt) cc_final: 0.7151 (mt) REVERT: D 266 LYS cc_start: 0.8836 (mmtp) cc_final: 0.8621 (mmmm) outliers start: 4 outliers final: 0 residues processed: 712 average time/residue: 0.1307 time to fit residues: 139.0780 Evaluate side-chains 622 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 622 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 6.9990 chunk 46 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 168 optimal weight: 5.9990 chunk 157 optimal weight: 0.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 34 HIS A 191 GLN A 232 ASN A 313 HIS A 320 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS A 545 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 28 GLN C 38 ASN C 52 GLN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.118122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.083953 restraints weight = 41347.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.087080 restraints weight = 21512.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.089218 restraints weight = 13455.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.090719 restraints weight = 9435.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.091679 restraints weight = 7190.147| |-----------------------------------------------------------------------------| r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3084 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3084 r_free = 0.3084 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3084 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.6196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16386 Z= 0.134 Angle : 0.578 7.478 22134 Z= 0.307 Chirality : 0.042 0.177 2360 Planarity : 0.003 0.048 2818 Dihedral : 10.837 175.516 2242 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.12 % Allowed : 1.98 % Favored : 97.90 % 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: 1119 sheet: 0.28 (0.43), residues: 100 loop : -0.06 (0.22), residues: 713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 243 TYR 0.036 0.001 TYR D 142 PHE 0.025 0.002 PHE C 166 TRP 0.034 0.002 TRP D 124 HIS 0.007 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00300 (16386) covalent geometry : angle 0.57809 (22134) hydrogen bonds : bond 0.03890 ( 871) hydrogen bonds : angle 4.82414 ( 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 733 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 731 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9246 (tptp) cc_final: 0.8949 (tppt) REVERT: A 12 LEU cc_start: 0.9617 (mt) cc_final: 0.9316 (mt) REVERT: A 30 LYS cc_start: 0.9496 (tptp) cc_final: 0.9263 (tptp) REVERT: A 95 MET cc_start: 0.9063 (mmm) cc_final: 0.8720 (tpp) REVERT: A 107 LYS cc_start: 0.9182 (mttm) cc_final: 0.8755 (mmmt) REVERT: A 147 GLN cc_start: 0.9280 (mt0) cc_final: 0.8860 (mt0) REVERT: A 149 TYR cc_start: 0.9104 (t80) cc_final: 0.8574 (t80) REVERT: A 158 ASN cc_start: 0.9374 (m-40) cc_final: 0.9095 (m-40) REVERT: A 161 ARG cc_start: 0.8316 (ttm110) cc_final: 0.7922 (mmm-85) REVERT: A 179 LEU cc_start: 0.9633 (tp) cc_final: 0.9431 (tp) REVERT: A 181 ASP cc_start: 0.8918 (m-30) cc_final: 0.8660 (m-30) REVERT: A 191 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8493 (mt0) REVERT: A 195 LEU cc_start: 0.9726 (mt) cc_final: 0.9481 (mt) REVERT: A 202 ASN cc_start: 0.9544 (t0) cc_final: 0.9336 (t0) REVERT: A 223 VAL cc_start: 0.9761 (m) cc_final: 0.9235 (p) REVERT: A 227 MET cc_start: 0.9317 (mtm) cc_final: 0.8828 (mtm) REVERT: A 231 ASP cc_start: 0.8780 (t0) cc_final: 0.8392 (t0) REVERT: A 238 ASP cc_start: 0.8345 (p0) cc_final: 0.7967 (p0) REVERT: A 257 ASP cc_start: 0.9055 (m-30) cc_final: 0.8631 (m-30) REVERT: A 262 LEU cc_start: 0.9879 (mt) cc_final: 0.9673 (mt) REVERT: A 270 ASP cc_start: 0.8999 (t0) cc_final: 0.8724 (t0) REVERT: A 301 PHE cc_start: 0.9195 (m-10) cc_final: 0.8661 (m-10) REVERT: A 314 MET cc_start: 0.9033 (tmm) cc_final: 0.8781 (ppp) REVERT: A 316 GLU cc_start: 0.8942 (tp30) cc_final: 0.8476 (tp30) REVERT: A 321 GLU cc_start: 0.8578 (pp20) cc_final: 0.8215 (pp20) REVERT: A 322 MET cc_start: 0.8499 (tpt) cc_final: 0.7919 (tpt) REVERT: A 344 GLU cc_start: 0.9307 (mt-10) cc_final: 0.8639 (mt-10) REVERT: A 345 LYS cc_start: 0.9819 (ttpt) cc_final: 0.9451 (ttmt) REVERT: A 349 LEU cc_start: 0.9699 (mt) cc_final: 0.9441 (mt) REVERT: A 375 LYS cc_start: 0.8732 (mmtt) cc_final: 0.8265 (mmtm) REVERT: A 390 GLN cc_start: 0.8767 (mt0) cc_final: 0.8566 (mt0) REVERT: A 393 SER cc_start: 0.9350 (m) cc_final: 0.8265 (p) REVERT: A 402 GLU cc_start: 0.8209 (mp0) cc_final: 0.7335 (mp0) REVERT: A 415 ASN cc_start: 0.9185 (t0) cc_final: 0.8787 (t0) REVERT: A 441 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8564 (mt-10) REVERT: A 459 LYS cc_start: 0.8946 (mttp) cc_final: 0.8485 (mtmt) REVERT: A 466 MET cc_start: 0.9045 (ptt) cc_final: 0.8768 (ptt) REVERT: A 474 GLN cc_start: 0.9317 (mt0) cc_final: 0.8990 (mm-40) REVERT: A 491 PHE cc_start: 0.9695 (t80) cc_final: 0.9487 (t80) REVERT: A 493 MET cc_start: 0.8935 (tmm) cc_final: 0.8645 (tmm) REVERT: A 501 GLN cc_start: 0.9364 (tt0) cc_final: 0.8718 (tm-30) REVERT: A 515 ASP cc_start: 0.8885 (m-30) cc_final: 0.8554 (m-30) REVERT: A 561 LEU cc_start: 0.9382 (tp) cc_final: 0.8937 (tp) REVERT: A 601 ILE cc_start: 0.9667 (mm) cc_final: 0.9298 (mm) REVERT: A 615 MET cc_start: 0.9027 (mmt) cc_final: 0.8799 (mmm) REVERT: A 632 MET cc_start: 0.8424 (mtt) cc_final: 0.8217 (mtt) REVERT: A 640 MET cc_start: 0.9295 (tpp) cc_final: 0.8737 (tpp) REVERT: A 645 GLN cc_start: 0.9170 (tp40) cc_final: 0.8817 (tp40) REVERT: A 669 ARG cc_start: 0.9061 (tpp-160) cc_final: 0.8768 (tpp-160) REVERT: B 8 LYS cc_start: 0.9446 (tptt) cc_final: 0.8964 (tppt) REVERT: B 21 ASP cc_start: 0.8603 (t70) cc_final: 0.8317 (t0) REVERT: B 55 LEU cc_start: 0.9779 (mt) cc_final: 0.9571 (mt) REVERT: B 58 LEU cc_start: 0.9768 (mt) cc_final: 0.9560 (mt) REVERT: B 119 GLU cc_start: 0.9370 (mp0) cc_final: 0.9050 (mp0) REVERT: B 139 GLU cc_start: 0.9376 (mm-30) cc_final: 0.9166 (mm-30) REVERT: B 143 LEU cc_start: 0.9286 (tp) cc_final: 0.8426 (tp) REVERT: B 148 GLU cc_start: 0.8869 (mp0) cc_final: 0.7897 (mp0) REVERT: B 149 TYR cc_start: 0.9194 (t80) cc_final: 0.8610 (t80) REVERT: B 167 LEU cc_start: 0.9178 (mt) cc_final: 0.8798 (mt) REVERT: B 172 LEU cc_start: 0.9417 (mp) cc_final: 0.9201 (mp) REVERT: B 173 LEU cc_start: 0.9404 (mt) cc_final: 0.9173 (mt) REVERT: B 176 ASN cc_start: 0.8774 (t0) cc_final: 0.8555 (t0) REVERT: B 181 ASP cc_start: 0.8710 (m-30) cc_final: 0.8357 (m-30) REVERT: B 184 ARG cc_start: 0.9431 (tpp80) cc_final: 0.8961 (tpp80) REVERT: B 191 GLN cc_start: 0.9393 (mm-40) cc_final: 0.8875 (mt0) REVERT: B 211 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8360 (mm-30) REVERT: B 239 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8331 (tm-30) REVERT: B 252 ASN cc_start: 0.9350 (t0) cc_final: 0.9098 (t0) REVERT: B 263 ASP cc_start: 0.9291 (m-30) cc_final: 0.8878 (m-30) REVERT: B 286 ASP cc_start: 0.8945 (m-30) cc_final: 0.8585 (m-30) REVERT: B 321 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8225 (tm-30) REVERT: B 322 MET cc_start: 0.9160 (mmm) cc_final: 0.8365 (mmm) REVERT: B 335 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8312 (mm-30) REVERT: B 348 MET cc_start: 0.9372 (ptp) cc_final: 0.9054 (ptp) REVERT: B 350 ARG cc_start: 0.9195 (mmm-85) cc_final: 0.8976 (mmm-85) REVERT: B 358 ILE cc_start: 0.9677 (mm) cc_final: 0.9416 (mm) REVERT: B 362 ASP cc_start: 0.8906 (m-30) cc_final: 0.8413 (m-30) REVERT: B 375 LYS cc_start: 0.9194 (mttm) cc_final: 0.8930 (mtpp) REVERT: B 393 SER cc_start: 0.9378 (m) cc_final: 0.9121 (p) REVERT: B 410 ASN cc_start: 0.8910 (m-40) cc_final: 0.8625 (m-40) REVERT: B 423 LYS cc_start: 0.9552 (mttt) cc_final: 0.9297 (mppt) REVERT: B 426 GLU cc_start: 0.8936 (pm20) cc_final: 0.8395 (pm20) REVERT: B 427 LYS cc_start: 0.9357 (ptpp) cc_final: 0.8716 (ptpp) REVERT: B 494 MET cc_start: 0.9344 (mtp) cc_final: 0.9037 (mmt) REVERT: B 550 MET cc_start: 0.8132 (mtp) cc_final: 0.7823 (mtm) REVERT: B 575 ARG cc_start: 0.8842 (mtm-85) cc_final: 0.8347 (mpp80) REVERT: B 576 LEU cc_start: 0.9431 (mt) cc_final: 0.9133 (mt) REVERT: B 606 TYR cc_start: 0.7892 (m-80) cc_final: 0.7633 (m-80) REVERT: B 615 MET cc_start: 0.9472 (mmp) cc_final: 0.9046 (mmp) REVERT: B 639 ASP cc_start: 0.9103 (m-30) cc_final: 0.8882 (m-30) REVERT: B 640 MET cc_start: 0.9179 (tpp) cc_final: 0.8652 (tpp) REVERT: C 20 MET cc_start: 0.9542 (tmm) cc_final: 0.9118 (ptp) REVERT: C 90 LEU cc_start: 0.9671 (mt) cc_final: 0.9311 (mt) REVERT: C 101 HIS cc_start: 0.7877 (m90) cc_final: 0.6694 (m90) REVERT: C 108 ILE cc_start: 0.8773 (mt) cc_final: 0.8511 (mt) REVERT: C 168 PHE cc_start: 0.9028 (m-80) cc_final: 0.8705 (m-80) REVERT: C 173 TYR cc_start: 0.7499 (t80) cc_final: 0.6607 (t80) REVERT: C 179 TYR cc_start: 0.8570 (t80) cc_final: 0.7872 (t80) REVERT: C 185 MET cc_start: 0.5498 (mmm) cc_final: 0.4337 (mpp) REVERT: C 201 HIS cc_start: 0.9083 (m170) cc_final: 0.8539 (m170) REVERT: C 233 ASN cc_start: 0.9368 (m110) cc_final: 0.8808 (m110) REVERT: C 252 LEU cc_start: 0.7595 (mt) cc_final: 0.7368 (mt) REVERT: C 260 ILE cc_start: 0.6936 (pt) cc_final: 0.6596 (pt) REVERT: C 278 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8355 (pm20) REVERT: D 20 MET cc_start: 0.9010 (mtm) cc_final: 0.8690 (mpp) REVERT: D 96 MET cc_start: 0.8971 (mmm) cc_final: 0.8734 (mmt) REVERT: D 148 ASP cc_start: 0.6949 (m-30) cc_final: 0.6640 (m-30) REVERT: D 185 MET cc_start: 0.5459 (ppp) cc_final: 0.4696 (mmm) REVERT: D 201 HIS cc_start: 0.9439 (m170) cc_final: 0.9125 (m170) REVERT: D 219 GLU cc_start: 0.9163 (tp30) cc_final: 0.8935 (tp30) REVERT: D 266 LYS cc_start: 0.8827 (mmtp) cc_final: 0.8623 (mmmm) outliers start: 2 outliers final: 0 residues processed: 732 average time/residue: 0.1306 time to fit residues: 143.2071 Evaluate side-chains 635 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 634 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 9.9990 chunk 183 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 27 optimal weight: 7.9990 chunk 136 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 242 GLN A 320 ASN ** A 410 ASN ** 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 390 GLN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN D 132 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.116327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.081987 restraints weight = 41820.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.085030 restraints weight = 21805.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.087096 restraints weight = 13738.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.088544 restraints weight = 9739.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.089430 restraints weight = 7483.882| |-----------------------------------------------------------------------------| r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3006 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.6487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16386 Z= 0.217 Angle : 0.627 8.387 22134 Z= 0.331 Chirality : 0.044 0.268 2360 Planarity : 0.004 0.043 2818 Dihedral : 10.673 173.074 2242 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.06 % Allowed : 1.57 % Favored : 98.37 % 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: 1.21 (0.15), residues: 1122 sheet: 0.30 (0.42), residues: 96 loop : -0.09 (0.23), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 243 TYR 0.035 0.002 TYR D 142 PHE 0.024 0.002 PHE C 227 TRP 0.038 0.002 TRP D 124 HIS 0.006 0.001 HIS A 551 Details of bonding type rmsd covalent geometry : bond 0.00469 (16386) covalent geometry : angle 0.62656 (22134) hydrogen bonds : bond 0.03960 ( 871) hydrogen bonds : angle 4.87815 ( 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 712 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 711 time to evaluate : 0.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9242 (tptp) cc_final: 0.8944 (tppt) REVERT: A 12 LEU cc_start: 0.9619 (mt) cc_final: 0.9329 (mt) REVERT: A 30 LYS cc_start: 0.9494 (tptp) cc_final: 0.9263 (tptp) REVERT: A 107 LYS cc_start: 0.9201 (mttm) cc_final: 0.8904 (mtpp) REVERT: A 129 PHE cc_start: 0.9560 (m-10) cc_final: 0.9258 (m-10) REVERT: A 147 GLN cc_start: 0.9353 (mt0) cc_final: 0.8674 (mt0) REVERT: A 149 TYR cc_start: 0.9316 (t80) cc_final: 0.8580 (t80) REVERT: A 158 ASN cc_start: 0.9410 (m-40) cc_final: 0.9147 (m-40) REVERT: A 161 ARG cc_start: 0.8406 (ttm110) cc_final: 0.7955 (mmm-85) REVERT: A 172 LEU cc_start: 0.9597 (mp) cc_final: 0.9278 (mp) REVERT: A 181 ASP cc_start: 0.8820 (m-30) cc_final: 0.8589 (m-30) REVERT: A 195 LEU cc_start: 0.9723 (mt) cc_final: 0.9482 (mt) REVERT: A 202 ASN cc_start: 0.9553 (t0) cc_final: 0.9323 (t0) REVERT: A 214 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8582 (mmtt) REVERT: A 218 ASN cc_start: 0.9554 (t0) cc_final: 0.9270 (t0) REVERT: A 223 VAL cc_start: 0.9792 (m) cc_final: 0.9271 (p) REVERT: A 227 MET cc_start: 0.9275 (mtm) cc_final: 0.8832 (mtm) REVERT: A 231 ASP cc_start: 0.8609 (t0) cc_final: 0.8204 (p0) REVERT: A 232 ASN cc_start: 0.8782 (m110) cc_final: 0.7735 (m110) REVERT: A 238 ASP cc_start: 0.8319 (p0) cc_final: 0.7964 (p0) REVERT: A 255 HIS cc_start: 0.8813 (t-90) cc_final: 0.7717 (t-90) REVERT: A 257 ASP cc_start: 0.9027 (m-30) cc_final: 0.8736 (m-30) REVERT: A 262 LEU cc_start: 0.9882 (mt) cc_final: 0.9640 (mt) REVERT: A 263 ASP cc_start: 0.9307 (m-30) cc_final: 0.9028 (m-30) REVERT: A 276 LYS cc_start: 0.9182 (mptt) cc_final: 0.8578 (mptt) REVERT: A 301 PHE cc_start: 0.9269 (m-10) cc_final: 0.8775 (m-10) REVERT: A 314 MET cc_start: 0.9109 (tmm) cc_final: 0.8836 (ppp) REVERT: A 316 GLU cc_start: 0.9028 (tp30) cc_final: 0.8621 (tp30) REVERT: A 322 MET cc_start: 0.8550 (tpt) cc_final: 0.8114 (tpp) REVERT: A 333 LYS cc_start: 0.9584 (tppt) cc_final: 0.9322 (tppp) REVERT: A 335 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8120 (mm-30) REVERT: A 344 GLU cc_start: 0.9323 (mt-10) cc_final: 0.8715 (mt-10) REVERT: A 345 LYS cc_start: 0.9813 (ttpt) cc_final: 0.9458 (ttmt) REVERT: A 349 LEU cc_start: 0.9697 (mt) cc_final: 0.9412 (mt) REVERT: A 366 LYS cc_start: 0.9421 (mtmm) cc_final: 0.9073 (mtmm) REVERT: A 375 LYS cc_start: 0.8985 (mmtt) cc_final: 0.8516 (mmtm) REVERT: A 390 GLN cc_start: 0.8860 (mt0) cc_final: 0.8647 (mt0) REVERT: A 393 SER cc_start: 0.9428 (m) cc_final: 0.9161 (t) REVERT: A 399 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8126 (tm-30) REVERT: A 402 GLU cc_start: 0.8269 (mp0) cc_final: 0.8060 (mp0) REVERT: A 407 ILE cc_start: 0.9311 (mt) cc_final: 0.9110 (mt) REVERT: A 415 ASN cc_start: 0.9281 (t0) cc_final: 0.8845 (t0) REVERT: A 459 LYS cc_start: 0.8947 (mttp) cc_final: 0.8528 (mtmt) REVERT: A 466 MET cc_start: 0.9161 (ptt) cc_final: 0.8908 (ptt) REVERT: A 493 MET cc_start: 0.8954 (tmm) cc_final: 0.8509 (tmm) REVERT: A 501 GLN cc_start: 0.9366 (tt0) cc_final: 0.8743 (tm-30) REVERT: A 515 ASP cc_start: 0.8966 (m-30) cc_final: 0.8695 (m-30) REVERT: A 561 LEU cc_start: 0.9449 (tp) cc_final: 0.9056 (tp) REVERT: A 601 ILE cc_start: 0.9438 (mm) cc_final: 0.8960 (tp) REVERT: A 615 MET cc_start: 0.9136 (mmt) cc_final: 0.8843 (mmm) REVERT: A 640 MET cc_start: 0.9282 (tpp) cc_final: 0.8766 (tpp) REVERT: A 645 GLN cc_start: 0.9184 (tp40) cc_final: 0.8810 (tp40) REVERT: A 667 LEU cc_start: 0.9417 (tt) cc_final: 0.9201 (tt) REVERT: A 669 ARG cc_start: 0.9099 (tpp-160) cc_final: 0.8875 (tpp-160) REVERT: B 8 LYS cc_start: 0.9388 (tptt) cc_final: 0.9038 (tppt) REVERT: B 12 LEU cc_start: 0.9603 (mt) cc_final: 0.9369 (mt) REVERT: B 55 LEU cc_start: 0.9766 (mt) cc_final: 0.9541 (mt) REVERT: B 87 LYS cc_start: 0.9387 (tptt) cc_final: 0.8984 (tttt) REVERT: B 88 LYS cc_start: 0.9404 (mptt) cc_final: 0.9143 (mmtt) REVERT: B 119 GLU cc_start: 0.9374 (mp0) cc_final: 0.9054 (mp0) REVERT: B 139 GLU cc_start: 0.9360 (mm-30) cc_final: 0.9144 (mm-30) REVERT: B 143 LEU cc_start: 0.9370 (tp) cc_final: 0.8417 (tp) REVERT: B 148 GLU cc_start: 0.8933 (mp0) cc_final: 0.7857 (mp0) REVERT: B 149 TYR cc_start: 0.9302 (t80) cc_final: 0.8436 (t80) REVERT: B 167 LEU cc_start: 0.9323 (mt) cc_final: 0.8877 (mt) REVERT: B 172 LEU cc_start: 0.9469 (mp) cc_final: 0.9223 (mp) REVERT: B 176 ASN cc_start: 0.8861 (t0) cc_final: 0.8658 (t0) REVERT: B 181 ASP cc_start: 0.8616 (m-30) cc_final: 0.8299 (m-30) REVERT: B 184 ARG cc_start: 0.9413 (tpp80) cc_final: 0.9143 (tpp80) REVERT: B 211 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8393 (mm-30) REVERT: B 235 ARG cc_start: 0.9232 (ttm110) cc_final: 0.8483 (mtm-85) REVERT: B 239 GLN cc_start: 0.8908 (tm-30) cc_final: 0.8320 (tm-30) REVERT: B 252 ASN cc_start: 0.9332 (t0) cc_final: 0.9053 (t0) REVERT: B 286 ASP cc_start: 0.9005 (m-30) cc_final: 0.8695 (m-30) REVERT: B 321 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8366 (tm-30) REVERT: B 322 MET cc_start: 0.9216 (mmm) cc_final: 0.8170 (mmm) REVERT: B 335 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8270 (mm-30) REVERT: B 358 ILE cc_start: 0.9694 (mm) cc_final: 0.9481 (mm) REVERT: B 393 SER cc_start: 0.9350 (m) cc_final: 0.9076 (p) REVERT: B 410 ASN cc_start: 0.8914 (m-40) cc_final: 0.8685 (m-40) REVERT: B 415 ASN cc_start: 0.9046 (t0) cc_final: 0.8743 (t0) REVERT: B 423 LYS cc_start: 0.9546 (mttt) cc_final: 0.9332 (mtpt) REVERT: B 426 GLU cc_start: 0.8958 (pm20) cc_final: 0.8739 (pm20) REVERT: B 427 LYS cc_start: 0.9370 (ptpp) cc_final: 0.8825 (ptpp) REVERT: B 475 ASN cc_start: 0.9189 (m-40) cc_final: 0.8909 (m110) REVERT: B 505 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8425 (mt-10) REVERT: B 550 MET cc_start: 0.8116 (mtp) cc_final: 0.7811 (mtm) REVERT: B 612 TYR cc_start: 0.8977 (m-80) cc_final: 0.8695 (m-80) REVERT: B 615 MET cc_start: 0.9473 (mmp) cc_final: 0.9035 (mmp) REVERT: B 640 MET cc_start: 0.9232 (tpp) cc_final: 0.8713 (tpp) REVERT: C 17 PHE cc_start: 0.9015 (p90) cc_final: 0.8699 (p90) REVERT: C 20 MET cc_start: 0.9548 (tmm) cc_final: 0.9173 (tmm) REVERT: C 90 LEU cc_start: 0.9587 (mt) cc_final: 0.9387 (mt) REVERT: C 168 PHE cc_start: 0.8948 (m-80) cc_final: 0.8685 (m-80) REVERT: C 173 TYR cc_start: 0.7549 (t80) cc_final: 0.6345 (t80) REVERT: C 177 TYR cc_start: 0.9145 (t80) cc_final: 0.8857 (t80) REVERT: C 179 TYR cc_start: 0.8676 (t80) cc_final: 0.7978 (t80) REVERT: C 185 MET cc_start: 0.5863 (mmm) cc_final: 0.4756 (mpp) REVERT: C 201 HIS cc_start: 0.8867 (m170) cc_final: 0.8558 (m170) REVERT: C 233 ASN cc_start: 0.9387 (m110) cc_final: 0.8700 (m110) REVERT: C 252 LEU cc_start: 0.7593 (mt) cc_final: 0.7104 (mt) REVERT: C 278 GLU cc_start: 0.8797 (mm-30) cc_final: 0.8395 (pm20) REVERT: D 20 MET cc_start: 0.9030 (mtm) cc_final: 0.8688 (mpp) REVERT: D 96 MET cc_start: 0.9041 (mmm) cc_final: 0.8771 (mmt) REVERT: D 148 ASP cc_start: 0.6993 (m-30) cc_final: 0.6721 (m-30) REVERT: D 176 LEU cc_start: 0.9622 (mt) cc_final: 0.9317 (tp) REVERT: D 201 HIS cc_start: 0.9458 (m170) cc_final: 0.9229 (m170) REVERT: D 219 GLU cc_start: 0.9229 (tp30) cc_final: 0.9010 (tp30) REVERT: D 233 ASN cc_start: 0.8614 (m110) cc_final: 0.8364 (p0) REVERT: D 240 LEU cc_start: 0.7695 (mt) cc_final: 0.7150 (mt) REVERT: D 270 ASN cc_start: 0.8401 (m-40) cc_final: 0.8173 (m-40) outliers start: 1 outliers final: 0 residues processed: 712 average time/residue: 0.1278 time to fit residues: 136.1338 Evaluate side-chains 617 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 617 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 chunk 105 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 186 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 9.9990 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 156 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 19 GLN A 320 ASN ** A 410 ASN ** 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 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 201 HIS D 270 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.119969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.085669 restraints weight = 41007.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.088787 restraints weight = 21454.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.090880 restraints weight = 13409.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.092395 restraints weight = 9418.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.093428 restraints weight = 7197.227| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.6733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16386 Z= 0.129 Angle : 0.610 9.750 22134 Z= 0.322 Chirality : 0.043 0.353 2360 Planarity : 0.004 0.046 2818 Dihedral : 10.188 164.800 2242 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.19), residues: 1932 helix: 1.19 (0.16), residues: 1121 sheet: -0.51 (0.38), residues: 144 loop : -0.03 (0.23), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 686 TYR 0.033 0.001 TYR D 142 PHE 0.022 0.002 PHE B 492 TRP 0.040 0.002 TRP D 124 HIS 0.006 0.001 HIS A 438 Details of bonding type rmsd covalent geometry : bond 0.00288 (16386) covalent geometry : angle 0.60964 (22134) hydrogen bonds : bond 0.03817 ( 871) hydrogen bonds : angle 4.84758 ( 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 713 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 713 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9233 (tptp) cc_final: 0.8912 (tppt) REVERT: A 12 LEU cc_start: 0.9619 (mt) cc_final: 0.9289 (mt) REVERT: A 107 LYS cc_start: 0.9204 (mttm) cc_final: 0.8708 (mtpp) REVERT: A 117 ARG cc_start: 0.9202 (tpp80) cc_final: 0.8862 (tpp80) REVERT: A 147 GLN cc_start: 0.9254 (mt0) cc_final: 0.8492 (mt0) REVERT: A 149 TYR cc_start: 0.9359 (t80) cc_final: 0.8715 (t80) REVERT: A 158 ASN cc_start: 0.9371 (m-40) cc_final: 0.9142 (m-40) REVERT: A 161 ARG cc_start: 0.8370 (ttm110) cc_final: 0.8009 (mmm-85) REVERT: A 172 LEU cc_start: 0.9526 (mp) cc_final: 0.9116 (mp) REVERT: A 181 ASP cc_start: 0.8842 (m-30) cc_final: 0.8592 (m-30) REVERT: A 195 LEU cc_start: 0.9711 (mt) cc_final: 0.9466 (mt) REVERT: A 214 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8573 (mmtt) REVERT: A 218 ASN cc_start: 0.9481 (t0) cc_final: 0.9270 (t0) REVERT: A 223 VAL cc_start: 0.9761 (m) cc_final: 0.9155 (p) REVERT: A 227 MET cc_start: 0.9274 (mtm) cc_final: 0.8812 (mtm) REVERT: A 231 ASP cc_start: 0.8530 (t0) cc_final: 0.8320 (t0) REVERT: A 236 TYR cc_start: 0.9246 (t80) cc_final: 0.8967 (t80) REVERT: A 255 HIS cc_start: 0.8753 (t-90) cc_final: 0.8082 (t-90) REVERT: A 257 ASP cc_start: 0.9083 (m-30) cc_final: 0.8797 (m-30) REVERT: A 262 LEU cc_start: 0.9878 (mt) cc_final: 0.9633 (mt) REVERT: A 263 ASP cc_start: 0.9289 (m-30) cc_final: 0.8988 (m-30) REVERT: A 301 PHE cc_start: 0.9152 (m-10) cc_final: 0.8588 (m-10) REVERT: A 316 GLU cc_start: 0.9065 (tp30) cc_final: 0.8589 (tp30) REVERT: A 321 GLU cc_start: 0.8637 (pp20) cc_final: 0.8068 (pp20) REVERT: A 322 MET cc_start: 0.8606 (tpt) cc_final: 0.7996 (tpp) REVERT: A 335 GLU cc_start: 0.8478 (mm-30) cc_final: 0.8156 (mm-30) REVERT: A 344 GLU cc_start: 0.9278 (mt-10) cc_final: 0.8629 (mt-10) REVERT: A 345 LYS cc_start: 0.9841 (ttpt) cc_final: 0.9519 (ttmt) REVERT: A 349 LEU cc_start: 0.9681 (mt) cc_final: 0.9441 (mt) REVERT: A 366 LYS cc_start: 0.9398 (mtmm) cc_final: 0.9095 (mtmm) REVERT: A 375 LYS cc_start: 0.8985 (mmtt) cc_final: 0.8637 (mmtm) REVERT: A 390 GLN cc_start: 0.8908 (mt0) cc_final: 0.8664 (mt0) REVERT: A 393 SER cc_start: 0.9384 (m) cc_final: 0.8933 (t) REVERT: A 402 GLU cc_start: 0.8300 (mp0) cc_final: 0.7930 (mp0) REVERT: A 407 ILE cc_start: 0.9257 (mt) cc_final: 0.8988 (mt) REVERT: A 415 ASN cc_start: 0.9219 (t0) cc_final: 0.8762 (t0) REVERT: A 459 LYS cc_start: 0.8937 (mttp) cc_final: 0.8431 (mtmt) REVERT: A 466 MET cc_start: 0.9052 (ptt) cc_final: 0.8825 (ptt) REVERT: A 474 GLN cc_start: 0.9370 (mt0) cc_final: 0.9004 (mm-40) REVERT: A 493 MET cc_start: 0.8913 (tmm) cc_final: 0.8701 (tmm) REVERT: A 501 GLN cc_start: 0.9305 (tt0) cc_final: 0.8763 (tm-30) REVERT: A 515 ASP cc_start: 0.8908 (m-30) cc_final: 0.8626 (m-30) REVERT: A 561 LEU cc_start: 0.9420 (tp) cc_final: 0.8999 (tp) REVERT: A 601 ILE cc_start: 0.9611 (mm) cc_final: 0.9002 (tp) REVERT: A 615 MET cc_start: 0.9098 (mmt) cc_final: 0.8766 (mmm) REVERT: A 640 MET cc_start: 0.9274 (tpp) cc_final: 0.8639 (tpp) REVERT: A 645 GLN cc_start: 0.9179 (tp40) cc_final: 0.8820 (tp-100) REVERT: A 669 ARG cc_start: 0.9120 (tpp-160) cc_final: 0.8841 (tpp-160) REVERT: B 8 LYS cc_start: 0.9392 (tptt) cc_final: 0.9041 (tppt) REVERT: B 12 LEU cc_start: 0.9592 (mt) cc_final: 0.9348 (mt) REVERT: B 20 LYS cc_start: 0.9672 (tmtt) cc_final: 0.9442 (tptp) REVERT: B 21 ASP cc_start: 0.8608 (t70) cc_final: 0.8317 (t0) REVERT: B 55 LEU cc_start: 0.9789 (mt) cc_final: 0.9575 (mt) REVERT: B 87 LYS cc_start: 0.9336 (tptt) cc_final: 0.8889 (tttt) REVERT: B 88 LYS cc_start: 0.9361 (mptt) cc_final: 0.9100 (mmtt) REVERT: B 119 GLU cc_start: 0.9337 (mp0) cc_final: 0.9028 (mp0) REVERT: B 127 LEU cc_start: 0.9781 (mm) cc_final: 0.9571 (mm) REVERT: B 139 GLU cc_start: 0.9392 (mm-30) cc_final: 0.9137 (mm-30) REVERT: B 149 TYR cc_start: 0.9266 (t80) cc_final: 0.8412 (t80) REVERT: B 167 LEU cc_start: 0.9275 (mt) cc_final: 0.8838 (mt) REVERT: B 172 LEU cc_start: 0.9404 (mp) cc_final: 0.9181 (mp) REVERT: B 176 ASN cc_start: 0.8753 (t0) cc_final: 0.8538 (t0) REVERT: B 181 ASP cc_start: 0.8728 (m-30) cc_final: 0.8349 (m-30) REVERT: B 184 ARG cc_start: 0.9451 (tpp80) cc_final: 0.9024 (tpp80) REVERT: B 211 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8500 (mm-30) REVERT: B 235 ARG cc_start: 0.9210 (ttm110) cc_final: 0.8402 (mtm-85) REVERT: B 239 GLN cc_start: 0.8931 (tm-30) cc_final: 0.8320 (tm-30) REVERT: B 252 ASN cc_start: 0.9335 (t0) cc_final: 0.9080 (t0) REVERT: B 263 ASP cc_start: 0.9259 (m-30) cc_final: 0.8823 (m-30) REVERT: B 321 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8366 (tm-30) REVERT: B 322 MET cc_start: 0.9263 (mmm) cc_final: 0.8578 (mmm) REVERT: B 335 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8421 (mm-30) REVERT: B 358 ILE cc_start: 0.9663 (mm) cc_final: 0.9452 (mm) REVERT: B 410 ASN cc_start: 0.8884 (m-40) cc_final: 0.8522 (m-40) REVERT: B 423 LYS cc_start: 0.9507 (mttt) cc_final: 0.9270 (mtpt) REVERT: B 426 GLU cc_start: 0.8973 (pm20) cc_final: 0.8461 (pm20) REVERT: B 427 LYS cc_start: 0.9342 (ptpp) cc_final: 0.8654 (ptpp) REVERT: B 475 ASN cc_start: 0.9117 (m-40) cc_final: 0.8906 (m110) REVERT: B 492 PHE cc_start: 0.9628 (m-80) cc_final: 0.9417 (m-10) REVERT: B 550 MET cc_start: 0.8065 (mtp) cc_final: 0.7823 (mtm) REVERT: B 576 LEU cc_start: 0.9347 (mt) cc_final: 0.9111 (mt) REVERT: B 612 TYR cc_start: 0.8902 (m-80) cc_final: 0.8637 (m-80) REVERT: B 640 MET cc_start: 0.9269 (tpp) cc_final: 0.8565 (tpp) REVERT: B 667 LEU cc_start: 0.9309 (tp) cc_final: 0.9034 (tp) REVERT: C 20 MET cc_start: 0.9540 (tmm) cc_final: 0.9024 (ptp) REVERT: C 101 HIS cc_start: 0.7690 (m90) cc_final: 0.6824 (m90) REVERT: C 110 MET cc_start: 0.5514 (mpp) cc_final: 0.5236 (mpp) REVERT: C 168 PHE cc_start: 0.8848 (m-80) cc_final: 0.8600 (m-80) REVERT: C 173 TYR cc_start: 0.7749 (t80) cc_final: 0.6622 (t80) REVERT: C 177 TYR cc_start: 0.9129 (t80) cc_final: 0.8852 (t80) REVERT: C 179 TYR cc_start: 0.8663 (t80) cc_final: 0.7971 (t80) REVERT: C 185 MET cc_start: 0.6166 (mmm) cc_final: 0.5174 (mpp) REVERT: C 208 LEU cc_start: 0.8879 (mm) cc_final: 0.8678 (mm) REVERT: C 231 LEU cc_start: 0.9058 (mt) cc_final: 0.8737 (pp) REVERT: C 233 ASN cc_start: 0.9427 (m110) cc_final: 0.8923 (m110) REVERT: C 252 LEU cc_start: 0.7541 (mt) cc_final: 0.6968 (mt) REVERT: C 278 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8403 (pm20) REVERT: C 321 TYR cc_start: 0.9103 (m-80) cc_final: 0.8857 (m-80) REVERT: D 20 MET cc_start: 0.9050 (mtm) cc_final: 0.8690 (mpp) REVERT: D 96 MET cc_start: 0.9056 (mmm) cc_final: 0.8852 (mmt) REVERT: D 148 ASP cc_start: 0.6900 (m-30) cc_final: 0.6610 (m-30) REVERT: D 176 LEU cc_start: 0.9596 (mt) cc_final: 0.9282 (tp) REVERT: D 201 HIS cc_start: 0.9363 (m-70) cc_final: 0.8838 (m-70) REVERT: D 219 GLU cc_start: 0.9182 (tp30) cc_final: 0.8957 (tp30) outliers start: 0 outliers final: 0 residues processed: 713 average time/residue: 0.1258 time to fit residues: 135.2182 Evaluate side-chains 633 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 633 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 6.9990 chunk 99 optimal weight: 0.0670 chunk 61 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN D 186 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.119454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.085833 restraints weight = 41994.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.088888 restraints weight = 21741.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.090986 restraints weight = 13518.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.092423 restraints weight = 9458.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.093422 restraints weight = 7230.119| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.6962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16386 Z= 0.145 Angle : 0.630 9.401 22134 Z= 0.330 Chirality : 0.044 0.333 2360 Planarity : 0.004 0.064 2818 Dihedral : 10.029 157.956 2242 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.06 % Allowed : 0.70 % Favored : 99.24 % 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: 0.76 (0.19), residues: 1932 helix: 1.05 (0.15), residues: 1141 sheet: 0.11 (0.43), residues: 110 loop : -0.20 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 235 TYR 0.031 0.001 TYR D 142 PHE 0.024 0.002 PHE C 227 TRP 0.042 0.002 TRP D 124 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00324 (16386) covalent geometry : angle 0.62951 (22134) hydrogen bonds : bond 0.03880 ( 871) hydrogen bonds : angle 4.81219 ( 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 699 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 698 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9223 (tptp) cc_final: 0.8918 (tppt) REVERT: A 12 LEU cc_start: 0.9590 (mt) cc_final: 0.9254 (mt) REVERT: A 107 LYS cc_start: 0.9245 (mttm) cc_final: 0.8780 (mtpp) REVERT: A 117 ARG cc_start: 0.9172 (tpp80) cc_final: 0.8846 (tpp80) REVERT: A 129 PHE cc_start: 0.9369 (m-10) cc_final: 0.9162 (m-80) REVERT: A 147 GLN cc_start: 0.9276 (mt0) cc_final: 0.8567 (mt0) REVERT: A 149 TYR cc_start: 0.9300 (t80) cc_final: 0.8685 (t80) REVERT: A 158 ASN cc_start: 0.9326 (m-40) cc_final: 0.9069 (m-40) REVERT: A 161 ARG cc_start: 0.8308 (ttm110) cc_final: 0.7897 (mmm-85) REVERT: A 164 ARG cc_start: 0.8903 (ptm-80) cc_final: 0.7643 (ptm-80) REVERT: A 172 LEU cc_start: 0.9606 (mp) cc_final: 0.9149 (mp) REVERT: A 181 ASP cc_start: 0.8868 (m-30) cc_final: 0.8526 (m-30) REVERT: A 195 LEU cc_start: 0.9652 (mt) cc_final: 0.9408 (mt) REVERT: A 223 VAL cc_start: 0.9767 (m) cc_final: 0.9250 (p) REVERT: A 227 MET cc_start: 0.9228 (mtm) cc_final: 0.8905 (mtm) REVERT: A 231 ASP cc_start: 0.8522 (t0) cc_final: 0.8192 (t0) REVERT: A 255 HIS cc_start: 0.8573 (t-90) cc_final: 0.8282 (t-90) REVERT: A 257 ASP cc_start: 0.9027 (m-30) cc_final: 0.8743 (m-30) REVERT: A 262 LEU cc_start: 0.9880 (mt) cc_final: 0.9641 (mt) REVERT: A 263 ASP cc_start: 0.9296 (m-30) cc_final: 0.8992 (m-30) REVERT: A 301 PHE cc_start: 0.9182 (m-10) cc_final: 0.8692 (m-10) REVERT: A 316 GLU cc_start: 0.9035 (tp30) cc_final: 0.8507 (tp30) REVERT: A 322 MET cc_start: 0.8629 (tpt) cc_final: 0.8187 (mmm) REVERT: A 333 LYS cc_start: 0.9558 (tppt) cc_final: 0.9176 (tppp) REVERT: A 335 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7875 (mm-30) REVERT: A 345 LYS cc_start: 0.9846 (ttpt) cc_final: 0.9524 (ttmt) REVERT: A 349 LEU cc_start: 0.9691 (mt) cc_final: 0.9449 (mt) REVERT: A 375 LYS cc_start: 0.9064 (mmtt) cc_final: 0.8695 (mmtm) REVERT: A 383 SER cc_start: 0.9538 (t) cc_final: 0.9323 (p) REVERT: A 390 GLN cc_start: 0.8888 (mt0) cc_final: 0.8617 (mt0) REVERT: A 393 SER cc_start: 0.9369 (m) cc_final: 0.8914 (t) REVERT: A 402 GLU cc_start: 0.8247 (mp0) cc_final: 0.7856 (mp0) REVERT: A 407 ILE cc_start: 0.9367 (mt) cc_final: 0.9093 (mt) REVERT: A 415 ASN cc_start: 0.9265 (t0) cc_final: 0.8891 (t0) REVERT: A 459 LYS cc_start: 0.8971 (mttp) cc_final: 0.8398 (mtmt) REVERT: A 474 GLN cc_start: 0.9365 (mt0) cc_final: 0.8980 (mm-40) REVERT: A 493 MET cc_start: 0.8966 (tmm) cc_final: 0.8527 (tmm) REVERT: A 501 GLN cc_start: 0.9316 (tt0) cc_final: 0.8823 (tm-30) REVERT: A 515 ASP cc_start: 0.8900 (m-30) cc_final: 0.8635 (m-30) REVERT: A 561 LEU cc_start: 0.9452 (tp) cc_final: 0.9076 (tp) REVERT: A 601 ILE cc_start: 0.9473 (mm) cc_final: 0.9094 (tp) REVERT: A 615 MET cc_start: 0.9139 (mmt) cc_final: 0.8850 (mmm) REVERT: A 636 LYS cc_start: 0.9402 (mmtm) cc_final: 0.9092 (mmmm) REVERT: A 640 MET cc_start: 0.9219 (tpp) cc_final: 0.9012 (tpp) REVERT: A 667 LEU cc_start: 0.9407 (tt) cc_final: 0.9202 (tt) REVERT: A 669 ARG cc_start: 0.9132 (tpp-160) cc_final: 0.8854 (tpp-160) REVERT: B 8 LYS cc_start: 0.9378 (tptt) cc_final: 0.9026 (tppt) REVERT: B 12 LEU cc_start: 0.9592 (mt) cc_final: 0.9355 (mt) REVERT: B 20 LYS cc_start: 0.9679 (tmtt) cc_final: 0.9474 (tptp) REVERT: B 55 LEU cc_start: 0.9796 (mt) cc_final: 0.9565 (mt) REVERT: B 87 LYS cc_start: 0.9334 (tptt) cc_final: 0.9125 (tppt) REVERT: B 119 GLU cc_start: 0.9317 (mp0) cc_final: 0.8999 (mp0) REVERT: B 128 PHE cc_start: 0.9569 (t80) cc_final: 0.9190 (t80) REVERT: B 139 GLU cc_start: 0.9380 (mm-30) cc_final: 0.9131 (mm-30) REVERT: B 149 TYR cc_start: 0.9317 (t80) cc_final: 0.8506 (t80) REVERT: B 167 LEU cc_start: 0.9236 (mt) cc_final: 0.8804 (mt) REVERT: B 173 LEU cc_start: 0.9401 (mt) cc_final: 0.9167 (mt) REVERT: B 181 ASP cc_start: 0.8675 (m-30) cc_final: 0.8314 (m-30) REVERT: B 184 ARG cc_start: 0.9402 (tpp80) cc_final: 0.9117 (tpp80) REVERT: B 191 GLN cc_start: 0.8763 (mt0) cc_final: 0.8238 (mt0) REVERT: B 235 ARG cc_start: 0.9207 (ttm110) cc_final: 0.8387 (mtm-85) REVERT: B 239 GLN cc_start: 0.8857 (tm-30) cc_final: 0.8236 (tm-30) REVERT: B 252 ASN cc_start: 0.9353 (t0) cc_final: 0.9045 (t0) REVERT: B 263 ASP cc_start: 0.9225 (m-30) cc_final: 0.8950 (m-30) REVERT: B 321 GLU cc_start: 0.8801 (tm-30) cc_final: 0.8329 (tm-30) REVERT: B 322 MET cc_start: 0.9241 (mmm) cc_final: 0.8144 (mmm) REVERT: B 335 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8374 (mm-30) REVERT: B 348 MET cc_start: 0.9405 (ptp) cc_final: 0.9022 (ptp) REVERT: B 355 TYR cc_start: 0.8778 (m-10) cc_final: 0.8468 (m-10) REVERT: B 403 ILE cc_start: 0.8845 (tp) cc_final: 0.8634 (tp) REVERT: B 410 ASN cc_start: 0.9024 (m-40) cc_final: 0.8566 (m-40) REVERT: B 423 LYS cc_start: 0.9519 (mttt) cc_final: 0.8992 (mtpt) REVERT: B 426 GLU cc_start: 0.9029 (pm20) cc_final: 0.8755 (pm20) REVERT: B 427 LYS cc_start: 0.9431 (ptpp) cc_final: 0.8857 (ptpp) REVERT: B 447 ASN cc_start: 0.8983 (m-40) cc_final: 0.8578 (m-40) REVERT: B 475 ASN cc_start: 0.9096 (m-40) cc_final: 0.8895 (m110) REVERT: B 550 MET cc_start: 0.8141 (mtp) cc_final: 0.7754 (mtp) REVERT: B 576 LEU cc_start: 0.9368 (mt) cc_final: 0.9153 (mt) REVERT: B 612 TYR cc_start: 0.8910 (m-80) cc_final: 0.8667 (m-80) REVERT: B 634 MET cc_start: 0.9439 (mmm) cc_final: 0.8858 (mpp) REVERT: B 640 MET cc_start: 0.9172 (tpp) cc_final: 0.8599 (tpp) REVERT: B 667 LEU cc_start: 0.9356 (tp) cc_final: 0.9065 (tp) REVERT: C 17 PHE cc_start: 0.9020 (p90) cc_final: 0.8746 (p90) REVERT: C 20 MET cc_start: 0.9521 (tmm) cc_final: 0.9256 (tmm) REVERT: C 101 HIS cc_start: 0.7767 (m90) cc_final: 0.7101 (m90) REVERT: C 110 MET cc_start: 0.5514 (mpp) cc_final: 0.5201 (mpp) REVERT: C 118 ILE cc_start: 0.9216 (pt) cc_final: 0.8640 (pt) REVERT: C 122 PHE cc_start: 0.8082 (m-80) cc_final: 0.7633 (m-80) REVERT: C 173 TYR cc_start: 0.7619 (t80) cc_final: 0.6468 (t80) REVERT: C 177 TYR cc_start: 0.9124 (t80) cc_final: 0.8839 (t80) REVERT: C 185 MET cc_start: 0.6189 (mmm) cc_final: 0.5433 (mpp) REVERT: C 233 ASN cc_start: 0.9401 (m110) cc_final: 0.8902 (m110) REVERT: C 252 LEU cc_start: 0.7505 (mt) cc_final: 0.6934 (mt) REVERT: C 278 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8366 (pm20) REVERT: D 20 MET cc_start: 0.9045 (mtm) cc_final: 0.8695 (mpp) REVERT: D 96 MET cc_start: 0.9102 (mmm) cc_final: 0.8872 (mmt) REVERT: D 148 ASP cc_start: 0.7021 (m-30) cc_final: 0.6726 (m-30) REVERT: D 176 LEU cc_start: 0.9629 (mt) cc_final: 0.9321 (tp) REVERT: D 219 GLU cc_start: 0.9194 (tp30) cc_final: 0.8967 (tp30) REVERT: D 240 LEU cc_start: 0.7653 (mt) cc_final: 0.6969 (mt) REVERT: D 270 ASN cc_start: 0.8655 (m110) cc_final: 0.8399 (m110) outliers start: 1 outliers final: 0 residues processed: 699 average time/residue: 0.1265 time to fit residues: 133.1989 Evaluate side-chains 629 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 629 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 0.9980 chunk 133 optimal weight: 0.5980 chunk 149 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 114 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 100 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 363 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 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 = 0.3588 r_free = 0.3588 target = 0.121364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.087170 restraints weight = 41328.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.090277 restraints weight = 21733.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.092402 restraints weight = 13593.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.093855 restraints weight = 9559.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.094916 restraints weight = 7336.429| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.7159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16386 Z= 0.130 Angle : 0.637 10.115 22134 Z= 0.334 Chirality : 0.044 0.277 2360 Planarity : 0.004 0.058 2818 Dihedral : 9.945 151.704 2242 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.06 % Allowed : 0.41 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.19), residues: 1932 helix: 1.00 (0.15), residues: 1144 sheet: 0.44 (0.47), residues: 100 loop : -0.23 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 243 TYR 0.033 0.001 TYR B 574 PHE 0.026 0.002 PHE C 168 TRP 0.043 0.002 TRP D 124 HIS 0.026 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00288 (16386) covalent geometry : angle 0.63701 (22134) hydrogen bonds : bond 0.03800 ( 871) hydrogen bonds : angle 4.77451 ( 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 711 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 710 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9228 (tptp) cc_final: 0.8904 (tppt) REVERT: A 12 LEU cc_start: 0.9584 (mt) cc_final: 0.9237 (mt) REVERT: A 107 LYS cc_start: 0.9221 (mttm) cc_final: 0.8776 (mtpp) REVERT: A 117 ARG cc_start: 0.9171 (tpp80) cc_final: 0.8965 (tpp80) REVERT: A 147 GLN cc_start: 0.9155 (mt0) cc_final: 0.8177 (mt0) REVERT: A 149 TYR cc_start: 0.9262 (t80) cc_final: 0.8775 (t80) REVERT: A 158 ASN cc_start: 0.9303 (m-40) cc_final: 0.9053 (m-40) REVERT: A 161 ARG cc_start: 0.8338 (ttm110) cc_final: 0.7762 (mmm-85) REVERT: A 164 ARG cc_start: 0.8887 (ptm-80) cc_final: 0.7692 (ptm-80) REVERT: A 172 LEU cc_start: 0.9521 (mp) cc_final: 0.9092 (mp) REVERT: A 181 ASP cc_start: 0.8896 (m-30) cc_final: 0.8542 (m-30) REVERT: A 195 LEU cc_start: 0.9688 (mt) cc_final: 0.9456 (mt) REVERT: A 214 LYS cc_start: 0.8791 (tppt) cc_final: 0.8354 (mmtt) REVERT: A 223 VAL cc_start: 0.9750 (m) cc_final: 0.9116 (p) REVERT: A 227 MET cc_start: 0.9289 (mtm) cc_final: 0.8744 (mtm) REVERT: A 232 ASN cc_start: 0.8910 (m110) cc_final: 0.8706 (m110) REVERT: A 255 HIS cc_start: 0.8494 (t-90) cc_final: 0.7975 (t-90) REVERT: A 257 ASP cc_start: 0.9052 (m-30) cc_final: 0.8738 (m-30) REVERT: A 262 LEU cc_start: 0.9872 (mt) cc_final: 0.9588 (mt) REVERT: A 263 ASP cc_start: 0.9288 (m-30) cc_final: 0.8955 (m-30) REVERT: A 276 LYS cc_start: 0.9313 (mptt) cc_final: 0.8990 (mmmt) REVERT: A 301 PHE cc_start: 0.9114 (m-10) cc_final: 0.8612 (m-10) REVERT: A 316 GLU cc_start: 0.9067 (tp30) cc_final: 0.8537 (tp30) REVERT: A 322 MET cc_start: 0.8712 (tpt) cc_final: 0.8271 (mmm) REVERT: A 333 LYS cc_start: 0.9554 (tppt) cc_final: 0.9198 (tppp) REVERT: A 335 GLU cc_start: 0.8391 (mm-30) cc_final: 0.7849 (mm-30) REVERT: A 345 LYS cc_start: 0.9840 (ttpt) cc_final: 0.9535 (ttmt) REVERT: A 349 LEU cc_start: 0.9697 (mt) cc_final: 0.9442 (mt) REVERT: A 375 LYS cc_start: 0.9029 (mmtt) cc_final: 0.8677 (mmtm) REVERT: A 390 GLN cc_start: 0.8934 (mt0) cc_final: 0.8646 (mt0) REVERT: A 393 SER cc_start: 0.9342 (m) cc_final: 0.8851 (t) REVERT: A 402 GLU cc_start: 0.8264 (mp0) cc_final: 0.7851 (mp0) REVERT: A 407 ILE cc_start: 0.9325 (mt) cc_final: 0.9053 (mt) REVERT: A 415 ASN cc_start: 0.9253 (t0) cc_final: 0.8381 (t0) REVERT: A 418 ASN cc_start: 0.9057 (m110) cc_final: 0.8546 (m-40) REVERT: A 459 LYS cc_start: 0.8959 (mttp) cc_final: 0.8292 (mtmm) REVERT: A 466 MET cc_start: 0.8837 (ptt) cc_final: 0.8575 (ptt) REVERT: A 474 GLN cc_start: 0.9305 (mt0) cc_final: 0.8971 (mm-40) REVERT: A 493 MET cc_start: 0.8902 (tmm) cc_final: 0.8642 (tmm) REVERT: A 501 GLN cc_start: 0.9334 (tt0) cc_final: 0.8854 (tm-30) REVERT: A 515 ASP cc_start: 0.8870 (m-30) cc_final: 0.8586 (m-30) REVERT: A 561 LEU cc_start: 0.9413 (tp) cc_final: 0.9032 (tp) REVERT: A 601 ILE cc_start: 0.9487 (mm) cc_final: 0.9091 (tp) REVERT: A 615 MET cc_start: 0.9165 (mmt) cc_final: 0.8875 (mmm) REVERT: A 636 LYS cc_start: 0.9404 (mmtm) cc_final: 0.9108 (mmmm) REVERT: A 640 MET cc_start: 0.9213 (tpp) cc_final: 0.8725 (tpp) REVERT: A 645 GLN cc_start: 0.9212 (tp40) cc_final: 0.7980 (tp-100) REVERT: A 648 ILE cc_start: 0.9550 (mm) cc_final: 0.9162 (mm) REVERT: A 650 GLN cc_start: 0.8598 (mt0) cc_final: 0.7670 (mt0) REVERT: A 667 LEU cc_start: 0.9411 (tt) cc_final: 0.9198 (tt) REVERT: A 669 ARG cc_start: 0.9100 (tpp-160) cc_final: 0.8828 (tpp-160) REVERT: A 680 LYS cc_start: 0.9362 (mttt) cc_final: 0.8824 (mttt) REVERT: B 8 LYS cc_start: 0.9384 (tptt) cc_final: 0.9041 (tppt) REVERT: B 12 LEU cc_start: 0.9591 (mt) cc_final: 0.9343 (mt) REVERT: B 20 LYS cc_start: 0.9669 (tmtt) cc_final: 0.9437 (tptp) REVERT: B 21 ASP cc_start: 0.8598 (t70) cc_final: 0.8312 (t0) REVERT: B 55 LEU cc_start: 0.9792 (mt) cc_final: 0.9572 (mt) REVERT: B 87 LYS cc_start: 0.9299 (tptt) cc_final: 0.8902 (tttt) REVERT: B 98 PHE cc_start: 0.9312 (t80) cc_final: 0.8972 (t80) REVERT: B 119 GLU cc_start: 0.9243 (mp0) cc_final: 0.8937 (mp0) REVERT: B 128 PHE cc_start: 0.9609 (t80) cc_final: 0.9257 (t80) REVERT: B 139 GLU cc_start: 0.9348 (mm-30) cc_final: 0.9135 (mm-30) REVERT: B 149 TYR cc_start: 0.9235 (t80) cc_final: 0.8604 (t80) REVERT: B 167 LEU cc_start: 0.9240 (mt) cc_final: 0.8840 (mt) REVERT: B 173 LEU cc_start: 0.9432 (mt) cc_final: 0.9199 (mt) REVERT: B 181 ASP cc_start: 0.8674 (m-30) cc_final: 0.8279 (m-30) REVERT: B 184 ARG cc_start: 0.9371 (tpp80) cc_final: 0.9077 (tpp80) REVERT: B 191 GLN cc_start: 0.8741 (mt0) cc_final: 0.8273 (mt0) REVERT: B 211 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8076 (mm-30) REVERT: B 228 LYS cc_start: 0.9468 (mmmm) cc_final: 0.9143 (mmtt) REVERT: B 235 ARG cc_start: 0.9175 (ttm110) cc_final: 0.8727 (ttp-110) REVERT: B 236 TYR cc_start: 0.9266 (t80) cc_final: 0.9063 (t80) REVERT: B 239 GLN cc_start: 0.8829 (tm-30) cc_final: 0.8211 (tm-30) REVERT: B 252 ASN cc_start: 0.9326 (t0) cc_final: 0.9048 (t0) REVERT: B 263 ASP cc_start: 0.9223 (m-30) cc_final: 0.8747 (m-30) REVERT: B 321 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8393 (tm-30) REVERT: B 322 MET cc_start: 0.9230 (mmm) cc_final: 0.8208 (mmm) REVERT: B 335 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8304 (mm-30) REVERT: B 355 TYR cc_start: 0.8806 (m-10) cc_final: 0.8468 (m-10) REVERT: B 374 SER cc_start: 0.9421 (t) cc_final: 0.8857 (p) REVERT: B 403 ILE cc_start: 0.8740 (tp) cc_final: 0.8474 (tp) REVERT: B 410 ASN cc_start: 0.8987 (m-40) cc_final: 0.8465 (m-40) REVERT: B 423 LYS cc_start: 0.9502 (mttt) cc_final: 0.9274 (mtpp) REVERT: B 426 GLU cc_start: 0.9044 (pm20) cc_final: 0.8570 (pm20) REVERT: B 427 LYS cc_start: 0.9392 (ptpp) cc_final: 0.8730 (ptpp) REVERT: B 440 SER cc_start: 0.9417 (p) cc_final: 0.9202 (p) REVERT: B 447 ASN cc_start: 0.8992 (m-40) cc_final: 0.8451 (m-40) REVERT: B 477 ILE cc_start: 0.9391 (mp) cc_final: 0.8864 (tt) REVERT: B 550 MET cc_start: 0.8143 (mtp) cc_final: 0.7631 (mtm) REVERT: B 576 LEU cc_start: 0.9391 (mt) cc_final: 0.9160 (mt) REVERT: B 612 TYR cc_start: 0.8845 (m-80) cc_final: 0.8517 (m-80) REVERT: B 634 MET cc_start: 0.9422 (mmm) cc_final: 0.8871 (mpp) REVERT: B 640 MET cc_start: 0.9203 (tpp) cc_final: 0.8665 (tpp) REVERT: B 671 ASP cc_start: 0.8913 (m-30) cc_final: 0.8708 (m-30) REVERT: C 17 PHE cc_start: 0.9041 (p90) cc_final: 0.8736 (p90) REVERT: C 20 MET cc_start: 0.9494 (tmm) cc_final: 0.9247 (tmm) REVERT: C 37 LEU cc_start: 0.3333 (tp) cc_final: 0.3131 (tp) REVERT: C 93 MET cc_start: 0.8289 (tmm) cc_final: 0.7948 (tmm) REVERT: C 101 HIS cc_start: 0.7522 (m90) cc_final: 0.6812 (m90) REVERT: C 109 PHE cc_start: 0.7384 (m-80) cc_final: 0.6941 (m-10) REVERT: C 110 MET cc_start: 0.5429 (mpp) cc_final: 0.5117 (mpp) REVERT: C 118 ILE cc_start: 0.9168 (pt) cc_final: 0.8686 (pt) REVERT: C 122 PHE cc_start: 0.8040 (m-80) cc_final: 0.7609 (m-80) REVERT: C 162 TYR cc_start: 0.9246 (m-10) cc_final: 0.8172 (m-10) REVERT: C 177 TYR cc_start: 0.9100 (t80) cc_final: 0.8828 (t80) REVERT: C 179 TYR cc_start: 0.8207 (t80) cc_final: 0.7846 (t80) REVERT: C 185 MET cc_start: 0.6256 (mmm) cc_final: 0.5011 (mpp) REVERT: C 231 LEU cc_start: 0.9067 (mt) cc_final: 0.8649 (pp) REVERT: C 233 ASN cc_start: 0.9401 (m110) cc_final: 0.8924 (m110) REVERT: C 278 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8425 (pm20) REVERT: D 20 MET cc_start: 0.9044 (mtm) cc_final: 0.8689 (mpp) REVERT: D 148 ASP cc_start: 0.7102 (m-30) cc_final: 0.6817 (m-30) REVERT: D 219 GLU cc_start: 0.9205 (tp30) cc_final: 0.8969 (tp30) REVERT: D 270 ASN cc_start: 0.8724 (m110) cc_final: 0.8483 (m110) outliers start: 1 outliers final: 0 residues processed: 711 average time/residue: 0.1249 time to fit residues: 133.3400 Evaluate side-chains 628 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 628 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 189 optimal weight: 5.9990 chunk 181 optimal weight: 10.0000 chunk 165 optimal weight: 0.0670 chunk 16 optimal weight: 5.9990 chunk 54 optimal weight: 5.9990 chunk 132 optimal weight: 0.4980 chunk 50 optimal weight: 5.9990 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** 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 363 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.123866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.089785 restraints weight = 41659.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.092989 restraints weight = 21850.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.095205 restraints weight = 13868.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.096604 restraints weight = 9820.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.097697 restraints weight = 7617.537| |-----------------------------------------------------------------------------| r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.7339 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 : 0.655 9.981 22134 Z= 0.346 Chirality : 0.044 0.270 2360 Planarity : 0.004 0.057 2818 Dihedral : 9.794 147.503 2242 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 0.71 (0.19), residues: 1932 helix: 0.98 (0.15), residues: 1145 sheet: 0.53 (0.48), residues: 100 loop : -0.25 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 243 TYR 0.033 0.002 TYR D 142 PHE 0.028 0.002 PHE B 129 TRP 0.046 0.002 TRP D 124 HIS 0.020 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00314 (16386) covalent geometry : angle 0.65520 (22134) hydrogen bonds : bond 0.03883 ( 871) hydrogen bonds : angle 4.88458 ( 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 728 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 728 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9243 (tptp) cc_final: 0.8916 (tppt) REVERT: A 12 LEU cc_start: 0.9549 (mt) cc_final: 0.9203 (mt) REVERT: A 107 LYS cc_start: 0.9223 (mttm) cc_final: 0.8779 (mtpp) REVERT: A 110 ASP cc_start: 0.9445 (p0) cc_final: 0.9157 (p0) REVERT: A 147 GLN cc_start: 0.9112 (mt0) cc_final: 0.8407 (mt0) REVERT: A 149 TYR cc_start: 0.9124 (t80) cc_final: 0.8698 (t80) REVERT: A 158 ASN cc_start: 0.9289 (m-40) cc_final: 0.9041 (m-40) REVERT: A 161 ARG cc_start: 0.8240 (ttm110) cc_final: 0.7739 (mmm-85) REVERT: A 164 ARG cc_start: 0.8937 (ptm-80) cc_final: 0.7716 (ptm-80) REVERT: A 181 ASP cc_start: 0.8851 (m-30) cc_final: 0.8548 (m-30) REVERT: A 195 LEU cc_start: 0.9670 (mt) cc_final: 0.9437 (mt) REVERT: A 214 LYS cc_start: 0.8739 (tppt) cc_final: 0.8302 (mmtt) REVERT: A 223 VAL cc_start: 0.9767 (m) cc_final: 0.9224 (p) REVERT: A 227 MET cc_start: 0.9226 (mtm) cc_final: 0.8931 (mtm) REVERT: A 232 ASN cc_start: 0.8913 (m110) cc_final: 0.8687 (m110) REVERT: A 238 ASP cc_start: 0.8074 (p0) cc_final: 0.7762 (p0) REVERT: A 257 ASP cc_start: 0.9019 (m-30) cc_final: 0.8734 (m-30) REVERT: A 262 LEU cc_start: 0.9865 (mt) cc_final: 0.9593 (mt) REVERT: A 263 ASP cc_start: 0.9276 (m-30) cc_final: 0.8997 (m-30) REVERT: A 276 LYS cc_start: 0.9293 (mptt) cc_final: 0.8940 (mmmt) REVERT: A 284 ILE cc_start: 0.9133 (mm) cc_final: 0.8848 (mm) REVERT: A 295 ASP cc_start: 0.9360 (t0) cc_final: 0.9105 (t0) REVERT: A 301 PHE cc_start: 0.9101 (m-10) cc_final: 0.8617 (m-10) REVERT: A 316 GLU cc_start: 0.9039 (tp30) cc_final: 0.8545 (tp30) REVERT: A 322 MET cc_start: 0.8712 (tpt) cc_final: 0.8281 (mmm) REVERT: A 324 ASP cc_start: 0.9331 (m-30) cc_final: 0.9085 (m-30) REVERT: A 333 LYS cc_start: 0.9549 (tppt) cc_final: 0.9201 (tppp) REVERT: A 335 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7843 (mm-30) REVERT: A 345 LYS cc_start: 0.9834 (ttpt) cc_final: 0.9427 (ttmt) REVERT: A 349 LEU cc_start: 0.9696 (mt) cc_final: 0.9455 (mt) REVERT: A 365 ASN cc_start: 0.9368 (m-40) cc_final: 0.8862 (m110) REVERT: A 375 LYS cc_start: 0.8999 (mmtt) cc_final: 0.8794 (mmtp) REVERT: A 390 GLN cc_start: 0.8874 (mt0) cc_final: 0.8599 (mt0) REVERT: A 393 SER cc_start: 0.9318 (m) cc_final: 0.8465 (t) REVERT: A 396 ASP cc_start: 0.8678 (p0) cc_final: 0.8345 (p0) REVERT: A 401 ASP cc_start: 0.9375 (m-30) cc_final: 0.8609 (m-30) REVERT: A 402 GLU cc_start: 0.8284 (mp0) cc_final: 0.7782 (mp0) REVERT: A 415 ASN cc_start: 0.9264 (t0) cc_final: 0.8652 (t0) REVERT: A 418 ASN cc_start: 0.8971 (m110) cc_final: 0.8642 (m-40) REVERT: A 420 MET cc_start: 0.9260 (mmm) cc_final: 0.8887 (mtp) REVERT: A 474 GLN cc_start: 0.9304 (mt0) cc_final: 0.8968 (mm-40) REVERT: A 491 PHE cc_start: 0.9647 (t80) cc_final: 0.9442 (t80) REVERT: A 493 MET cc_start: 0.8883 (tmm) cc_final: 0.8609 (tmm) REVERT: A 501 GLN cc_start: 0.9322 (tt0) cc_final: 0.8845 (tm-30) REVERT: A 515 ASP cc_start: 0.8893 (m-30) cc_final: 0.8594 (m-30) REVERT: A 529 ASP cc_start: 0.8866 (m-30) cc_final: 0.8664 (m-30) REVERT: A 561 LEU cc_start: 0.9397 (tp) cc_final: 0.9051 (tp) REVERT: A 590 SER cc_start: 0.9522 (t) cc_final: 0.9121 (p) REVERT: A 601 ILE cc_start: 0.9473 (mm) cc_final: 0.8981 (tp) REVERT: A 615 MET cc_start: 0.9169 (mmt) cc_final: 0.8842 (mmm) REVERT: A 628 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8398 (mm-30) REVERT: A 633 ASP cc_start: 0.9034 (t0) cc_final: 0.8207 (t0) REVERT: A 636 LYS cc_start: 0.9367 (mmtm) cc_final: 0.8890 (mmtt) REVERT: A 639 ASP cc_start: 0.9243 (t70) cc_final: 0.8495 (t70) REVERT: A 640 MET cc_start: 0.9213 (tpp) cc_final: 0.8752 (tpp) REVERT: A 645 GLN cc_start: 0.9130 (tp40) cc_final: 0.7778 (tp-100) REVERT: A 648 ILE cc_start: 0.9537 (mm) cc_final: 0.9123 (mm) REVERT: A 667 LEU cc_start: 0.9428 (tt) cc_final: 0.9213 (tt) REVERT: A 669 ARG cc_start: 0.9029 (tpp-160) cc_final: 0.8761 (tpp-160) REVERT: A 680 LYS cc_start: 0.9371 (mttt) cc_final: 0.8790 (mttt) REVERT: B 8 LYS cc_start: 0.9381 (tptt) cc_final: 0.9038 (tppt) REVERT: B 12 LEU cc_start: 0.9586 (mt) cc_final: 0.9343 (mt) REVERT: B 20 LYS cc_start: 0.9678 (tmtt) cc_final: 0.9474 (tptp) REVERT: B 55 LEU cc_start: 0.9788 (mt) cc_final: 0.9574 (mt) REVERT: B 87 LYS cc_start: 0.9267 (tptt) cc_final: 0.8937 (tttt) REVERT: B 88 LYS cc_start: 0.8999 (tttp) cc_final: 0.8626 (tptt) REVERT: B 98 PHE cc_start: 0.9334 (t80) cc_final: 0.8962 (t80) REVERT: B 107 LYS cc_start: 0.9248 (mmmt) cc_final: 0.8872 (mmmt) REVERT: B 111 LYS cc_start: 0.9643 (mptt) cc_final: 0.9384 (mmtt) REVERT: B 119 GLU cc_start: 0.9218 (mp0) cc_final: 0.8958 (mp0) REVERT: B 149 TYR cc_start: 0.9226 (t80) cc_final: 0.8594 (t80) REVERT: B 167 LEU cc_start: 0.9246 (mt) cc_final: 0.8863 (mt) REVERT: B 181 ASP cc_start: 0.8576 (m-30) cc_final: 0.8119 (m-30) REVERT: B 211 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8288 (mm-30) REVERT: B 214 LYS cc_start: 0.8492 (mmtp) cc_final: 0.8223 (mmtt) REVERT: B 235 ARG cc_start: 0.9178 (ttm110) cc_final: 0.8724 (ttp-110) REVERT: B 239 GLN cc_start: 0.8829 (tm-30) cc_final: 0.8261 (tm-30) REVERT: B 252 ASN cc_start: 0.9274 (t0) cc_final: 0.8930 (t0) REVERT: B 263 ASP cc_start: 0.9203 (m-30) cc_final: 0.8926 (m-30) REVERT: B 286 ASP cc_start: 0.9104 (m-30) cc_final: 0.8836 (m-30) REVERT: B 321 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8404 (tm-30) REVERT: B 322 MET cc_start: 0.9234 (mmm) cc_final: 0.8140 (mmm) REVERT: B 335 GLU cc_start: 0.8522 (mm-30) cc_final: 0.8195 (mm-30) REVERT: B 355 TYR cc_start: 0.8775 (m-10) cc_final: 0.8454 (m-10) REVERT: B 362 ASP cc_start: 0.8617 (m-30) cc_final: 0.8391 (m-30) REVERT: B 374 SER cc_start: 0.9429 (t) cc_final: 0.8887 (p) REVERT: B 426 GLU cc_start: 0.8992 (pm20) cc_final: 0.8675 (pm20) REVERT: B 427 LYS cc_start: 0.9338 (ptpp) cc_final: 0.8862 (ptpp) REVERT: B 576 LEU cc_start: 0.9366 (mt) cc_final: 0.9157 (mt) REVERT: B 612 TYR cc_start: 0.8852 (m-80) cc_final: 0.8547 (m-80) REVERT: B 634 MET cc_start: 0.9461 (mmm) cc_final: 0.8903 (mpp) REVERT: B 640 MET cc_start: 0.9171 (tpp) cc_final: 0.8538 (tpp) REVERT: B 671 ASP cc_start: 0.8938 (m-30) cc_final: 0.8654 (m-30) REVERT: C 17 PHE cc_start: 0.9003 (p90) cc_final: 0.8668 (p90) REVERT: C 20 MET cc_start: 0.9515 (tmm) cc_final: 0.9271 (tmm) REVERT: C 93 MET cc_start: 0.8303 (tmm) cc_final: 0.7960 (tmm) REVERT: C 101 HIS cc_start: 0.7641 (m90) cc_final: 0.6954 (m90) REVERT: C 109 PHE cc_start: 0.7588 (m-80) cc_final: 0.7293 (m-10) REVERT: C 110 MET cc_start: 0.5460 (mpp) cc_final: 0.5142 (mpp) REVERT: C 118 ILE cc_start: 0.9108 (pt) cc_final: 0.8661 (pt) REVERT: C 122 PHE cc_start: 0.8135 (m-80) cc_final: 0.7681 (m-80) REVERT: C 162 TYR cc_start: 0.9245 (m-10) cc_final: 0.8642 (m-10) REVERT: C 169 TYR cc_start: 0.9271 (m-80) cc_final: 0.9008 (m-80) REVERT: C 173 TYR cc_start: 0.7874 (t80) cc_final: 0.7218 (t80) REVERT: C 177 TYR cc_start: 0.9134 (t80) cc_final: 0.8786 (t80) REVERT: C 179 TYR cc_start: 0.8204 (t80) cc_final: 0.7843 (t80) REVERT: C 185 MET cc_start: 0.6197 (mmm) cc_final: 0.5020 (mpp) REVERT: C 233 ASN cc_start: 0.9310 (m110) cc_final: 0.8974 (m110) REVERT: C 237 GLU cc_start: 0.9611 (mm-30) cc_final: 0.9320 (pp20) REVERT: C 269 MET cc_start: 0.9291 (pmm) cc_final: 0.9080 (pmm) REVERT: C 278 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8401 (pm20) REVERT: D 20 MET cc_start: 0.9010 (mtm) cc_final: 0.8649 (mpp) REVERT: D 109 PHE cc_start: 0.8471 (m-80) cc_final: 0.8068 (m-80) REVERT: D 148 ASP cc_start: 0.7252 (m-30) cc_final: 0.6978 (m-30) REVERT: D 176 LEU cc_start: 0.9606 (mt) cc_final: 0.9318 (tp) REVERT: D 191 ILE cc_start: 0.9579 (mm) cc_final: 0.9378 (mm) REVERT: D 219 GLU cc_start: 0.9175 (tp30) cc_final: 0.8918 (tp30) REVERT: D 224 LEU cc_start: 0.8273 (mt) cc_final: 0.8008 (mt) REVERT: D 270 ASN cc_start: 0.8735 (m110) cc_final: 0.8481 (m110) REVERT: D 313 GLU cc_start: 0.8228 (mp0) cc_final: 0.7686 (mp0) outliers start: 0 outliers final: 0 residues processed: 728 average time/residue: 0.1205 time to fit residues: 132.3243 Evaluate side-chains 628 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 628 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 148 optimal weight: 20.0000 chunk 125 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** 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 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 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 = 0.3632 r_free = 0.3632 target = 0.125135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.091176 restraints weight = 41337.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.094366 restraints weight = 21633.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.096501 restraints weight = 13554.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.097830 restraints weight = 9582.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.098923 restraints weight = 7451.058| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3199 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.7498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16386 Z= 0.149 Angle : 0.657 9.272 22134 Z= 0.347 Chirality : 0.044 0.258 2360 Planarity : 0.004 0.059 2818 Dihedral : 9.718 144.875 2242 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.19), residues: 1932 helix: 0.91 (0.15), residues: 1148 sheet: 0.50 (0.48), residues: 100 loop : -0.27 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 686 TYR 0.029 0.001 TYR D 142 PHE 0.046 0.002 PHE B 129 TRP 0.044 0.002 TRP D 124 HIS 0.023 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00334 (16386) covalent geometry : angle 0.65652 (22134) hydrogen bonds : bond 0.03940 ( 871) hydrogen bonds : angle 4.95519 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3551.44 seconds wall clock time: 62 minutes 15.49 seconds (3735.49 seconds total)