Starting phenix.real_space_refine on Sat Jun 14 06:44:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bze_45065/06_2025/9bze_45065_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bze_45065/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9bze_45065/06_2025/9bze_45065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bze_45065/06_2025/9bze_45065.map" model { file = "/net/cci-nas-00/data/ceres_data/9bze_45065/06_2025/9bze_45065_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bze_45065/06_2025/9bze_45065_neut.cif" } resolution = 4.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 8.78, per 1000 atoms: 0.55 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: 3.65 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.69 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: 4.87 Time building geometry restraints manager: 4.37 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: 0.910 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: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.230 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.580 ------------------------------------------------------------------------------- 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 : 8.44 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE C 227 TYR 0.021 0.002 TYR D 179 ARG 0.004 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.15421 ( 871) hydrogen bonds : angle 6.51768 ( 2571) covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74007 (22134) *********************** 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 : 1.628 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: A 41 ILE cc_start: 0.8698 (mm) cc_final: 0.8401 (mm) REVERT: A 51 LEU cc_start: 0.8139 (tp) cc_final: 0.7885 (tp) REVERT: A 81 PHE cc_start: 0.8260 (m-80) cc_final: 0.7979 (m-10) REVERT: A 123 SER cc_start: 0.9320 (m) cc_final: 0.9092 (m) REVERT: A 172 LEU cc_start: 0.9490 (mp) cc_final: 0.9140 (mp) REVERT: A 181 ASP cc_start: 0.8241 (m-30) cc_final: 0.7570 (m-30) REVERT: A 191 GLN cc_start: 0.8014 (mm-40) cc_final: 0.7703 (mm-40) REVERT: A 211 GLU cc_start: 0.6931 (mt-10) cc_final: 0.6385 (tp30) REVERT: A 258 ILE cc_start: 0.9219 (tp) cc_final: 0.8834 (tp) REVERT: A 265 LYS cc_start: 0.9075 (mmtt) cc_final: 0.8771 (mmmt) REVERT: A 267 ILE cc_start: 0.8833 (mp) cc_final: 0.8346 (pt) REVERT: A 315 ASP cc_start: 0.8472 (p0) cc_final: 0.7926 (p0) REVERT: A 345 LYS cc_start: 0.8888 (tttt) cc_final: 0.8369 (ttmt) REVERT: A 362 ASP cc_start: 0.6076 (m-30) cc_final: 0.5755 (m-30) REVERT: A 365 ASN cc_start: 0.8288 (m-40) cc_final: 0.8042 (m-40) REVERT: A 377 LYS cc_start: 0.8818 (mttt) cc_final: 0.8472 (mttp) REVERT: A 378 PHE cc_start: 0.8896 (p90) cc_final: 0.8650 (p90) REVERT: A 387 GLN cc_start: 0.7497 (mt0) cc_final: 0.7162 (mt0) REVERT: A 408 SER cc_start: 0.8599 (p) cc_final: 0.8393 (p) REVERT: A 420 MET cc_start: 0.7468 (mmm) cc_final: 0.7262 (mmm) REVERT: A 435 SER cc_start: 0.9408 (p) cc_final: 0.8804 (p) REVERT: A 447 ASN cc_start: 0.7313 (m-40) cc_final: 0.6835 (m-40) REVERT: A 501 GLN cc_start: 0.8285 (tt0) cc_final: 0.8063 (tt0) REVERT: A 576 LEU cc_start: 0.8683 (mt) cc_final: 0.8127 (mt) REVERT: A 583 SER cc_start: 0.8180 (m) cc_final: 0.7871 (t) REVERT: A 590 SER cc_start: 0.9100 (p) cc_final: 0.8344 (p) REVERT: A 595 MET cc_start: 0.8050 (mmp) cc_final: 0.7620 (mmp) REVERT: A 655 THR cc_start: 0.9477 (m) cc_final: 0.9168 (t) REVERT: A 670 ILE cc_start: 0.8913 (mt) cc_final: 0.8508 (mt) REVERT: A 687 THR cc_start: 0.7729 (m) cc_final: 0.7477 (m) REVERT: B 11 GLN cc_start: 0.7654 (mt0) cc_final: 0.6756 (mt0) REVERT: B 41 ILE cc_start: 0.8792 (mm) cc_final: 0.8340 (mm) REVERT: B 99 LYS cc_start: 0.9064 (mmtt) cc_final: 0.8419 (tppt) REVERT: B 127 LEU cc_start: 0.8999 (mt) cc_final: 0.8789 (mt) REVERT: B 147 GLN cc_start: 0.8314 (mt0) cc_final: 0.7999 (mt0) REVERT: B 172 LEU cc_start: 0.9342 (mp) cc_final: 0.8982 (mp) REVERT: B 175 VAL cc_start: 0.9207 (t) cc_final: 0.8995 (t) REVERT: B 177 ASP cc_start: 0.8671 (t0) cc_final: 0.8090 (t70) REVERT: B 181 ASP cc_start: 0.8122 (m-30) cc_final: 0.7650 (m-30) REVERT: B 192 LEU cc_start: 0.9272 (mt) cc_final: 0.8944 (mt) REVERT: B 204 SER cc_start: 0.9054 (m) cc_final: 0.8225 (t) REVERT: B 226 VAL cc_start: 0.9079 (t) cc_final: 0.8717 (t) REVERT: B 256 ARG cc_start: 0.7885 (ttp80) cc_final: 0.7217 (tpt90) REVERT: B 288 PHE cc_start: 0.7689 (t80) cc_final: 0.7230 (t80) REVERT: B 315 ASP cc_start: 0.8777 (p0) cc_final: 0.8407 (p0) REVERT: B 322 MET cc_start: 0.7584 (mmm) cc_final: 0.7155 (mmm) REVERT: B 345 LYS cc_start: 0.8290 (tttt) cc_final: 0.7954 (ttpt) REVERT: B 346 LEU cc_start: 0.8863 (mt) cc_final: 0.8463 (mt) REVERT: B 359 MET cc_start: 0.8061 (ttt) cc_final: 0.7714 (ttt) REVERT: B 374 SER cc_start: 0.8716 (t) cc_final: 0.8474 (p) REVERT: B 381 LEU cc_start: 0.8730 (tp) cc_final: 0.8505 (tp) REVERT: B 387 GLN cc_start: 0.7301 (mt0) cc_final: 0.6851 (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: 0.7805 (m-40) REVERT: B 425 ILE cc_start: 0.8953 (mt) cc_final: 0.8668 (mt) REVERT: B 474 GLN cc_start: 0.7992 (mt0) cc_final: 0.7700 (mt0) REVERT: B 494 MET cc_start: 0.7983 (mtp) cc_final: 0.7783 (mtp) REVERT: B 500 ILE cc_start: 0.9441 (mt) cc_final: 0.9001 (mt) REVERT: B 550 MET cc_start: 0.7876 (mtm) cc_final: 0.6902 (mtm) REVERT: B 587 VAL cc_start: 0.8690 (t) cc_final: 0.8465 (t) REVERT: B 597 ILE cc_start: 0.9427 (pt) cc_final: 0.9223 (pt) REVERT: B 644 ILE cc_start: 0.8904 (mt) cc_final: 0.8660 (mt) REVERT: B 655 THR cc_start: 0.9501 (m) cc_final: 0.9291 (t) REVERT: C 27 LYS cc_start: 0.8055 (ptmm) cc_final: 0.7852 (tmtt) REVERT: C 37 LEU cc_start: 0.5102 (mt) cc_final: 0.4514 (tp) REVERT: C 101 HIS cc_start: 0.5573 (m170) cc_final: 0.5352 (m90) REVERT: C 114 PRO cc_start: 0.5223 (Cg_endo) cc_final: 0.4821 (Cg_exo) REVERT: C 153 LEU cc_start: 0.6366 (tp) cc_final: 0.6043 (tp) REVERT: C 163 LEU cc_start: 0.6465 (tt) cc_final: 0.6161 (tt) REVERT: C 178 PHE cc_start: 0.4924 (m-80) cc_final: 0.4682 (m-80) REVERT: D 47 LEU cc_start: 0.5071 (mt) cc_final: 0.3959 (mp) REVERT: D 96 MET cc_start: 0.5835 (mmm) cc_final: 0.5506 (mmm) REVERT: D 141 LEU cc_start: 0.6273 (mt) cc_final: 0.5937 (mp) REVERT: D 186 GLN cc_start: 0.4627 (mm-40) cc_final: 0.3832 (mm-40) outliers start: 23 outliers final: 6 residues processed: 1020 average time/residue: 0.3123 time to fit residues: 449.7440 Evaluate side-chains 701 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 695 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 8.9990 chunk 145 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 77 optimal weight: 3.9990 chunk 150 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 112 optimal weight: 0.6980 chunk 174 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN B 43 GLN B 61 ASN B 102 ASN B 191 GLN 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 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 HIS ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS ** C 85 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 D 80 HIS D 186 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.126886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.091649 restraints weight = 39160.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.094762 restraints weight = 20234.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.097064 restraints weight = 13069.850| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3088 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3088 r_free = 0.3088 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16386 Z= 0.189 Angle : 0.626 7.817 22134 Z= 0.334 Chirality : 0.043 0.253 2360 Planarity : 0.004 0.036 2818 Dihedral : 11.455 178.510 2242 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.12 % Allowed : 2.80 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.19), residues: 1932 helix: 1.36 (0.15), residues: 1109 sheet: 0.20 (0.42), residues: 126 loop : 0.47 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D 124 HIS 0.010 0.001 HIS A 255 PHE 0.030 0.003 PHE C 168 TYR 0.022 0.002 TYR D 174 ARG 0.007 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.04780 ( 871) hydrogen bonds : angle 5.07981 ( 2571) covalent geometry : bond 0.00406 (16386) covalent geometry : angle 0.62609 (22134) *********************** 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 804 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 802 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9252 (tptp) cc_final: 0.8886 (tppt) REVERT: A 41 ILE cc_start: 0.9368 (mm) cc_final: 0.9078 (mm) REVERT: A 52 LYS cc_start: 0.9679 (tppt) cc_final: 0.9359 (tppp) REVERT: A 95 MET cc_start: 0.9115 (mmm) cc_final: 0.8670 (mmm) REVERT: A 118 TYR cc_start: 0.9377 (t80) cc_final: 0.9108 (t80) REVERT: A 143 LEU cc_start: 0.9309 (tp) cc_final: 0.9098 (tp) REVERT: A 147 GLN cc_start: 0.9451 (mt0) cc_final: 0.8534 (mt0) REVERT: A 158 ASN cc_start: 0.9396 (m110) cc_final: 0.9006 (m-40) REVERT: A 162 LYS cc_start: 0.8812 (ttmm) cc_final: 0.8523 (ttmm) REVERT: A 181 ASP cc_start: 0.8899 (m-30) cc_final: 0.8673 (m-30) REVERT: A 191 GLN cc_start: 0.9118 (mm-40) cc_final: 0.8905 (mm-40) REVERT: A 195 LEU cc_start: 0.9603 (mt) cc_final: 0.9315 (mt) REVERT: A 227 MET cc_start: 0.9337 (mtm) cc_final: 0.9046 (mtm) REVERT: A 238 ASP cc_start: 0.8560 (p0) cc_final: 0.8072 (p0) REVERT: A 255 HIS cc_start: 0.8979 (t-90) cc_final: 0.7968 (t-90) REVERT: A 257 ASP cc_start: 0.9304 (m-30) cc_final: 0.8852 (m-30) REVERT: A 262 LEU cc_start: 0.9830 (mt) cc_final: 0.9584 (mt) REVERT: A 270 ASP cc_start: 0.8887 (t0) cc_final: 0.8608 (t0) REVERT: A 291 LEU cc_start: 0.9687 (mt) cc_final: 0.9472 (mt) REVERT: A 322 MET cc_start: 0.8051 (mmp) cc_final: 0.7610 (mmm) REVERT: A 335 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7627 (mm-30) REVERT: A 344 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8917 (mt-10) REVERT: A 349 LEU cc_start: 0.9641 (mt) cc_final: 0.9354 (mt) REVERT: A 359 MET cc_start: 0.8944 (ttp) cc_final: 0.8740 (ttp) REVERT: A 366 LYS cc_start: 0.9274 (mtmm) cc_final: 0.8836 (mtmm) REVERT: A 375 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8231 (mmtm) REVERT: A 415 ASN cc_start: 0.9317 (t0) cc_final: 0.9007 (t0) REVERT: A 447 ASN cc_start: 0.8170 (m-40) cc_final: 0.7875 (t0) REVERT: A 466 MET cc_start: 0.9143 (ptt) cc_final: 0.8733 (ptt) REVERT: A 493 MET cc_start: 0.9062 (tmm) cc_final: 0.8698 (tmm) REVERT: A 494 MET cc_start: 0.9399 (mtp) cc_final: 0.9157 (mtp) REVERT: A 510 LYS cc_start: 0.9004 (mtpt) cc_final: 0.8700 (mtpt) REVERT: A 528 PHE cc_start: 0.9327 (m-80) cc_final: 0.8975 (m-80) REVERT: A 553 PRO cc_start: 0.9576 (Cg_exo) cc_final: 0.9106 (Cg_endo) REVERT: A 602 GLU cc_start: 0.7736 (pt0) cc_final: 0.7089 (pt0) REVERT: A 604 ARG cc_start: 0.9091 (mmm160) cc_final: 0.8889 (mmm-85) REVERT: A 636 LYS cc_start: 0.9404 (mptt) cc_final: 0.9172 (mmmt) REVERT: A 645 GLN cc_start: 0.8842 (tp40) cc_final: 0.8583 (tp40) REVERT: A 655 THR cc_start: 0.9417 (m) cc_final: 0.9152 (t) REVERT: A 657 PHE cc_start: 0.8991 (m-80) cc_final: 0.8687 (m-80) REVERT: B 8 LYS cc_start: 0.9472 (tptt) cc_final: 0.9055 (tppt) REVERT: B 41 ILE cc_start: 0.9433 (mm) cc_final: 0.9098 (mt) REVERT: B 119 GLU cc_start: 0.9293 (mp0) cc_final: 0.9077 (mp0) REVERT: B 147 GLN cc_start: 0.8715 (mt0) cc_final: 0.8485 (mt0) REVERT: B 172 LEU cc_start: 0.9135 (mp) cc_final: 0.8904 (mp) REVERT: B 184 ARG cc_start: 0.9414 (tpp80) cc_final: 0.9114 (tpp80) REVERT: B 191 GLN cc_start: 0.9281 (mm-40) cc_final: 0.9050 (mm-40) REVERT: B 202 ASN cc_start: 0.9342 (t0) cc_final: 0.8891 (t0) REVERT: B 211 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8284 (mm-30) REVERT: B 236 TYR cc_start: 0.9315 (t80) cc_final: 0.8868 (t80) REVERT: B 288 PHE cc_start: 0.9399 (t80) cc_final: 0.9117 (t80) REVERT: B 308 LYS cc_start: 0.9433 (mttm) cc_final: 0.9091 (mmmm) REVERT: B 315 ASP cc_start: 0.8893 (p0) cc_final: 0.8362 (p0) REVERT: B 321 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8406 (tm-30) REVERT: B 322 MET cc_start: 0.8835 (mmm) cc_final: 0.8393 (mmm) REVERT: B 348 MET cc_start: 0.9509 (ptm) cc_final: 0.9124 (ptm) REVERT: B 374 SER cc_start: 0.9052 (t) cc_final: 0.8122 (p) REVERT: B 378 PHE cc_start: 0.9210 (p90) cc_final: 0.8999 (p90) REVERT: B 387 GLN cc_start: 0.9213 (mt0) cc_final: 0.8949 (mt0) REVERT: B 390 GLN cc_start: 0.9237 (mt0) cc_final: 0.8982 (mm110) REVERT: B 393 SER cc_start: 0.9370 (m) cc_final: 0.9031 (p) REVERT: B 398 ASP cc_start: 0.8076 (t0) cc_final: 0.7842 (t0) REVERT: B 407 ILE cc_start: 0.9000 (mp) cc_final: 0.8780 (mp) REVERT: B 410 ASN cc_start: 0.8767 (m110) cc_final: 0.8295 (m110) REVERT: B 423 LYS cc_start: 0.9569 (mttt) cc_final: 0.9253 (mppt) REVERT: B 426 GLU cc_start: 0.9068 (pm20) cc_final: 0.8858 (pm20) REVERT: B 427 LYS cc_start: 0.9370 (mmmm) cc_final: 0.9075 (mmmm) REVERT: B 474 GLN cc_start: 0.8769 (mt0) cc_final: 0.8526 (mt0) REVERT: B 493 MET cc_start: 0.9656 (tmm) cc_final: 0.9411 (tmm) REVERT: B 516 GLN cc_start: 0.8784 (tp-100) cc_final: 0.8070 (tp40) REVERT: B 543 ILE cc_start: 0.9716 (mm) cc_final: 0.9421 (mm) REVERT: B 558 TRP cc_start: 0.9321 (m100) cc_final: 0.8605 (m100) REVERT: B 575 ARG cc_start: 0.8812 (mtm-85) cc_final: 0.8409 (mtm-85) REVERT: B 612 TYR cc_start: 0.9144 (m-80) cc_final: 0.8630 (m-10) REVERT: B 615 MET cc_start: 0.9149 (mmp) cc_final: 0.8699 (mmp) REVERT: B 639 ASP cc_start: 0.9223 (m-30) cc_final: 0.8847 (m-30) REVERT: B 640 MET cc_start: 0.9442 (tpp) cc_final: 0.9080 (tpp) REVERT: B 677 ARG cc_start: 0.9350 (mmm-85) cc_final: 0.9118 (mmm-85) REVERT: C 21 PHE cc_start: 0.8986 (m-80) cc_final: 0.8785 (m-80) REVERT: C 35 ILE cc_start: 0.7048 (tt) cc_final: 0.6810 (tt) REVERT: C 93 MET cc_start: 0.8685 (ttm) cc_final: 0.8366 (ttp) REVERT: C 101 HIS cc_start: 0.7867 (m170) cc_final: 0.6465 (m90) REVERT: C 157 MET cc_start: 0.9173 (mtm) cc_final: 0.8733 (mtm) REVERT: C 162 TYR cc_start: 0.9281 (m-10) cc_final: 0.8550 (m-10) REVERT: C 163 LEU cc_start: 0.9629 (tt) cc_final: 0.9253 (tt) REVERT: C 173 TYR cc_start: 0.7413 (t80) cc_final: 0.6460 (t80) REVERT: C 201 HIS cc_start: 0.9126 (m170) cc_final: 0.8799 (m170) REVERT: C 233 ASN cc_start: 0.9303 (m110) cc_final: 0.8812 (m110) REVERT: C 239 GLU cc_start: 0.9472 (pt0) cc_final: 0.9106 (pt0) REVERT: C 260 ILE cc_start: 0.6874 (pt) cc_final: 0.6459 (pt) REVERT: D 20 MET cc_start: 0.8967 (mtm) cc_final: 0.8734 (mpp) REVERT: D 148 ASP cc_start: 0.7418 (m-30) cc_final: 0.7101 (m-30) REVERT: D 184 LEU cc_start: 0.6841 (mt) cc_final: 0.6472 (mt) REVERT: D 186 GLN cc_start: 0.7783 (mm110) cc_final: 0.7402 (mm110) REVERT: D 281 ASP cc_start: 0.8203 (p0) cc_final: 0.7788 (t0) REVERT: D 315 LEU cc_start: 0.9273 (tp) cc_final: 0.8996 (tp) outliers start: 2 outliers final: 0 residues processed: 803 average time/residue: 0.2790 time to fit residues: 330.7635 Evaluate side-chains 659 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 659 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 191 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 171 optimal weight: 7.9990 chunk 189 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 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 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 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 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.116672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.082047 restraints weight = 41659.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.085189 restraints weight = 21516.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.087342 restraints weight = 13395.488| |-----------------------------------------------------------------------------| r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2985 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16386 Z= 0.249 Angle : 0.644 7.543 22134 Z= 0.343 Chirality : 0.044 0.229 2360 Planarity : 0.004 0.036 2818 Dihedral : 11.317 172.934 2242 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.23 % Allowed : 2.68 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.19), residues: 1932 helix: 1.24 (0.15), residues: 1156 sheet: 0.21 (0.42), residues: 126 loop : 0.38 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 124 HIS 0.007 0.002 HIS B 368 PHE 0.027 0.002 PHE A 654 TYR 0.039 0.002 TYR B 574 ARG 0.008 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.04290 ( 871) hydrogen bonds : angle 4.98671 ( 2571) covalent geometry : bond 0.00526 (16386) covalent geometry : angle 0.64386 (22134) *********************** 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 761 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 757 time to evaluate : 1.893 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: 0.9226 (tptp) cc_final: 0.8900 (tppt) REVERT: A 12 LEU cc_start: 0.9648 (mt) cc_final: 0.9354 (mt) REVERT: A 95 MET cc_start: 0.9143 (mmm) cc_final: 0.8558 (mmm) REVERT: A 129 PHE cc_start: 0.9520 (m-10) cc_final: 0.9258 (m-80) REVERT: A 147 GLN cc_start: 0.9417 (mt0) cc_final: 0.8672 (mt0) REVERT: A 149 TYR cc_start: 0.9195 (t80) cc_final: 0.8471 (t80) REVERT: A 157 LEU cc_start: 0.9443 (tp) cc_final: 0.9157 (tp) REVERT: A 158 ASN cc_start: 0.9432 (m110) cc_final: 0.9053 (m-40) REVERT: A 181 ASP cc_start: 0.8982 (m-30) cc_final: 0.8664 (m-30) REVERT: A 195 LEU cc_start: 0.9705 (mt) cc_final: 0.9430 (mt) REVERT: A 223 VAL cc_start: 0.9781 (m) cc_final: 0.9317 (p) REVERT: A 227 MET cc_start: 0.9314 (mtm) cc_final: 0.8914 (mtm) REVERT: A 238 ASP cc_start: 0.8340 (p0) cc_final: 0.7892 (p0) REVERT: A 255 HIS cc_start: 0.8839 (t-90) cc_final: 0.8129 (t-90) REVERT: A 257 ASP cc_start: 0.9187 (m-30) cc_final: 0.8954 (m-30) REVERT: A 262 LEU cc_start: 0.9855 (mt) cc_final: 0.9618 (mt) REVERT: A 270 ASP cc_start: 0.8980 (t0) cc_final: 0.8702 (t0) REVERT: A 335 GLU cc_start: 0.8014 (mm-30) cc_final: 0.7718 (mm-30) REVERT: A 344 GLU cc_start: 0.9275 (mt-10) cc_final: 0.8781 (mt-10) REVERT: A 349 LEU cc_start: 0.9675 (mt) cc_final: 0.9471 (mt) REVERT: A 375 LYS cc_start: 0.8955 (mmtt) cc_final: 0.8493 (mmtm) REVERT: A 378 PHE cc_start: 0.9059 (p90) cc_final: 0.8859 (p90) REVERT: A 390 GLN cc_start: 0.8704 (mt0) cc_final: 0.8500 (mt0) REVERT: A 393 SER cc_start: 0.9386 (m) cc_final: 0.9050 (t) REVERT: A 415 ASN cc_start: 0.9392 (t0) cc_final: 0.9136 (t0) REVERT: A 459 LYS cc_start: 0.9019 (mttp) cc_final: 0.8563 (mtmt) REVERT: A 466 MET cc_start: 0.9199 (ptt) cc_final: 0.8854 (ptt) REVERT: A 491 PHE cc_start: 0.9724 (t80) cc_final: 0.9434 (t80) REVERT: A 493 MET cc_start: 0.9029 (tmm) cc_final: 0.8638 (tmm) REVERT: A 494 MET cc_start: 0.9381 (mtp) cc_final: 0.9066 (mtp) REVERT: A 512 GLU cc_start: 0.8432 (pm20) cc_final: 0.8139 (pm20) REVERT: A 515 ASP cc_start: 0.9035 (m-30) cc_final: 0.8724 (m-30) REVERT: A 561 LEU cc_start: 0.9343 (tp) cc_final: 0.8838 (tp) REVERT: A 604 ARG cc_start: 0.9107 (mmm160) cc_final: 0.8594 (mmp80) REVERT: A 615 MET cc_start: 0.9071 (mmt) cc_final: 0.8826 (mmm) REVERT: A 636 LYS cc_start: 0.9434 (mptt) cc_final: 0.9182 (mmmm) REVERT: A 640 MET cc_start: 0.9224 (tpp) cc_final: 0.8899 (tpp) REVERT: A 645 GLN cc_start: 0.9146 (tp40) cc_final: 0.8850 (tp40) REVERT: A 655 THR cc_start: 0.9506 (m) cc_final: 0.9066 (p) REVERT: A 686 ARG cc_start: 0.8455 (mmm-85) cc_final: 0.7881 (mtm180) REVERT: B 8 LYS cc_start: 0.9455 (tptt) cc_final: 0.9023 (tppt) REVERT: B 41 ILE cc_start: 0.9459 (mm) cc_final: 0.9171 (mt) REVERT: B 55 LEU cc_start: 0.9744 (mt) cc_final: 0.9541 (mt) REVERT: B 58 LEU cc_start: 0.9784 (mt) cc_final: 0.9557 (mt) REVERT: B 109 ASN cc_start: 0.9230 (m110) cc_final: 0.8788 (m-40) REVERT: B 111 LYS cc_start: 0.9708 (mptt) cc_final: 0.9486 (mmtt) REVERT: B 117 ARG cc_start: 0.9409 (mmm-85) cc_final: 0.9071 (mmm-85) REVERT: B 119 GLU cc_start: 0.9365 (mp0) cc_final: 0.9093 (mp0) REVERT: B 143 LEU cc_start: 0.9224 (tp) cc_final: 0.8416 (tp) REVERT: B 148 GLU cc_start: 0.9040 (mp0) cc_final: 0.8026 (mp0) REVERT: B 150 GLN cc_start: 0.9438 (tp-100) cc_final: 0.9136 (tp-100) REVERT: B 167 LEU cc_start: 0.9136 (mt) cc_final: 0.8802 (mt) REVERT: B 172 LEU cc_start: 0.9406 (mp) cc_final: 0.9132 (mp) REVERT: B 176 ASN cc_start: 0.8810 (t0) cc_final: 0.8609 (t0) REVERT: B 184 ARG cc_start: 0.9449 (tpp80) cc_final: 0.9076 (tpp80) REVERT: B 211 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8536 (mm-30) REVERT: B 236 TYR cc_start: 0.9315 (t80) cc_final: 0.9076 (t80) REVERT: B 252 ASN cc_start: 0.9331 (t0) cc_final: 0.8937 (t0) REVERT: B 279 SER cc_start: 0.8263 (m) cc_final: 0.8004 (t) REVERT: B 288 PHE cc_start: 0.9515 (t80) cc_final: 0.9272 (t80) REVERT: B 290 GLU cc_start: 0.9471 (tt0) cc_final: 0.9239 (tm-30) REVERT: B 291 LEU cc_start: 0.9656 (mt) cc_final: 0.9446 (mp) REVERT: B 321 GLU cc_start: 0.8851 (tm-30) cc_final: 0.8277 (tm-30) REVERT: B 322 MET cc_start: 0.9095 (mmm) cc_final: 0.8279 (mmm) REVERT: B 335 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8138 (mm-30) REVERT: B 348 MET cc_start: 0.9497 (ptm) cc_final: 0.9292 (ptm) REVERT: B 358 ILE cc_start: 0.9761 (mm) cc_final: 0.9559 (mm) REVERT: B 375 LYS cc_start: 0.9048 (mmtp) cc_final: 0.8782 (mmmm) REVERT: B 378 PHE cc_start: 0.9182 (p90) cc_final: 0.8886 (p90) REVERT: B 390 GLN cc_start: 0.9242 (mt0) cc_final: 0.8929 (mm-40) REVERT: B 393 SER cc_start: 0.9325 (m) cc_final: 0.9050 (p) REVERT: B 398 ASP cc_start: 0.8303 (t0) cc_final: 0.8038 (t0) REVERT: B 410 ASN cc_start: 0.9026 (m-40) cc_final: 0.8689 (m-40) REVERT: B 415 ASN cc_start: 0.9515 (t0) cc_final: 0.9245 (t0) REVERT: B 423 LYS cc_start: 0.9555 (mttt) cc_final: 0.9345 (mtpt) REVERT: B 425 ILE cc_start: 0.9557 (mt) cc_final: 0.9341 (mt) REVERT: B 427 LYS cc_start: 0.9416 (mmmm) cc_final: 0.8954 (tppt) REVERT: B 437 THR cc_start: 0.9709 (m) cc_final: 0.9501 (m) REVERT: B 543 ILE cc_start: 0.9760 (mm) cc_final: 0.9470 (mm) REVERT: B 550 MET cc_start: 0.8109 (mtp) cc_final: 0.7728 (mtm) REVERT: B 576 LEU cc_start: 0.9491 (mt) cc_final: 0.9144 (mt) REVERT: B 588 GLN cc_start: 0.9371 (mm-40) cc_final: 0.8776 (mm-40) REVERT: B 612 TYR cc_start: 0.9252 (m-80) cc_final: 0.8767 (m-10) REVERT: B 615 MET cc_start: 0.9437 (mmp) cc_final: 0.9156 (mmp) REVERT: B 636 LYS cc_start: 0.9660 (mmmt) cc_final: 0.9390 (mmmm) REVERT: B 639 ASP cc_start: 0.9184 (m-30) cc_final: 0.8802 (m-30) REVERT: B 640 MET cc_start: 0.9400 (tpp) cc_final: 0.8962 (tpp) REVERT: C 20 MET cc_start: 0.9502 (tmm) cc_final: 0.9035 (ptp) REVERT: C 21 PHE cc_start: 0.9123 (m-80) cc_final: 0.8766 (m-80) REVERT: C 101 HIS cc_start: 0.8393 (m170) cc_final: 0.7312 (m170) REVERT: C 108 ILE cc_start: 0.8798 (mt) cc_final: 0.8491 (mt) REVERT: C 162 TYR cc_start: 0.9312 (m-10) cc_final: 0.8706 (m-10) REVERT: C 163 LEU cc_start: 0.9684 (tt) cc_final: 0.9289 (tt) REVERT: C 168 PHE cc_start: 0.9030 (m-80) cc_final: 0.8725 (m-80) REVERT: C 173 TYR cc_start: 0.7459 (t80) cc_final: 0.6559 (t80) REVERT: C 177 TYR cc_start: 0.9123 (t80) cc_final: 0.8876 (t80) REVERT: C 179 TYR cc_start: 0.8072 (t80) cc_final: 0.7555 (t80) REVERT: C 185 MET cc_start: 0.4795 (mmm) cc_final: 0.3546 (mpp) REVERT: C 201 HIS cc_start: 0.9166 (m170) cc_final: 0.8845 (m170) REVERT: C 278 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8044 (pm20) REVERT: D 20 MET cc_start: 0.8967 (mtm) cc_final: 0.8700 (mpp) REVERT: D 148 ASP cc_start: 0.7357 (m-30) cc_final: 0.7079 (m-30) REVERT: D 176 LEU cc_start: 0.9642 (mt) cc_final: 0.9249 (tp) REVERT: D 186 GLN cc_start: 0.7749 (mm110) cc_final: 0.7404 (mm110) REVERT: D 201 HIS cc_start: 0.9006 (m170) cc_final: 0.8615 (m170) REVERT: D 219 GLU cc_start: 0.9172 (tp30) cc_final: 0.8938 (tp30) REVERT: D 266 LYS cc_start: 0.8743 (mmtp) cc_final: 0.8514 (mmmm) REVERT: D 281 ASP cc_start: 0.8341 (p0) cc_final: 0.7909 (t0) REVERT: D 282 ILE cc_start: 0.5929 (OUTLIER) cc_final: 0.5260 (tp) outliers start: 4 outliers final: 0 residues processed: 758 average time/residue: 0.2910 time to fit residues: 325.5957 Evaluate side-chains 649 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 648 time to evaluate : 1.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 180 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 71 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 148 optimal weight: 20.0000 chunk 90 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 304 HIS ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 25 ASN C 28 GLN ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.118214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.083986 restraints weight = 41129.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.086847 restraints weight = 21556.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.089014 restraints weight = 13698.651| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 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 = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.5802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16386 Z= 0.190 Angle : 0.596 7.588 22134 Z= 0.316 Chirality : 0.042 0.240 2360 Planarity : 0.004 0.042 2818 Dihedral : 11.083 177.191 2242 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.29 % Allowed : 2.21 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.19), residues: 1932 helix: 1.24 (0.15), residues: 1133 sheet: 0.66 (0.44), residues: 106 loop : 0.19 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 124 HIS 0.006 0.001 HIS A 438 PHE 0.024 0.002 PHE A 261 TYR 0.029 0.002 TYR C 174 ARG 0.007 0.001 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 871) hydrogen bonds : angle 4.89127 ( 2571) covalent geometry : bond 0.00410 (16386) covalent geometry : angle 0.59558 (22134) *********************** 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 760 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 755 time to evaluate : 1.704 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: 0.9239 (tptp) cc_final: 0.8919 (tppt) REVERT: A 12 LEU cc_start: 0.9632 (mt) cc_final: 0.9341 (mt) REVERT: A 65 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8335 (mp0) REVERT: A 95 MET cc_start: 0.9090 (mmm) cc_final: 0.8489 (mmm) REVERT: A 107 LYS cc_start: 0.9140 (mttm) cc_final: 0.8784 (mtpp) REVERT: A 129 PHE cc_start: 0.9539 (m-10) cc_final: 0.9303 (m-80) REVERT: A 147 GLN cc_start: 0.9430 (mt0) cc_final: 0.8603 (mt0) REVERT: A 149 TYR cc_start: 0.9219 (t80) cc_final: 0.8598 (t80) REVERT: A 158 ASN cc_start: 0.9326 (m110) cc_final: 0.9113 (m-40) REVERT: A 172 LEU cc_start: 0.9507 (mp) cc_final: 0.9234 (mp) REVERT: A 181 ASP cc_start: 0.8916 (m-30) cc_final: 0.8637 (m-30) REVERT: A 195 LEU cc_start: 0.9700 (mt) cc_final: 0.9410 (mt) REVERT: A 214 LYS cc_start: 0.8855 (tppt) cc_final: 0.8400 (mmtt) REVERT: A 223 VAL cc_start: 0.9742 (m) cc_final: 0.9169 (p) REVERT: A 227 MET cc_start: 0.9350 (mtm) cc_final: 0.8851 (mtm) REVERT: A 232 ASN cc_start: 0.8953 (m-40) cc_final: 0.8675 (m-40) REVERT: A 235 ARG cc_start: 0.9109 (ttm110) cc_final: 0.8812 (ttm-80) REVERT: A 255 HIS cc_start: 0.8720 (t-90) cc_final: 0.7640 (t-90) REVERT: A 257 ASP cc_start: 0.9201 (m-30) cc_final: 0.8887 (m-30) REVERT: A 262 LEU cc_start: 0.9878 (mt) cc_final: 0.9626 (mt) REVERT: A 263 ASP cc_start: 0.9277 (m-30) cc_final: 0.9075 (m-30) REVERT: A 276 LYS cc_start: 0.9186 (mmpt) cc_final: 0.8787 (mmpt) REVERT: A 290 GLU cc_start: 0.9344 (pt0) cc_final: 0.8635 (pp20) REVERT: A 291 LEU cc_start: 0.9733 (mt) cc_final: 0.9258 (mt) REVERT: A 335 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7802 (mm-30) REVERT: A 344 GLU cc_start: 0.9302 (mt-10) cc_final: 0.8783 (mt-10) REVERT: A 345 LYS cc_start: 0.9782 (ttpt) cc_final: 0.9478 (ttmt) REVERT: A 349 LEU cc_start: 0.9687 (mt) cc_final: 0.9461 (mt) REVERT: A 375 LYS cc_start: 0.8935 (mmtt) cc_final: 0.8518 (mmtm) REVERT: A 390 GLN cc_start: 0.8885 (mt0) cc_final: 0.8605 (mt0) REVERT: A 393 SER cc_start: 0.9350 (m) cc_final: 0.9043 (t) REVERT: A 407 ILE cc_start: 0.9274 (mt) cc_final: 0.9012 (mt) REVERT: A 415 ASN cc_start: 0.9422 (t0) cc_final: 0.8864 (t0) REVERT: A 447 ASN cc_start: 0.8664 (m-40) cc_final: 0.8368 (m-40) REVERT: A 459 LYS cc_start: 0.9027 (mttp) cc_final: 0.8525 (mtmt) REVERT: A 466 MET cc_start: 0.9294 (ptt) cc_final: 0.8950 (ptt) REVERT: A 491 PHE cc_start: 0.9703 (t80) cc_final: 0.9403 (t80) REVERT: A 493 MET cc_start: 0.8979 (tmm) cc_final: 0.8500 (tmm) REVERT: A 494 MET cc_start: 0.9345 (mtp) cc_final: 0.8988 (mtp) REVERT: A 501 GLN cc_start: 0.9365 (tt0) cc_final: 0.8623 (tm-30) REVERT: A 515 ASP cc_start: 0.8982 (m-30) cc_final: 0.8644 (m-30) REVERT: A 561 LEU cc_start: 0.9382 (tp) cc_final: 0.8896 (tp) REVERT: A 598 MET cc_start: 0.8335 (mtp) cc_final: 0.7609 (mtp) REVERT: A 599 GLU cc_start: 0.9187 (pt0) cc_final: 0.8693 (pt0) REVERT: A 601 ILE cc_start: 0.9516 (mm) cc_final: 0.9124 (tp) REVERT: A 615 MET cc_start: 0.9100 (mmt) cc_final: 0.8781 (mmm) REVERT: A 636 LYS cc_start: 0.9474 (mptt) cc_final: 0.9163 (mmmm) REVERT: A 640 MET cc_start: 0.9317 (tpp) cc_final: 0.8899 (tpp) REVERT: A 645 GLN cc_start: 0.9196 (tp40) cc_final: 0.8868 (tp40) REVERT: A 655 THR cc_start: 0.9435 (m) cc_final: 0.8721 (t) REVERT: A 657 PHE cc_start: 0.9158 (m-80) cc_final: 0.8644 (m-80) REVERT: A 667 LEU cc_start: 0.9352 (tt) cc_final: 0.9145 (tt) REVERT: A 686 ARG cc_start: 0.8510 (mmm-85) cc_final: 0.7862 (mtm180) REVERT: B 8 LYS cc_start: 0.9425 (tptt) cc_final: 0.8982 (tppt) REVERT: B 41 ILE cc_start: 0.9442 (mm) cc_final: 0.9201 (mt) REVERT: B 55 LEU cc_start: 0.9758 (mt) cc_final: 0.9548 (mt) REVERT: B 58 LEU cc_start: 0.9782 (mt) cc_final: 0.9570 (mt) REVERT: B 109 ASN cc_start: 0.9360 (m110) cc_final: 0.8978 (m-40) REVERT: B 111 LYS cc_start: 0.9711 (mptt) cc_final: 0.9476 (mmtt) REVERT: B 119 GLU cc_start: 0.9394 (mp0) cc_final: 0.9077 (mp0) REVERT: B 143 LEU cc_start: 0.9278 (tp) cc_final: 0.8712 (tp) REVERT: B 148 GLU cc_start: 0.8996 (mp0) cc_final: 0.8343 (mp0) REVERT: B 150 GLN cc_start: 0.9448 (tp-100) cc_final: 0.9183 (tp-100) REVERT: B 167 LEU cc_start: 0.9207 (mt) cc_final: 0.8848 (mt) REVERT: B 172 LEU cc_start: 0.9398 (mp) cc_final: 0.9149 (mp) REVERT: B 176 ASN cc_start: 0.8722 (t0) cc_final: 0.8471 (t0) REVERT: B 181 ASP cc_start: 0.8710 (m-30) cc_final: 0.8326 (m-30) REVERT: B 184 ARG cc_start: 0.9444 (tpp80) cc_final: 0.9026 (tpp80) REVERT: B 211 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8323 (mm-30) REVERT: B 252 ASN cc_start: 0.9357 (t0) cc_final: 0.9075 (t0) REVERT: B 279 SER cc_start: 0.8300 (m) cc_final: 0.8077 (t) REVERT: B 286 ASP cc_start: 0.9049 (m-30) cc_final: 0.8766 (m-30) REVERT: B 291 LEU cc_start: 0.9676 (mt) cc_final: 0.9369 (mt) REVERT: B 321 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8495 (tm-30) REVERT: B 322 MET cc_start: 0.9184 (mmm) cc_final: 0.8366 (mmm) REVERT: B 335 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8171 (mm-30) REVERT: B 348 MET cc_start: 0.9457 (ptm) cc_final: 0.9093 (ptm) REVERT: B 358 ILE cc_start: 0.9751 (mm) cc_final: 0.9516 (mm) REVERT: B 362 ASP cc_start: 0.9010 (m-30) cc_final: 0.8757 (m-30) REVERT: B 375 LYS cc_start: 0.9041 (mmtp) cc_final: 0.8657 (mmmm) REVERT: B 390 GLN cc_start: 0.9219 (mt0) cc_final: 0.8997 (mm-40) REVERT: B 393 SER cc_start: 0.9348 (m) cc_final: 0.9014 (p) REVERT: B 399 GLU cc_start: 0.8967 (mm-30) cc_final: 0.8685 (mp0) REVERT: B 402 GLU cc_start: 0.9090 (tp30) cc_final: 0.8836 (tp30) REVERT: B 407 ILE cc_start: 0.9039 (mp) cc_final: 0.8826 (mp) REVERT: B 410 ASN cc_start: 0.8990 (m-40) cc_final: 0.8776 (m-40) REVERT: B 415 ASN cc_start: 0.9360 (t0) cc_final: 0.9042 (t0) REVERT: B 423 LYS cc_start: 0.9573 (mttt) cc_final: 0.9326 (mtpt) REVERT: B 427 LYS cc_start: 0.9443 (mmmm) cc_final: 0.9100 (mmmm) REVERT: B 493 MET cc_start: 0.9547 (tmm) cc_final: 0.9316 (tmm) REVERT: B 543 ILE cc_start: 0.9750 (mm) cc_final: 0.9465 (mm) REVERT: B 550 MET cc_start: 0.8238 (mtp) cc_final: 0.7892 (mtm) REVERT: B 576 LEU cc_start: 0.9496 (mt) cc_final: 0.9196 (mt) REVERT: B 588 GLN cc_start: 0.9428 (mm-40) cc_final: 0.9004 (mm-40) REVERT: B 603 GLU cc_start: 0.8499 (tm-30) cc_final: 0.7908 (tp30) REVERT: B 612 TYR cc_start: 0.9136 (m-80) cc_final: 0.8072 (m-80) REVERT: B 639 ASP cc_start: 0.9176 (m-30) cc_final: 0.8890 (m-30) REVERT: B 640 MET cc_start: 0.9207 (tpp) cc_final: 0.8663 (tpp) REVERT: C 68 GLU cc_start: 0.9223 (tp30) cc_final: 0.9023 (tp30) REVERT: C 101 HIS cc_start: 0.8368 (m170) cc_final: 0.7297 (m170) REVERT: C 157 MET cc_start: 0.9290 (mtm) cc_final: 0.8971 (mtm) REVERT: C 163 LEU cc_start: 0.9677 (tt) cc_final: 0.9235 (tt) REVERT: C 168 PHE cc_start: 0.8995 (m-80) cc_final: 0.8702 (m-80) REVERT: C 173 TYR cc_start: 0.7353 (t80) cc_final: 0.6563 (t80) REVERT: C 177 TYR cc_start: 0.9139 (t80) cc_final: 0.8889 (t80) REVERT: C 179 TYR cc_start: 0.8388 (t80) cc_final: 0.8108 (t80) REVERT: C 185 MET cc_start: 0.4824 (mmm) cc_final: 0.4602 (mpp) REVERT: C 208 LEU cc_start: 0.8560 (mm) cc_final: 0.8338 (mt) REVERT: C 233 ASN cc_start: 0.9350 (m110) cc_final: 0.8772 (m-40) REVERT: C 252 LEU cc_start: 0.7573 (mt) cc_final: 0.7297 (mt) REVERT: C 281 ASP cc_start: 0.8548 (m-30) cc_final: 0.8307 (m-30) REVERT: D 20 MET cc_start: 0.9056 (mtm) cc_final: 0.8770 (mpp) REVERT: D 138 ILE cc_start: 0.9812 (mm) cc_final: 0.9610 (mm) REVERT: D 139 VAL cc_start: 0.8134 (m) cc_final: 0.7886 (p) REVERT: D 148 ASP cc_start: 0.7266 (m-30) cc_final: 0.6969 (m-30) REVERT: D 208 LEU cc_start: 0.8601 (mt) cc_final: 0.8343 (mt) REVERT: D 219 GLU cc_start: 0.9184 (tp30) cc_final: 0.8957 (tp30) REVERT: D 266 LYS cc_start: 0.8794 (mmtp) cc_final: 0.8587 (mmmm) outliers start: 5 outliers final: 1 residues processed: 756 average time/residue: 0.2793 time to fit residues: 311.6389 Evaluate side-chains 654 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 653 time to evaluate : 1.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 67 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 175 optimal weight: 8.9990 chunk 182 optimal weight: 0.2980 chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS ** A 410 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 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 85 GLN C 132 GLN C 238 ASN D 127 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.117540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.083128 restraints weight = 42466.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.086191 restraints weight = 21883.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.088278 restraints weight = 13686.084| |-----------------------------------------------------------------------------| r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.6184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16386 Z= 0.171 Angle : 0.590 7.028 22134 Z= 0.315 Chirality : 0.043 0.286 2360 Planarity : 0.004 0.052 2818 Dihedral : 10.947 177.632 2242 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.19), residues: 1932 helix: 1.33 (0.15), residues: 1143 sheet: 0.55 (0.45), residues: 100 loop : 0.20 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 124 HIS 0.006 0.001 HIS D 84 PHE 0.029 0.002 PHE C 166 TYR 0.039 0.002 TYR D 142 ARG 0.008 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 871) hydrogen bonds : angle 4.86591 ( 2571) covalent geometry : bond 0.00374 (16386) covalent geometry : angle 0.58979 (22134) *********************** 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 749 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 748 time to evaluate : 1.727 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: 0.9258 (tptp) cc_final: 0.8925 (tppt) REVERT: A 12 LEU cc_start: 0.9630 (mt) cc_final: 0.9327 (mt) REVERT: A 107 LYS cc_start: 0.9132 (mttm) cc_final: 0.8783 (mtpp) REVERT: A 117 ARG cc_start: 0.9202 (ttm-80) cc_final: 0.8976 (ttm-80) REVERT: A 129 PHE cc_start: 0.9543 (m-10) cc_final: 0.9252 (m-80) REVERT: A 147 GLN cc_start: 0.9436 (mt0) cc_final: 0.9178 (mt0) REVERT: A 149 TYR cc_start: 0.9254 (t80) cc_final: 0.8610 (t80) REVERT: A 172 LEU cc_start: 0.9592 (mp) cc_final: 0.9225 (mp) REVERT: A 181 ASP cc_start: 0.8891 (m-30) cc_final: 0.8620 (m-30) REVERT: A 191 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.8487 (mt0) REVERT: A 195 LEU cc_start: 0.9695 (mt) cc_final: 0.9403 (mt) REVERT: A 214 LYS cc_start: 0.8772 (tppt) cc_final: 0.8336 (mmtt) REVERT: A 223 VAL cc_start: 0.9779 (m) cc_final: 0.9265 (p) REVERT: A 227 MET cc_start: 0.9276 (mtm) cc_final: 0.8925 (mtm) REVERT: A 232 ASN cc_start: 0.8940 (m-40) cc_final: 0.8691 (m-40) REVERT: A 257 ASP cc_start: 0.9096 (m-30) cc_final: 0.8851 (m-30) REVERT: A 262 LEU cc_start: 0.9882 (mt) cc_final: 0.9623 (mt) REVERT: A 263 ASP cc_start: 0.9290 (m-30) cc_final: 0.9061 (m-30) REVERT: A 301 PHE cc_start: 0.9158 (m-10) cc_final: 0.8758 (m-10) REVERT: A 321 GLU cc_start: 0.8426 (pm20) cc_final: 0.8058 (pm20) REVERT: A 335 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7647 (mm-30) REVERT: A 344 GLU cc_start: 0.9295 (mt-10) cc_final: 0.8761 (mt-10) REVERT: A 349 LEU cc_start: 0.9685 (mt) cc_final: 0.9464 (mt) REVERT: A 375 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8685 (mmtm) REVERT: A 393 SER cc_start: 0.9375 (m) cc_final: 0.9083 (t) REVERT: A 407 ILE cc_start: 0.9321 (mt) cc_final: 0.9043 (mt) REVERT: A 415 ASN cc_start: 0.9350 (t0) cc_final: 0.9064 (t0) REVERT: A 459 LYS cc_start: 0.8982 (mttp) cc_final: 0.8494 (mtmt) REVERT: A 466 MET cc_start: 0.9232 (ptt) cc_final: 0.8949 (ptt) REVERT: A 468 LEU cc_start: 0.9615 (tp) cc_final: 0.9386 (tp) REVERT: A 493 MET cc_start: 0.8987 (tmm) cc_final: 0.8469 (tmm) REVERT: A 494 MET cc_start: 0.9346 (mtp) cc_final: 0.8930 (mtp) REVERT: A 501 GLN cc_start: 0.9365 (tt0) cc_final: 0.8701 (tm-30) REVERT: A 515 ASP cc_start: 0.8954 (m-30) cc_final: 0.8614 (m-30) REVERT: A 561 LEU cc_start: 0.9350 (tp) cc_final: 0.8887 (tp) REVERT: A 598 MET cc_start: 0.8324 (mtp) cc_final: 0.6986 (mtp) REVERT: A 599 GLU cc_start: 0.9212 (pt0) cc_final: 0.8732 (pt0) REVERT: A 601 ILE cc_start: 0.9524 (mm) cc_final: 0.9162 (tp) REVERT: A 604 ARG cc_start: 0.9299 (mmm-85) cc_final: 0.8752 (mmp80) REVERT: A 615 MET cc_start: 0.9146 (mmt) cc_final: 0.8814 (mmm) REVERT: A 636 LYS cc_start: 0.9438 (mptt) cc_final: 0.9155 (mmmm) REVERT: A 640 MET cc_start: 0.9367 (tpp) cc_final: 0.8746 (tpp) REVERT: A 645 GLN cc_start: 0.9215 (tp40) cc_final: 0.8863 (tp-100) REVERT: A 655 THR cc_start: 0.9417 (m) cc_final: 0.8912 (t) REVERT: A 657 PHE cc_start: 0.9270 (m-80) cc_final: 0.8803 (m-80) REVERT: A 686 ARG cc_start: 0.8533 (mmm-85) cc_final: 0.7668 (mtm180) REVERT: B 8 LYS cc_start: 0.9435 (tptt) cc_final: 0.8993 (tppt) REVERT: B 41 ILE cc_start: 0.9473 (mm) cc_final: 0.9205 (mt) REVERT: B 55 LEU cc_start: 0.9768 (mt) cc_final: 0.9550 (mt) REVERT: B 58 LEU cc_start: 0.9780 (mt) cc_final: 0.9576 (mt) REVERT: B 60 GLU cc_start: 0.9381 (mt-10) cc_final: 0.9177 (tm-30) REVERT: B 119 GLU cc_start: 0.9372 (mp0) cc_final: 0.9060 (mp0) REVERT: B 150 GLN cc_start: 0.9465 (tp-100) cc_final: 0.9232 (tp-100) REVERT: B 167 LEU cc_start: 0.9279 (mt) cc_final: 0.8847 (mt) REVERT: B 172 LEU cc_start: 0.9381 (mp) cc_final: 0.9122 (mp) REVERT: B 181 ASP cc_start: 0.8655 (m-30) cc_final: 0.8325 (m-30) REVERT: B 184 ARG cc_start: 0.9392 (tpp80) cc_final: 0.8952 (tpp80) REVERT: B 211 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8373 (mm-30) REVERT: B 238 ASP cc_start: 0.8384 (t0) cc_final: 0.7781 (t70) REVERT: B 239 GLN cc_start: 0.8832 (tm-30) cc_final: 0.8316 (tm-30) REVERT: B 252 ASN cc_start: 0.9380 (t0) cc_final: 0.9083 (t0) REVERT: B 276 LYS cc_start: 0.9088 (ptmm) cc_final: 0.8872 (ptmm) REVERT: B 321 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8405 (tm-30) REVERT: B 322 MET cc_start: 0.9196 (mmm) cc_final: 0.8609 (mmm) REVERT: B 335 GLU cc_start: 0.8459 (mm-30) cc_final: 0.8130 (mm-30) REVERT: B 375 LYS cc_start: 0.9004 (mmtp) cc_final: 0.8741 (mmmm) REVERT: B 387 GLN cc_start: 0.8972 (mt0) cc_final: 0.8454 (mp10) REVERT: B 393 SER cc_start: 0.9369 (m) cc_final: 0.9053 (p) REVERT: B 398 ASP cc_start: 0.8649 (m-30) cc_final: 0.8440 (m-30) REVERT: B 399 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8726 (mp0) REVERT: B 407 ILE cc_start: 0.9043 (mp) cc_final: 0.8772 (mp) REVERT: B 410 ASN cc_start: 0.9012 (m-40) cc_final: 0.8780 (m-40) REVERT: B 415 ASN cc_start: 0.9273 (t0) cc_final: 0.8979 (t0) REVERT: B 423 LYS cc_start: 0.9552 (mttt) cc_final: 0.9349 (mtpt) REVERT: B 543 ILE cc_start: 0.9740 (mm) cc_final: 0.9444 (mm) REVERT: B 550 MET cc_start: 0.8117 (mtp) cc_final: 0.7834 (mtm) REVERT: B 576 LEU cc_start: 0.9526 (mt) cc_final: 0.9212 (mt) REVERT: B 588 GLN cc_start: 0.9435 (mm-40) cc_final: 0.9049 (mm-40) REVERT: B 612 TYR cc_start: 0.8946 (m-80) cc_final: 0.8260 (m-10) REVERT: B 639 ASP cc_start: 0.9100 (m-30) cc_final: 0.8897 (m-30) REVERT: B 640 MET cc_start: 0.9185 (tpp) cc_final: 0.8488 (tpp) REVERT: B 680 LYS cc_start: 0.9100 (mttt) cc_final: 0.8876 (mtpt) REVERT: C 20 MET cc_start: 0.9328 (tpt) cc_final: 0.9121 (ptp) REVERT: C 21 PHE cc_start: 0.9345 (m-80) cc_final: 0.8673 (m-80) REVERT: C 79 GLU cc_start: 0.6719 (tm-30) cc_final: 0.5658 (pt0) REVERT: C 90 LEU cc_start: 0.9704 (mt) cc_final: 0.9495 (mt) REVERT: C 101 HIS cc_start: 0.8391 (m170) cc_final: 0.7701 (m170) REVERT: C 157 MET cc_start: 0.9301 (mtm) cc_final: 0.9015 (mtm) REVERT: C 163 LEU cc_start: 0.9708 (tt) cc_final: 0.9489 (pp) REVERT: C 168 PHE cc_start: 0.8914 (m-80) cc_final: 0.8654 (m-80) REVERT: C 173 TYR cc_start: 0.7463 (t80) cc_final: 0.6684 (t80) REVERT: C 177 TYR cc_start: 0.9135 (t80) cc_final: 0.8917 (t80) REVERT: C 179 TYR cc_start: 0.8414 (t80) cc_final: 0.8213 (t80) REVERT: C 185 MET cc_start: 0.5688 (mmm) cc_final: 0.4747 (mpp) REVERT: C 208 LEU cc_start: 0.8869 (mm) cc_final: 0.8577 (mm) REVERT: C 233 ASN cc_start: 0.9437 (m110) cc_final: 0.8901 (m110) REVERT: C 252 LEU cc_start: 0.7473 (mt) cc_final: 0.7193 (mt) REVERT: C 281 ASP cc_start: 0.8599 (m-30) cc_final: 0.8369 (m-30) REVERT: C 313 GLU cc_start: 0.8984 (tt0) cc_final: 0.8535 (tp30) REVERT: D 20 MET cc_start: 0.9002 (mtm) cc_final: 0.8705 (mpp) REVERT: D 30 TRP cc_start: 0.8169 (p-90) cc_final: 0.7659 (p-90) REVERT: D 42 LEU cc_start: 0.9094 (mp) cc_final: 0.8634 (mp) REVERT: D 148 ASP cc_start: 0.7057 (m-30) cc_final: 0.6765 (m-30) REVERT: D 201 HIS cc_start: 0.9329 (m170) cc_final: 0.8913 (m170) REVERT: D 207 LEU cc_start: 0.8437 (mt) cc_final: 0.8217 (mt) REVERT: D 219 GLU cc_start: 0.9190 (tp30) cc_final: 0.8978 (tp30) REVERT: D 270 ASN cc_start: 0.8710 (m-40) cc_final: 0.8503 (m-40) outliers start: 1 outliers final: 0 residues processed: 748 average time/residue: 0.2702 time to fit residues: 299.6277 Evaluate side-chains 643 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 642 time to evaluate : 1.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 31 optimal weight: 5.9990 chunk 126 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 156 optimal weight: 9.9990 chunk 21 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 169 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 177 optimal weight: 30.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 180 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN ** 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** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.115853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.081860 restraints weight = 42255.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.084736 restraints weight = 21933.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.086755 restraints weight = 14129.172| |-----------------------------------------------------------------------------| r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 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 = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.6535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16386 Z= 0.211 Angle : 0.615 9.507 22134 Z= 0.327 Chirality : 0.044 0.248 2360 Planarity : 0.004 0.047 2818 Dihedral : 11.053 179.624 2242 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.06 % Allowed : 1.17 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.19), residues: 1932 helix: 1.25 (0.15), residues: 1134 sheet: 0.35 (0.44), residues: 100 loop : -0.01 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP D 124 HIS 0.006 0.001 HIS A 438 PHE 0.027 0.002 PHE B 492 TYR 0.035 0.002 TYR C 130 ARG 0.008 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 871) hydrogen bonds : angle 4.88739 ( 2571) covalent geometry : bond 0.00455 (16386) covalent geometry : angle 0.61512 (22134) *********************** 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 736 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 735 time to evaluate : 1.807 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: 0.9250 (tptp) cc_final: 0.8961 (tppt) REVERT: A 12 LEU cc_start: 0.9625 (mt) cc_final: 0.9317 (mt) REVERT: A 65 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8178 (mp0) REVERT: A 107 LYS cc_start: 0.9161 (mttm) cc_final: 0.8904 (mtpp) REVERT: A 129 PHE cc_start: 0.9541 (m-10) cc_final: 0.9256 (m-10) REVERT: A 147 GLN cc_start: 0.9414 (mt0) cc_final: 0.8739 (mt0) REVERT: A 149 TYR cc_start: 0.9297 (t80) cc_final: 0.8679 (t80) REVERT: A 172 LEU cc_start: 0.9575 (mp) cc_final: 0.9224 (mp) REVERT: A 181 ASP cc_start: 0.8947 (m-30) cc_final: 0.8634 (m-30) REVERT: A 195 LEU cc_start: 0.9722 (mt) cc_final: 0.9466 (mt) REVERT: A 214 LYS cc_start: 0.8832 (tppt) cc_final: 0.8592 (tppt) REVERT: A 223 VAL cc_start: 0.9762 (m) cc_final: 0.9189 (p) REVERT: A 227 MET cc_start: 0.9307 (mtm) cc_final: 0.8855 (mtm) REVERT: A 232 ASN cc_start: 0.8961 (m-40) cc_final: 0.8586 (m-40) REVERT: A 255 HIS cc_start: 0.8646 (t-90) cc_final: 0.7760 (t-90) REVERT: A 257 ASP cc_start: 0.9127 (m-30) cc_final: 0.8861 (m-30) REVERT: A 262 LEU cc_start: 0.9893 (mt) cc_final: 0.9614 (mt) REVERT: A 301 PHE cc_start: 0.9232 (m-10) cc_final: 0.8731 (m-10) REVERT: A 335 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7668 (mm-30) REVERT: A 344 GLU cc_start: 0.9277 (mt-10) cc_final: 0.8705 (mt-10) REVERT: A 349 LEU cc_start: 0.9700 (mt) cc_final: 0.9450 (mt) REVERT: A 375 LYS cc_start: 0.9136 (mmtt) cc_final: 0.8865 (mmtm) REVERT: A 390 GLN cc_start: 0.8956 (mt0) cc_final: 0.8723 (mt0) REVERT: A 393 SER cc_start: 0.9348 (m) cc_final: 0.9067 (t) REVERT: A 415 ASN cc_start: 0.9324 (t0) cc_final: 0.8961 (t0) REVERT: A 420 MET cc_start: 0.9547 (tpp) cc_final: 0.9222 (mmm) REVERT: A 459 LYS cc_start: 0.9042 (mttp) cc_final: 0.8455 (mtmm) REVERT: A 466 MET cc_start: 0.9257 (ptt) cc_final: 0.8974 (ptt) REVERT: A 493 MET cc_start: 0.8985 (tmm) cc_final: 0.8463 (tmm) REVERT: A 494 MET cc_start: 0.9317 (mtp) cc_final: 0.8914 (mtp) REVERT: A 501 GLN cc_start: 0.9389 (tt0) cc_final: 0.8730 (tm-30) REVERT: A 515 ASP cc_start: 0.8965 (m-30) cc_final: 0.8657 (m-30) REVERT: A 550 MET cc_start: 0.8400 (mtm) cc_final: 0.7833 (mtm) REVERT: A 561 LEU cc_start: 0.9417 (tp) cc_final: 0.8963 (tp) REVERT: A 571 TYR cc_start: 0.8582 (t80) cc_final: 0.8361 (t80) REVERT: A 598 MET cc_start: 0.8377 (mtp) cc_final: 0.7967 (mtp) REVERT: A 599 GLU cc_start: 0.9174 (pt0) cc_final: 0.8822 (pt0) REVERT: A 601 ILE cc_start: 0.9534 (mm) cc_final: 0.9248 (tp) REVERT: A 615 MET cc_start: 0.9163 (mmt) cc_final: 0.8912 (mmp) REVERT: A 640 MET cc_start: 0.9352 (tpp) cc_final: 0.8759 (tpp) REVERT: A 645 GLN cc_start: 0.9232 (tp40) cc_final: 0.8844 (tp-100) REVERT: A 667 LEU cc_start: 0.9436 (tt) cc_final: 0.9210 (tt) REVERT: B 8 LYS cc_start: 0.9387 (tptt) cc_final: 0.9047 (tppt) REVERT: B 12 LEU cc_start: 0.9631 (mt) cc_final: 0.9393 (mt) REVERT: B 41 ILE cc_start: 0.9464 (mm) cc_final: 0.9258 (mt) REVERT: B 55 LEU cc_start: 0.9760 (mt) cc_final: 0.9543 (mt) REVERT: B 119 GLU cc_start: 0.9396 (mp0) cc_final: 0.9000 (mp0) REVERT: B 143 LEU cc_start: 0.9357 (tp) cc_final: 0.8339 (tp) REVERT: B 148 GLU cc_start: 0.9061 (mp0) cc_final: 0.7852 (mp0) REVERT: B 149 TYR cc_start: 0.9119 (t80) cc_final: 0.8550 (t80) REVERT: B 167 LEU cc_start: 0.9305 (mt) cc_final: 0.8985 (mt) REVERT: B 172 LEU cc_start: 0.9387 (mp) cc_final: 0.9124 (mp) REVERT: B 181 ASP cc_start: 0.8591 (m-30) cc_final: 0.8288 (m-30) REVERT: B 184 ARG cc_start: 0.9377 (tpp80) cc_final: 0.8856 (tpp80) REVERT: B 211 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8448 (mm-30) REVERT: B 235 ARG cc_start: 0.9246 (ttm110) cc_final: 0.8444 (ptp-110) REVERT: B 238 ASP cc_start: 0.8392 (t0) cc_final: 0.7777 (t70) REVERT: B 239 GLN cc_start: 0.8845 (tm-30) cc_final: 0.8299 (tm-30) REVERT: B 252 ASN cc_start: 0.9420 (t0) cc_final: 0.9136 (t0) REVERT: B 263 ASP cc_start: 0.9314 (m-30) cc_final: 0.8902 (m-30) REVERT: B 276 LYS cc_start: 0.9146 (ptmm) cc_final: 0.8900 (ptmm) REVERT: B 286 ASP cc_start: 0.9128 (m-30) cc_final: 0.8818 (m-30) REVERT: B 321 GLU cc_start: 0.8886 (tm-30) cc_final: 0.8372 (tm-30) REVERT: B 322 MET cc_start: 0.9174 (mmm) cc_final: 0.8432 (mmm) REVERT: B 335 GLU cc_start: 0.8470 (mm-30) cc_final: 0.8129 (mm-30) REVERT: B 348 MET cc_start: 0.9410 (ptm) cc_final: 0.9137 (ptp) REVERT: B 355 TYR cc_start: 0.8705 (m-10) cc_final: 0.8239 (m-10) REVERT: B 362 ASP cc_start: 0.8950 (m-30) cc_final: 0.8589 (m-30) REVERT: B 375 LYS cc_start: 0.8990 (mmtp) cc_final: 0.8687 (mmmm) REVERT: B 387 GLN cc_start: 0.8974 (mt0) cc_final: 0.8324 (mp10) REVERT: B 390 GLN cc_start: 0.9239 (mm-40) cc_final: 0.8867 (mm-40) REVERT: B 393 SER cc_start: 0.9358 (m) cc_final: 0.9040 (p) REVERT: B 398 ASP cc_start: 0.8723 (m-30) cc_final: 0.8514 (m-30) REVERT: B 399 GLU cc_start: 0.9047 (mm-30) cc_final: 0.8753 (mp0) REVERT: B 402 GLU cc_start: 0.9082 (tp30) cc_final: 0.8857 (tp30) REVERT: B 403 ILE cc_start: 0.9045 (tp) cc_final: 0.8820 (tp) REVERT: B 407 ILE cc_start: 0.9146 (mp) cc_final: 0.8857 (mp) REVERT: B 415 ASN cc_start: 0.9385 (t0) cc_final: 0.9098 (t0) REVERT: B 543 ILE cc_start: 0.9741 (mm) cc_final: 0.9441 (mm) REVERT: B 550 MET cc_start: 0.8157 (mtp) cc_final: 0.7482 (mtm) REVERT: B 588 GLN cc_start: 0.9419 (mm-40) cc_final: 0.8967 (mm-40) REVERT: B 606 TYR cc_start: 0.7998 (m-80) cc_final: 0.7731 (m-80) REVERT: B 615 MET cc_start: 0.9465 (mmp) cc_final: 0.9146 (mmp) REVERT: B 640 MET cc_start: 0.9060 (tpp) cc_final: 0.8428 (tpp) REVERT: B 680 LYS cc_start: 0.9089 (mttt) cc_final: 0.8853 (mtpt) REVERT: C 17 PHE cc_start: 0.9020 (p90) cc_final: 0.8449 (p90) REVERT: C 21 PHE cc_start: 0.9235 (m-80) cc_final: 0.8564 (m-80) REVERT: C 69 GLN cc_start: 0.9050 (tm-30) cc_final: 0.8846 (tm-30) REVERT: C 79 GLU cc_start: 0.6859 (tm-30) cc_final: 0.6046 (pt0) REVERT: C 89 VAL cc_start: 0.6201 (t) cc_final: 0.5965 (m) REVERT: C 90 LEU cc_start: 0.9674 (mt) cc_final: 0.9444 (mt) REVERT: C 101 HIS cc_start: 0.8292 (m170) cc_final: 0.7381 (m170) REVERT: C 109 PHE cc_start: 0.7686 (m-80) cc_final: 0.7466 (m-10) REVERT: C 157 MET cc_start: 0.9274 (mtm) cc_final: 0.9014 (mtm) REVERT: C 168 PHE cc_start: 0.8943 (m-80) cc_final: 0.8738 (m-80) REVERT: C 173 TYR cc_start: 0.7430 (t80) cc_final: 0.6669 (t80) REVERT: C 177 TYR cc_start: 0.9129 (t80) cc_final: 0.8910 (t80) REVERT: C 185 MET cc_start: 0.5970 (mmm) cc_final: 0.5045 (mpp) REVERT: C 208 LEU cc_start: 0.8876 (mm) cc_final: 0.8578 (mt) REVERT: C 233 ASN cc_start: 0.9431 (m110) cc_final: 0.8880 (m-40) REVERT: C 252 LEU cc_start: 0.7497 (mt) cc_final: 0.7207 (mt) REVERT: C 278 GLU cc_start: 0.8839 (mm-30) cc_final: 0.8281 (pm20) REVERT: C 281 ASP cc_start: 0.8593 (m-30) cc_final: 0.8339 (m-30) REVERT: C 313 GLU cc_start: 0.9005 (tt0) cc_final: 0.8114 (tp30) REVERT: D 30 TRP cc_start: 0.8239 (p-90) cc_final: 0.7517 (p-90) REVERT: D 148 ASP cc_start: 0.7000 (m-30) cc_final: 0.6701 (m-30) REVERT: D 176 LEU cc_start: 0.9634 (mt) cc_final: 0.9338 (tp) REVERT: D 191 ILE cc_start: 0.9507 (mm) cc_final: 0.9296 (mm) REVERT: D 240 LEU cc_start: 0.8118 (mt) cc_final: 0.7792 (mt) REVERT: D 270 ASN cc_start: 0.8556 (m-40) cc_final: 0.8335 (m-40) outliers start: 1 outliers final: 0 residues processed: 735 average time/residue: 0.2689 time to fit residues: 293.5395 Evaluate side-chains 631 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 631 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 39 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 161 optimal weight: 9.9990 chunk 23 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 184 optimal weight: 6.9990 chunk 119 optimal weight: 0.0000 chunk 175 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** 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** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.118689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.084727 restraints weight = 41447.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.087829 restraints weight = 21463.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.089931 restraints weight = 13400.717| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3017 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3017 r_free = 0.3017 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 = 0.3017 r_free = 0.3017 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3017 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.6753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16386 Z= 0.153 Angle : 0.605 10.099 22134 Z= 0.320 Chirality : 0.043 0.343 2360 Planarity : 0.003 0.043 2818 Dihedral : 10.964 179.673 2242 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.19), residues: 1932 helix: 1.19 (0.15), residues: 1137 sheet: 0.15 (0.43), residues: 110 loop : -0.00 (0.23), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 124 HIS 0.008 0.001 HIS C 201 PHE 0.029 0.002 PHE B 492 TYR 0.036 0.002 TYR D 142 ARG 0.009 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 871) hydrogen bonds : angle 4.86950 ( 2571) covalent geometry : bond 0.00341 (16386) covalent geometry : angle 0.60473 (22134) *********************** 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 733 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 733 time to evaluate : 1.859 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: A 8 LYS cc_start: 0.9252 (tptp) cc_final: 0.8935 (tppt) REVERT: A 12 LEU cc_start: 0.9623 (mt) cc_final: 0.9280 (mt) REVERT: A 65 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8023 (mp0) REVERT: A 107 LYS cc_start: 0.9166 (mttm) cc_final: 0.8733 (mtpp) REVERT: A 129 PHE cc_start: 0.9539 (m-10) cc_final: 0.9249 (m-10) REVERT: A 147 GLN cc_start: 0.9370 (mt0) cc_final: 0.8659 (mt0) REVERT: A 149 TYR cc_start: 0.9317 (t80) cc_final: 0.8718 (t80) REVERT: A 172 LEU cc_start: 0.9533 (mp) cc_final: 0.9191 (mp) REVERT: A 175 VAL cc_start: 0.9251 (t) cc_final: 0.9050 (t) REVERT: A 181 ASP cc_start: 0.8879 (m-30) cc_final: 0.8583 (m-30) REVERT: A 195 LEU cc_start: 0.9742 (mt) cc_final: 0.9533 (mt) REVERT: A 214 LYS cc_start: 0.8772 (tppt) cc_final: 0.8519 (tppt) REVERT: A 223 VAL cc_start: 0.9764 (m) cc_final: 0.9247 (p) REVERT: A 227 MET cc_start: 0.9274 (mtm) cc_final: 0.8933 (mtm) REVERT: A 232 ASN cc_start: 0.8779 (m-40) cc_final: 0.8402 (m-40) REVERT: A 255 HIS cc_start: 0.8659 (t-90) cc_final: 0.7780 (t-90) REVERT: A 257 ASP cc_start: 0.9094 (m-30) cc_final: 0.8854 (m-30) REVERT: A 262 LEU cc_start: 0.9898 (mt) cc_final: 0.9658 (mt) REVERT: A 276 LYS cc_start: 0.9111 (mmpt) cc_final: 0.8873 (mmtm) REVERT: A 301 PHE cc_start: 0.9159 (m-10) cc_final: 0.8673 (m-10) REVERT: A 322 MET cc_start: 0.9065 (mmm) cc_final: 0.8134 (mmm) REVERT: A 335 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7580 (mm-30) REVERT: A 344 GLU cc_start: 0.9267 (mt-10) cc_final: 0.8626 (mt-10) REVERT: A 345 LYS cc_start: 0.9784 (ttpt) cc_final: 0.9482 (ttmt) REVERT: A 349 LEU cc_start: 0.9685 (mt) cc_final: 0.9468 (mt) REVERT: A 375 LYS cc_start: 0.9082 (mmtt) cc_final: 0.8827 (mmtm) REVERT: A 393 SER cc_start: 0.9342 (m) cc_final: 0.8373 (p) REVERT: A 402 GLU cc_start: 0.8170 (mp0) cc_final: 0.7236 (mp0) REVERT: A 407 ILE cc_start: 0.9322 (mt) cc_final: 0.8969 (mt) REVERT: A 415 ASN cc_start: 0.9326 (t0) cc_final: 0.8911 (t0) REVERT: A 420 MET cc_start: 0.9498 (tpp) cc_final: 0.9151 (mmm) REVERT: A 459 LYS cc_start: 0.9010 (mttp) cc_final: 0.8378 (mtmm) REVERT: A 466 MET cc_start: 0.9171 (ptt) cc_final: 0.8830 (ptt) REVERT: A 493 MET cc_start: 0.8968 (tmm) cc_final: 0.8437 (tmm) REVERT: A 494 MET cc_start: 0.9336 (mtp) cc_final: 0.8894 (mtp) REVERT: A 501 GLN cc_start: 0.9371 (tt0) cc_final: 0.8728 (tm-30) REVERT: A 515 ASP cc_start: 0.8907 (m-30) cc_final: 0.8579 (m-30) REVERT: A 550 MET cc_start: 0.8335 (mtm) cc_final: 0.7694 (mtm) REVERT: A 561 LEU cc_start: 0.9419 (tp) cc_final: 0.8962 (tp) REVERT: A 571 TYR cc_start: 0.8509 (t80) cc_final: 0.8212 (t80) REVERT: A 595 MET cc_start: 0.9095 (mmp) cc_final: 0.8465 (mmp) REVERT: A 598 MET cc_start: 0.8425 (mtp) cc_final: 0.7752 (mtp) REVERT: A 601 ILE cc_start: 0.9510 (mm) cc_final: 0.9225 (tp) REVERT: A 615 MET cc_start: 0.9161 (mmt) cc_final: 0.8910 (mmm) REVERT: A 640 MET cc_start: 0.9367 (tpp) cc_final: 0.8779 (tpp) REVERT: A 645 GLN cc_start: 0.9210 (tp40) cc_final: 0.8834 (tp-100) REVERT: A 655 THR cc_start: 0.9334 (m) cc_final: 0.9052 (m) REVERT: A 667 LEU cc_start: 0.9383 (tt) cc_final: 0.9161 (tt) REVERT: A 686 ARG cc_start: 0.8469 (mmm-85) cc_final: 0.7804 (mtm180) REVERT: B 8 LYS cc_start: 0.9390 (tptt) cc_final: 0.8935 (tppt) REVERT: B 20 LYS cc_start: 0.9683 (tmtt) cc_final: 0.9473 (tptp) REVERT: B 21 ASP cc_start: 0.8687 (t70) cc_final: 0.8393 (t0) REVERT: B 41 ILE cc_start: 0.9441 (mm) cc_final: 0.9196 (mt) REVERT: B 55 LEU cc_start: 0.9778 (mt) cc_final: 0.9565 (mt) REVERT: B 87 LYS cc_start: 0.9325 (tptt) cc_final: 0.8959 (tttt) REVERT: B 119 GLU cc_start: 0.9371 (mp0) cc_final: 0.9020 (mp0) REVERT: B 122 ILE cc_start: 0.9752 (mt) cc_final: 0.9491 (mt) REVERT: B 143 LEU cc_start: 0.9289 (tp) cc_final: 0.8375 (tp) REVERT: B 148 GLU cc_start: 0.9111 (mp0) cc_final: 0.7837 (mp0) REVERT: B 149 TYR cc_start: 0.9188 (t80) cc_final: 0.8509 (t80) REVERT: B 167 LEU cc_start: 0.9310 (mt) cc_final: 0.8779 (mt) REVERT: B 172 LEU cc_start: 0.9372 (mp) cc_final: 0.9024 (mp) REVERT: B 181 ASP cc_start: 0.8545 (m-30) cc_final: 0.8263 (m-30) REVERT: B 184 ARG cc_start: 0.9363 (tpp80) cc_final: 0.8943 (tpp80) REVERT: B 211 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8435 (mm-30) REVERT: B 238 ASP cc_start: 0.8418 (t0) cc_final: 0.7831 (t70) REVERT: B 239 GLN cc_start: 0.8931 (tm-30) cc_final: 0.8357 (tm-30) REVERT: B 252 ASN cc_start: 0.9440 (t0) cc_final: 0.9134 (t0) REVERT: B 263 ASP cc_start: 0.9301 (m-30) cc_final: 0.8871 (m-30) REVERT: B 286 ASP cc_start: 0.8976 (m-30) cc_final: 0.8692 (m-30) REVERT: B 321 GLU cc_start: 0.8888 (tm-30) cc_final: 0.8370 (tm-30) REVERT: B 322 MET cc_start: 0.9194 (mmm) cc_final: 0.8400 (mmm) REVERT: B 335 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8130 (mm-30) REVERT: B 348 MET cc_start: 0.9398 (ptm) cc_final: 0.9185 (ptp) REVERT: B 355 TYR cc_start: 0.8732 (m-10) cc_final: 0.8293 (m-10) REVERT: B 362 ASP cc_start: 0.8838 (m-30) cc_final: 0.8319 (m-30) REVERT: B 374 SER cc_start: 0.9450 (t) cc_final: 0.8967 (p) REVERT: B 375 LYS cc_start: 0.8918 (mmtp) cc_final: 0.8656 (mmmm) REVERT: B 384 GLU cc_start: 0.8794 (pm20) cc_final: 0.8272 (pm20) REVERT: B 387 GLN cc_start: 0.8987 (mt0) cc_final: 0.8300 (mp10) REVERT: B 393 SER cc_start: 0.9339 (m) cc_final: 0.9015 (p) REVERT: B 398 ASP cc_start: 0.8641 (m-30) cc_final: 0.8420 (m-30) REVERT: B 399 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8791 (mp0) REVERT: B 402 GLU cc_start: 0.9037 (tp30) cc_final: 0.8799 (tp30) REVERT: B 403 ILE cc_start: 0.8966 (tp) cc_final: 0.8673 (tp) REVERT: B 407 ILE cc_start: 0.9049 (mp) cc_final: 0.8752 (mp) REVERT: B 415 ASN cc_start: 0.9324 (t0) cc_final: 0.9009 (t0) REVERT: B 427 LYS cc_start: 0.9433 (mmtt) cc_final: 0.9117 (mmmm) REVERT: B 543 ILE cc_start: 0.9733 (mm) cc_final: 0.9425 (mm) REVERT: B 575 ARG cc_start: 0.8862 (mtm-85) cc_final: 0.8616 (mtm-85) REVERT: B 576 LEU cc_start: 0.9484 (mt) cc_final: 0.9227 (mt) REVERT: B 588 GLN cc_start: 0.9419 (mm-40) cc_final: 0.9008 (mm-40) REVERT: B 615 MET cc_start: 0.9465 (mmp) cc_final: 0.9128 (mmp) REVERT: B 640 MET cc_start: 0.9147 (tpp) cc_final: 0.8520 (tpp) REVERT: B 680 LYS cc_start: 0.9012 (mttt) cc_final: 0.8776 (mtpt) REVERT: B 686 ARG cc_start: 0.8709 (ttm110) cc_final: 0.8179 (mtt90) REVERT: C 17 PHE cc_start: 0.9076 (p90) cc_final: 0.8760 (p90) REVERT: C 20 MET cc_start: 0.9493 (tmm) cc_final: 0.9110 (ptp) REVERT: C 21 PHE cc_start: 0.9304 (m-80) cc_final: 0.8612 (m-80) REVERT: C 37 LEU cc_start: 0.3352 (tp) cc_final: 0.3149 (tp) REVERT: C 79 GLU cc_start: 0.6556 (tm-30) cc_final: 0.5360 (pt0) REVERT: C 90 LEU cc_start: 0.9645 (mt) cc_final: 0.9441 (mt) REVERT: C 101 HIS cc_start: 0.8289 (m170) cc_final: 0.7669 (m170) REVERT: C 157 MET cc_start: 0.9293 (mtm) cc_final: 0.9006 (mtm) REVERT: C 174 TYR cc_start: 0.7712 (t80) cc_final: 0.7177 (t80) REVERT: C 177 TYR cc_start: 0.9082 (t80) cc_final: 0.8874 (t80) REVERT: C 185 MET cc_start: 0.6317 (mmm) cc_final: 0.5113 (mpp) REVERT: C 208 LEU cc_start: 0.8857 (mm) cc_final: 0.8559 (mt) REVERT: C 227 PHE cc_start: 0.9236 (m-80) cc_final: 0.8985 (m-10) REVERT: C 231 LEU cc_start: 0.9118 (mt) cc_final: 0.8762 (pp) REVERT: C 233 ASN cc_start: 0.9459 (m110) cc_final: 0.8925 (m110) REVERT: C 260 ILE cc_start: 0.7189 (pt) cc_final: 0.6851 (pt) REVERT: C 278 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8351 (pm20) REVERT: C 281 ASP cc_start: 0.8548 (m-30) cc_final: 0.8296 (m-30) REVERT: D 30 TRP cc_start: 0.8189 (p-90) cc_final: 0.7260 (p-90) REVERT: D 96 MET cc_start: 0.8964 (mmm) cc_final: 0.8726 (mmm) REVERT: D 148 ASP cc_start: 0.7000 (m-30) cc_final: 0.6713 (m-30) REVERT: D 176 LEU cc_start: 0.9624 (mt) cc_final: 0.9344 (tp) REVERT: D 185 MET cc_start: 0.7837 (ptp) cc_final: 0.5853 (mmp) REVERT: D 201 HIS cc_start: 0.9237 (m170) cc_final: 0.8928 (m170) REVERT: D 240 LEU cc_start: 0.8023 (mt) cc_final: 0.7675 (mt) outliers start: 0 outliers final: 0 residues processed: 733 average time/residue: 0.2730 time to fit residues: 298.4614 Evaluate side-chains 643 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 643 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 159 optimal weight: 20.0000 chunk 72 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 183 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 108 optimal weight: 0.0010 overall best weight: 1.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 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** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 363 ASN ** 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** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN D 270 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.118863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.084577 restraints weight = 41455.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.087594 restraints weight = 21360.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.089681 restraints weight = 13390.170| |-----------------------------------------------------------------------------| r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3015 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3015 r_free = 0.3015 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 = 0.3015 r_free = 0.3015 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3015 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.6934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16386 Z= 0.154 Angle : 0.614 8.685 22134 Z= 0.324 Chirality : 0.043 0.314 2360 Planarity : 0.003 0.040 2818 Dihedral : 10.804 177.932 2242 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.19), residues: 1932 helix: 1.17 (0.15), residues: 1125 sheet: -0.31 (0.40), residues: 134 loop : 0.05 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 124 HIS 0.005 0.001 HIS A 438 PHE 0.028 0.002 PHE C 166 TYR 0.031 0.001 TYR D 142 ARG 0.010 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 871) hydrogen bonds : angle 4.82376 ( 2571) covalent geometry : bond 0.00343 (16386) covalent geometry : angle 0.61390 (22134) *********************** 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 738 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 738 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9236 (tptp) cc_final: 0.8916 (tppt) REVERT: A 12 LEU cc_start: 0.9609 (mt) cc_final: 0.9263 (mt) REVERT: A 65 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8106 (mp0) REVERT: A 107 LYS cc_start: 0.9218 (mttm) cc_final: 0.8775 (mtpp) REVERT: A 129 PHE cc_start: 0.9548 (m-10) cc_final: 0.9278 (m-10) REVERT: A 147 GLN cc_start: 0.9417 (mt0) cc_final: 0.8759 (mt0) REVERT: A 149 TYR cc_start: 0.9316 (t80) cc_final: 0.8705 (t80) REVERT: A 172 LEU cc_start: 0.9530 (mp) cc_final: 0.9225 (mp) REVERT: A 181 ASP cc_start: 0.8890 (m-30) cc_final: 0.8572 (m-30) REVERT: A 195 LEU cc_start: 0.9735 (mt) cc_final: 0.9491 (mt) REVERT: A 214 LYS cc_start: 0.8823 (tppt) cc_final: 0.8577 (tppt) REVERT: A 223 VAL cc_start: 0.9721 (m) cc_final: 0.9048 (p) REVERT: A 227 MET cc_start: 0.9278 (mtm) cc_final: 0.8818 (mtm) REVERT: A 232 ASN cc_start: 0.8636 (m-40) cc_final: 0.8432 (m-40) REVERT: A 255 HIS cc_start: 0.8556 (t-90) cc_final: 0.8256 (t-90) REVERT: A 257 ASP cc_start: 0.9091 (m-30) cc_final: 0.8825 (m-30) REVERT: A 262 LEU cc_start: 0.9887 (mt) cc_final: 0.9602 (mt) REVERT: A 276 LYS cc_start: 0.9038 (mmpt) cc_final: 0.8696 (mmtm) REVERT: A 301 PHE cc_start: 0.9152 (m-10) cc_final: 0.8609 (m-10) REVERT: A 322 MET cc_start: 0.8522 (mmm) cc_final: 0.8095 (mmm) REVERT: A 335 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7828 (mm-30) REVERT: A 344 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8591 (mt-10) REVERT: A 345 LYS cc_start: 0.9776 (ttpt) cc_final: 0.9468 (ttmt) REVERT: A 349 LEU cc_start: 0.9701 (mt) cc_final: 0.9466 (mt) REVERT: A 350 ARG cc_start: 0.8997 (mtp-110) cc_final: 0.8594 (mtp180) REVERT: A 375 LYS cc_start: 0.9021 (mmtt) cc_final: 0.8784 (mmtm) REVERT: A 390 GLN cc_start: 0.8957 (mt0) cc_final: 0.8709 (mt0) REVERT: A 393 SER cc_start: 0.9313 (m) cc_final: 0.8193 (t) REVERT: A 402 GLU cc_start: 0.8217 (mp0) cc_final: 0.7232 (mp0) REVERT: A 407 ILE cc_start: 0.9315 (mt) cc_final: 0.8985 (mt) REVERT: A 415 ASN cc_start: 0.9344 (t0) cc_final: 0.9006 (t0) REVERT: A 444 ASP cc_start: 0.8732 (t0) cc_final: 0.8175 (t0) REVERT: A 459 LYS cc_start: 0.8991 (mttp) cc_final: 0.8378 (mtmm) REVERT: A 493 MET cc_start: 0.8983 (tmm) cc_final: 0.8417 (tmm) REVERT: A 501 GLN cc_start: 0.9362 (tt0) cc_final: 0.8758 (tm-30) REVERT: A 515 ASP cc_start: 0.8908 (m-30) cc_final: 0.8576 (m-30) REVERT: A 550 MET cc_start: 0.8226 (mtm) cc_final: 0.7688 (mtm) REVERT: A 561 LEU cc_start: 0.9404 (tp) cc_final: 0.8933 (tp) REVERT: A 571 TYR cc_start: 0.8602 (t80) cc_final: 0.8228 (t80) REVERT: A 598 MET cc_start: 0.8492 (mtp) cc_final: 0.7754 (mtp) REVERT: A 601 ILE cc_start: 0.9577 (mm) cc_final: 0.9289 (tp) REVERT: A 615 MET cc_start: 0.9111 (mmt) cc_final: 0.8896 (mmm) REVERT: A 640 MET cc_start: 0.9332 (tpp) cc_final: 0.8731 (tpp) REVERT: A 645 GLN cc_start: 0.9211 (tp40) cc_final: 0.8869 (tp-100) REVERT: A 654 PHE cc_start: 0.9340 (t80) cc_final: 0.9113 (t80) REVERT: A 667 LEU cc_start: 0.9376 (tt) cc_final: 0.9148 (tt) REVERT: A 686 ARG cc_start: 0.8438 (mmm-85) cc_final: 0.7799 (mtm180) REVERT: B 8 LYS cc_start: 0.9402 (tptt) cc_final: 0.9053 (tppt) REVERT: B 12 LEU cc_start: 0.9625 (mt) cc_final: 0.9391 (mt) REVERT: B 41 ILE cc_start: 0.9440 (mm) cc_final: 0.9211 (mt) REVERT: B 55 LEU cc_start: 0.9782 (mt) cc_final: 0.9551 (mt) REVERT: B 87 LYS cc_start: 0.9339 (tptt) cc_final: 0.8934 (tttt) REVERT: B 88 LYS cc_start: 0.9006 (tttm) cc_final: 0.8718 (tttp) REVERT: B 111 LYS cc_start: 0.9690 (mptt) cc_final: 0.9414 (mmtt) REVERT: B 119 GLU cc_start: 0.9375 (mp0) cc_final: 0.9043 (mp0) REVERT: B 139 GLU cc_start: 0.9396 (mm-30) cc_final: 0.9178 (mm-30) REVERT: B 143 LEU cc_start: 0.9237 (tp) cc_final: 0.8304 (tp) REVERT: B 148 GLU cc_start: 0.9111 (mp0) cc_final: 0.7885 (mp0) REVERT: B 149 TYR cc_start: 0.9232 (t80) cc_final: 0.8391 (t80) REVERT: B 167 LEU cc_start: 0.9266 (mt) cc_final: 0.9040 (mt) REVERT: B 168 VAL cc_start: 0.9380 (t) cc_final: 0.9149 (m) REVERT: B 172 LEU cc_start: 0.9381 (mp) cc_final: 0.9029 (mp) REVERT: B 181 ASP cc_start: 0.8650 (m-30) cc_final: 0.8307 (m-30) REVERT: B 184 ARG cc_start: 0.9328 (tpp80) cc_final: 0.8962 (tpp80) REVERT: B 191 GLN cc_start: 0.9139 (mm110) cc_final: 0.8861 (mt0) REVERT: B 211 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8474 (mm-30) REVERT: B 228 LYS cc_start: 0.9520 (mmmm) cc_final: 0.9126 (mmtt) REVERT: B 239 GLN cc_start: 0.8933 (tm-30) cc_final: 0.8321 (tm-30) REVERT: B 252 ASN cc_start: 0.9440 (t0) cc_final: 0.8940 (t0) REVERT: B 263 ASP cc_start: 0.9294 (m-30) cc_final: 0.8865 (m-30) REVERT: B 274 ARG cc_start: 0.8680 (tpp80) cc_final: 0.8438 (tpp80) REVERT: B 286 ASP cc_start: 0.8990 (m-30) cc_final: 0.8669 (m-30) REVERT: B 321 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8508 (tm-30) REVERT: B 322 MET cc_start: 0.9229 (mmm) cc_final: 0.8848 (mmm) REVERT: B 335 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8115 (mm-30) REVERT: B 348 MET cc_start: 0.9410 (ptm) cc_final: 0.9197 (ptp) REVERT: B 355 TYR cc_start: 0.8721 (m-10) cc_final: 0.8469 (m-10) REVERT: B 362 ASP cc_start: 0.8858 (m-30) cc_final: 0.8466 (m-30) REVERT: B 375 LYS cc_start: 0.8890 (mmtp) cc_final: 0.8644 (mmmm) REVERT: B 384 GLU cc_start: 0.8782 (pm20) cc_final: 0.8293 (pm20) REVERT: B 393 SER cc_start: 0.9287 (m) cc_final: 0.8986 (p) REVERT: B 398 ASP cc_start: 0.8683 (m-30) cc_final: 0.8456 (m-30) REVERT: B 402 GLU cc_start: 0.9045 (tp30) cc_final: 0.8783 (tp30) REVERT: B 403 ILE cc_start: 0.8879 (tp) cc_final: 0.8628 (tp) REVERT: B 410 ASN cc_start: 0.8860 (m-40) cc_final: 0.8597 (m-40) REVERT: B 415 ASN cc_start: 0.9322 (t0) cc_final: 0.8987 (t0) REVERT: B 426 GLU cc_start: 0.9006 (pm20) cc_final: 0.8603 (pm20) REVERT: B 543 ILE cc_start: 0.9728 (mm) cc_final: 0.9437 (mm) REVERT: B 575 ARG cc_start: 0.8864 (mtm-85) cc_final: 0.8575 (mtm-85) REVERT: B 576 LEU cc_start: 0.9458 (mt) cc_final: 0.9223 (mt) REVERT: B 588 GLN cc_start: 0.9398 (mm-40) cc_final: 0.8985 (mm-40) REVERT: B 615 MET cc_start: 0.9472 (mmp) cc_final: 0.9067 (mmp) REVERT: B 640 MET cc_start: 0.9127 (tpp) cc_final: 0.8527 (tpp) REVERT: B 671 ASP cc_start: 0.8947 (m-30) cc_final: 0.8728 (m-30) REVERT: B 680 LYS cc_start: 0.9120 (mttt) cc_final: 0.8876 (mtpt) REVERT: C 17 PHE cc_start: 0.9091 (p90) cc_final: 0.8512 (p90) REVERT: C 21 PHE cc_start: 0.9319 (m-80) cc_final: 0.8676 (m-80) REVERT: C 79 GLU cc_start: 0.6620 (tm-30) cc_final: 0.5488 (pt0) REVERT: C 101 HIS cc_start: 0.8273 (m170) cc_final: 0.7744 (m170) REVERT: C 157 MET cc_start: 0.9280 (mtm) cc_final: 0.9002 (mtm) REVERT: C 168 PHE cc_start: 0.8831 (m-80) cc_final: 0.8492 (m-80) REVERT: C 173 TYR cc_start: 0.7658 (t80) cc_final: 0.6694 (t80) REVERT: C 174 TYR cc_start: 0.7784 (t80) cc_final: 0.7233 (t80) REVERT: C 177 TYR cc_start: 0.9113 (t80) cc_final: 0.8857 (t80) REVERT: C 185 MET cc_start: 0.6508 (mmm) cc_final: 0.5452 (mpp) REVERT: C 201 HIS cc_start: 0.9194 (m170) cc_final: 0.8943 (m170) REVERT: C 208 LEU cc_start: 0.8876 (mm) cc_final: 0.8559 (mt) REVERT: C 227 PHE cc_start: 0.9271 (m-80) cc_final: 0.9000 (m-10) REVERT: C 231 LEU cc_start: 0.9137 (mt) cc_final: 0.8790 (pp) REVERT: C 233 ASN cc_start: 0.9438 (m110) cc_final: 0.8900 (m110) REVERT: C 252 LEU cc_start: 0.7472 (mt) cc_final: 0.7180 (mt) REVERT: C 278 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8413 (pm20) REVERT: C 281 ASP cc_start: 0.8639 (m-30) cc_final: 0.8383 (m-30) REVERT: D 30 TRP cc_start: 0.8185 (p-90) cc_final: 0.7257 (p-90) REVERT: D 96 MET cc_start: 0.9010 (mmm) cc_final: 0.8795 (mmm) REVERT: D 148 ASP cc_start: 0.7097 (m-30) cc_final: 0.6815 (m-30) REVERT: D 184 LEU cc_start: 0.6992 (mt) cc_final: 0.6769 (mt) REVERT: D 240 LEU cc_start: 0.8077 (mt) cc_final: 0.7808 (mt) outliers start: 0 outliers final: 0 residues processed: 738 average time/residue: 0.2648 time to fit residues: 291.8483 Evaluate side-chains 630 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 630 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 111 optimal weight: 7.9990 chunk 102 optimal weight: 0.6980 chunk 182 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 96 optimal weight: 0.9980 chunk 115 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 chunk 27 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.120994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.087109 restraints weight = 41957.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.090212 restraints weight = 21786.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.092329 restraints weight = 13651.925| |-----------------------------------------------------------------------------| r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.7111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16386 Z= 0.150 Angle : 0.619 10.031 22134 Z= 0.325 Chirality : 0.043 0.275 2360 Planarity : 0.003 0.040 2818 Dihedral : 10.605 176.497 2242 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.19), residues: 1932 helix: 1.16 (0.15), residues: 1140 sheet: -0.36 (0.40), residues: 134 loop : 0.08 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 124 HIS 0.007 0.001 HIS D 201 PHE 0.029 0.002 PHE D 109 TYR 0.030 0.002 TYR D 142 ARG 0.011 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.03819 ( 871) hydrogen bonds : angle 4.85236 ( 2571) covalent geometry : bond 0.00338 (16386) covalent geometry : angle 0.61879 (22134) *********************** 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 729 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 729 time to evaluate : 1.858 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: A 8 LYS cc_start: 0.9221 (tptp) cc_final: 0.8907 (tppt) REVERT: A 12 LEU cc_start: 0.9566 (mt) cc_final: 0.9205 (mt) REVERT: A 65 GLU cc_start: 0.8875 (mm-30) cc_final: 0.8467 (mp0) REVERT: A 107 LYS cc_start: 0.9253 (mttm) cc_final: 0.8815 (mtpp) REVERT: A 129 PHE cc_start: 0.9492 (m-10) cc_final: 0.9256 (m-10) REVERT: A 147 GLN cc_start: 0.9351 (mt0) cc_final: 0.8680 (mt0) REVERT: A 149 TYR cc_start: 0.9207 (t80) cc_final: 0.8643 (t80) REVERT: A 181 ASP cc_start: 0.8841 (m-30) cc_final: 0.8578 (m-30) REVERT: A 190 MET cc_start: 0.9254 (mtm) cc_final: 0.9001 (mtm) REVERT: A 195 LEU cc_start: 0.9733 (mt) cc_final: 0.9491 (mt) REVERT: A 214 LYS cc_start: 0.8820 (tppt) cc_final: 0.8575 (tppt) REVERT: A 223 VAL cc_start: 0.9767 (m) cc_final: 0.9167 (p) REVERT: A 227 MET cc_start: 0.9279 (mtm) cc_final: 0.8911 (mtm) REVERT: A 228 LYS cc_start: 0.9375 (mmmt) cc_final: 0.8813 (mmtt) REVERT: A 255 HIS cc_start: 0.8544 (t-90) cc_final: 0.8209 (t-90) REVERT: A 257 ASP cc_start: 0.9072 (m-30) cc_final: 0.8819 (m-30) REVERT: A 262 LEU cc_start: 0.9873 (mt) cc_final: 0.9553 (mt) REVERT: A 276 LYS cc_start: 0.9025 (mmpt) cc_final: 0.8710 (mmtm) REVERT: A 301 PHE cc_start: 0.9148 (m-10) cc_final: 0.8632 (m-10) REVERT: A 318 ASP cc_start: 0.9330 (t0) cc_final: 0.8588 (t0) REVERT: A 322 MET cc_start: 0.9011 (mmm) cc_final: 0.8532 (mmm) REVERT: A 335 GLU cc_start: 0.8125 (mm-30) cc_final: 0.7881 (mm-30) REVERT: A 344 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8563 (mt-10) REVERT: A 349 LEU cc_start: 0.9701 (mt) cc_final: 0.9454 (mt) REVERT: A 350 ARG cc_start: 0.8984 (mtp-110) cc_final: 0.8638 (mtp180) REVERT: A 365 ASN cc_start: 0.9257 (m-40) cc_final: 0.9052 (m110) REVERT: A 390 GLN cc_start: 0.8897 (mt0) cc_final: 0.8686 (mt0) REVERT: A 393 SER cc_start: 0.9343 (m) cc_final: 0.8843 (t) REVERT: A 402 GLU cc_start: 0.8234 (mp0) cc_final: 0.7819 (mp0) REVERT: A 415 ASN cc_start: 0.9342 (t0) cc_final: 0.9022 (t0) REVERT: A 444 ASP cc_start: 0.8708 (t0) cc_final: 0.8164 (t0) REVERT: A 459 LYS cc_start: 0.9022 (mttp) cc_final: 0.8373 (mtmm) REVERT: A 493 MET cc_start: 0.8960 (tmm) cc_final: 0.8573 (tmm) REVERT: A 501 GLN cc_start: 0.9359 (tt0) cc_final: 0.8755 (tm-30) REVERT: A 515 ASP cc_start: 0.8968 (m-30) cc_final: 0.8696 (m-30) REVERT: A 561 LEU cc_start: 0.9427 (tp) cc_final: 0.8957 (tp) REVERT: A 571 TYR cc_start: 0.8673 (t80) cc_final: 0.8177 (t80) REVERT: A 595 MET cc_start: 0.9027 (mmp) cc_final: 0.8386 (mmp) REVERT: A 598 MET cc_start: 0.8565 (mtp) cc_final: 0.7744 (mtp) REVERT: A 599 GLU cc_start: 0.9110 (pm20) cc_final: 0.8839 (pm20) REVERT: A 601 ILE cc_start: 0.9554 (mm) cc_final: 0.9106 (tp) REVERT: A 615 MET cc_start: 0.9204 (mmt) cc_final: 0.8873 (mmm) REVERT: A 628 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8431 (mm-30) REVERT: A 640 MET cc_start: 0.9340 (tpp) cc_final: 0.8754 (tpp) REVERT: A 645 GLN cc_start: 0.9229 (tp40) cc_final: 0.8886 (tp-100) REVERT: A 657 PHE cc_start: 0.9056 (m-80) cc_final: 0.8672 (m-80) REVERT: A 667 LEU cc_start: 0.9390 (tt) cc_final: 0.9153 (tt) REVERT: A 686 ARG cc_start: 0.8460 (mmm-85) cc_final: 0.7767 (mtm180) REVERT: B 8 LYS cc_start: 0.9399 (tptt) cc_final: 0.9054 (tppt) REVERT: B 12 LEU cc_start: 0.9614 (mt) cc_final: 0.9380 (mt) REVERT: B 16 ILE cc_start: 0.9344 (tp) cc_final: 0.9003 (tp) REVERT: B 20 LYS cc_start: 0.9680 (tmtt) cc_final: 0.9467 (tptp) REVERT: B 21 ASP cc_start: 0.8768 (t70) cc_final: 0.8487 (t0) REVERT: B 41 ILE cc_start: 0.9465 (mm) cc_final: 0.9178 (mt) REVERT: B 55 LEU cc_start: 0.9774 (mt) cc_final: 0.9552 (mt) REVERT: B 87 LYS cc_start: 0.9329 (tptt) cc_final: 0.8868 (tttt) REVERT: B 88 LYS cc_start: 0.8983 (tttm) cc_final: 0.8703 (tttp) REVERT: B 111 LYS cc_start: 0.9669 (mptt) cc_final: 0.9376 (mmtt) REVERT: B 117 ARG cc_start: 0.9375 (mmm-85) cc_final: 0.8944 (mmm-85) REVERT: B 119 GLU cc_start: 0.9349 (mp0) cc_final: 0.9054 (mp0) REVERT: B 143 LEU cc_start: 0.9251 (tp) cc_final: 0.8383 (tp) REVERT: B 148 GLU cc_start: 0.9078 (mp0) cc_final: 0.8010 (mp0) REVERT: B 149 TYR cc_start: 0.9202 (t80) cc_final: 0.8428 (t80) REVERT: B 150 GLN cc_start: 0.9497 (tp-100) cc_final: 0.9206 (tp-100) REVERT: B 172 LEU cc_start: 0.9398 (mp) cc_final: 0.9067 (mp) REVERT: B 173 LEU cc_start: 0.9409 (mt) cc_final: 0.9201 (mt) REVERT: B 181 ASP cc_start: 0.8642 (m-30) cc_final: 0.8289 (m-30) REVERT: B 184 ARG cc_start: 0.9291 (tpp80) cc_final: 0.8934 (tpp80) REVERT: B 211 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8409 (mm-30) REVERT: B 228 LYS cc_start: 0.9476 (mmmm) cc_final: 0.9246 (tppt) REVERT: B 239 GLN cc_start: 0.8899 (tm-30) cc_final: 0.8318 (tm-30) REVERT: B 252 ASN cc_start: 0.9455 (t0) cc_final: 0.9042 (t0) REVERT: B 263 ASP cc_start: 0.9258 (m-30) cc_final: 0.8838 (m-30) REVERT: B 274 ARG cc_start: 0.8696 (tpp80) cc_final: 0.8440 (tpp80) REVERT: B 321 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8551 (tm-30) REVERT: B 322 MET cc_start: 0.9234 (mmm) cc_final: 0.8828 (mmm) REVERT: B 335 GLU cc_start: 0.8485 (mm-30) cc_final: 0.8106 (mm-30) REVERT: B 348 MET cc_start: 0.9393 (ptm) cc_final: 0.9179 (ptp) REVERT: B 355 TYR cc_start: 0.8793 (m-10) cc_final: 0.8330 (m-10) REVERT: B 374 SER cc_start: 0.9412 (t) cc_final: 0.8916 (p) REVERT: B 375 LYS cc_start: 0.8888 (mmtp) cc_final: 0.8662 (mmmm) REVERT: B 384 GLU cc_start: 0.8801 (pm20) cc_final: 0.8298 (pm20) REVERT: B 393 SER cc_start: 0.9385 (m) cc_final: 0.9136 (p) REVERT: B 402 GLU cc_start: 0.9009 (tp30) cc_final: 0.8797 (tp30) REVERT: B 403 ILE cc_start: 0.9033 (tp) cc_final: 0.8675 (tp) REVERT: B 410 ASN cc_start: 0.8849 (m-40) cc_final: 0.8609 (m-40) REVERT: B 415 ASN cc_start: 0.9342 (t0) cc_final: 0.9023 (t0) REVERT: B 426 GLU cc_start: 0.9041 (pm20) cc_final: 0.8748 (pm20) REVERT: B 543 ILE cc_start: 0.9732 (mm) cc_final: 0.9456 (mm) REVERT: B 575 ARG cc_start: 0.8789 (mtm-85) cc_final: 0.8571 (mtm-85) REVERT: B 576 LEU cc_start: 0.9449 (mt) cc_final: 0.9225 (mt) REVERT: B 588 GLN cc_start: 0.9294 (mm-40) cc_final: 0.8930 (mm-40) REVERT: B 612 TYR cc_start: 0.8558 (m-10) cc_final: 0.8262 (m-10) REVERT: B 615 MET cc_start: 0.9448 (mmp) cc_final: 0.9100 (mmp) REVERT: B 634 MET cc_start: 0.9332 (mmm) cc_final: 0.8837 (mpp) REVERT: B 640 MET cc_start: 0.9085 (tpp) cc_final: 0.8469 (tpp) REVERT: B 671 ASP cc_start: 0.8960 (m-30) cc_final: 0.8748 (m-30) REVERT: B 680 LYS cc_start: 0.9133 (mttt) cc_final: 0.8907 (mtpt) REVERT: B 686 ARG cc_start: 0.8682 (ttm110) cc_final: 0.8238 (mtt90) REVERT: C 17 PHE cc_start: 0.9063 (p90) cc_final: 0.8503 (p90) REVERT: C 21 PHE cc_start: 0.9362 (m-80) cc_final: 0.8725 (m-80) REVERT: C 79 GLU cc_start: 0.6797 (tm-30) cc_final: 0.5551 (pt0) REVERT: C 101 HIS cc_start: 0.8205 (m170) cc_final: 0.7734 (m170) REVERT: C 123 GLU cc_start: 0.9603 (mm-30) cc_final: 0.9380 (mm-30) REVERT: C 157 MET cc_start: 0.9271 (mtm) cc_final: 0.8979 (mtm) REVERT: C 173 TYR cc_start: 0.7504 (t80) cc_final: 0.6691 (t80) REVERT: C 174 TYR cc_start: 0.7795 (t80) cc_final: 0.7016 (t80) REVERT: C 177 TYR cc_start: 0.9087 (t80) cc_final: 0.8814 (t80) REVERT: C 184 LEU cc_start: 0.4434 (mt) cc_final: 0.4090 (pp) REVERT: C 185 MET cc_start: 0.6432 (mmm) cc_final: 0.5549 (mpp) REVERT: C 201 HIS cc_start: 0.9137 (m170) cc_final: 0.8865 (m170) REVERT: C 208 LEU cc_start: 0.8995 (mm) cc_final: 0.8718 (mt) REVERT: C 252 LEU cc_start: 0.7396 (mt) cc_final: 0.7118 (mt) REVERT: C 278 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8405 (pm20) REVERT: C 281 ASP cc_start: 0.8664 (m-30) cc_final: 0.8399 (m-30) REVERT: D 30 TRP cc_start: 0.8174 (p-90) cc_final: 0.7145 (p-90) REVERT: D 96 MET cc_start: 0.9033 (mmm) cc_final: 0.8769 (mmm) REVERT: D 109 PHE cc_start: 0.8388 (m-80) cc_final: 0.7662 (m-80) REVERT: D 148 ASP cc_start: 0.7140 (m-30) cc_final: 0.6887 (m-30) REVERT: D 167 LEU cc_start: 0.9440 (mm) cc_final: 0.9238 (mm) REVERT: D 176 LEU cc_start: 0.9602 (mt) cc_final: 0.9331 (tp) REVERT: D 185 MET cc_start: 0.7450 (ptp) cc_final: 0.6390 (mmp) REVERT: D 201 HIS cc_start: 0.9250 (m170) cc_final: 0.8921 (m170) REVERT: D 240 LEU cc_start: 0.8063 (mt) cc_final: 0.7748 (mt) REVERT: D 270 ASN cc_start: 0.8674 (m110) cc_final: 0.8413 (m110) REVERT: D 311 THR cc_start: 0.9300 (p) cc_final: 0.8663 (t) outliers start: 0 outliers final: 0 residues processed: 729 average time/residue: 0.2728 time to fit residues: 295.7353 Evaluate side-chains 631 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 631 time to evaluate : 1.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 137 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 160 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 120 optimal weight: 6.9990 chunk 135 optimal weight: 0.4980 chunk 148 optimal weight: 9.9990 chunk 127 optimal weight: 0.4980 chunk 68 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** 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 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.118935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.085164 restraints weight = 42300.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.088289 restraints weight = 22018.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.090410 restraints weight = 13775.076| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3046 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3046 r_free = 0.3046 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3046 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.7266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16386 Z= 0.174 Angle : 0.649 9.919 22134 Z= 0.340 Chirality : 0.044 0.264 2360 Planarity : 0.004 0.050 2818 Dihedral : 10.485 175.660 2242 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.06 % Allowed : 0.06 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.19), residues: 1932 helix: 1.00 (0.15), residues: 1154 sheet: -0.38 (0.40), residues: 134 loop : 0.05 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP D 124 HIS 0.007 0.001 HIS A 469 PHE 0.034 0.002 PHE D 109 TYR 0.031 0.002 TYR D 142 ARG 0.008 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 871) hydrogen bonds : angle 4.87925 ( 2571) covalent geometry : bond 0.00388 (16386) covalent geometry : angle 0.64894 (22134) ********************** 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 718 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 717 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9234 (tptp) cc_final: 0.8926 (tppt) REVERT: A 12 LEU cc_start: 0.9566 (mt) cc_final: 0.9208 (mt) REVERT: A 65 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8488 (mp0) REVERT: A 107 LYS cc_start: 0.9277 (mttm) cc_final: 0.8818 (mtpp) REVERT: A 129 PHE cc_start: 0.9512 (m-10) cc_final: 0.9225 (m-10) REVERT: A 143 LEU cc_start: 0.9490 (tp) cc_final: 0.9019 (tp) REVERT: A 144 MET cc_start: 0.9127 (mmm) cc_final: 0.8779 (mmm) REVERT: A 147 GLN cc_start: 0.9398 (mt0) cc_final: 0.8749 (mt0) REVERT: A 149 TYR cc_start: 0.9477 (t80) cc_final: 0.8433 (t80) REVERT: A 164 ARG cc_start: 0.9232 (ptt90) cc_final: 0.8690 (ptt90) REVERT: A 172 LEU cc_start: 0.9559 (mp) cc_final: 0.9211 (mp) REVERT: A 181 ASP cc_start: 0.8890 (m-30) cc_final: 0.8601 (m-30) REVERT: A 190 MET cc_start: 0.9302 (mtm) cc_final: 0.9005 (mtm) REVERT: A 195 LEU cc_start: 0.9731 (mt) cc_final: 0.9493 (mt) REVERT: A 223 VAL cc_start: 0.9745 (m) cc_final: 0.9053 (p) REVERT: A 227 MET cc_start: 0.9291 (mtm) cc_final: 0.8808 (mtm) REVERT: A 257 ASP cc_start: 0.9074 (m-30) cc_final: 0.8812 (m-30) REVERT: A 262 LEU cc_start: 0.9899 (mt) cc_final: 0.9629 (mt) REVERT: A 276 LYS cc_start: 0.9059 (mmpt) cc_final: 0.8714 (mmpt) REVERT: A 301 PHE cc_start: 0.9146 (m-10) cc_final: 0.8633 (m-10) REVERT: A 318 ASP cc_start: 0.8801 (t0) cc_final: 0.8537 (t0) REVERT: A 321 GLU cc_start: 0.8495 (pm20) cc_final: 0.8159 (pm20) REVERT: A 335 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7847 (mm-30) REVERT: A 344 GLU cc_start: 0.9245 (mt-10) cc_final: 0.8595 (mt-10) REVERT: A 345 LYS cc_start: 0.9758 (ttpt) cc_final: 0.9558 (ttmt) REVERT: A 349 LEU cc_start: 0.9689 (mt) cc_final: 0.9469 (mt) REVERT: A 350 ARG cc_start: 0.8982 (mtp-110) cc_final: 0.8643 (mtp180) REVERT: A 365 ASN cc_start: 0.9151 (m-40) cc_final: 0.8923 (m110) REVERT: A 390 GLN cc_start: 0.8962 (mt0) cc_final: 0.8723 (mt0) REVERT: A 393 SER cc_start: 0.9334 (m) cc_final: 0.8819 (t) REVERT: A 402 GLU cc_start: 0.8243 (mp0) cc_final: 0.7821 (mp0) REVERT: A 407 ILE cc_start: 0.9359 (mt) cc_final: 0.9027 (mt) REVERT: A 415 ASN cc_start: 0.9363 (t0) cc_final: 0.9093 (t0) REVERT: A 421 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8618 (tm-30) REVERT: A 444 ASP cc_start: 0.8729 (t0) cc_final: 0.8187 (t0) REVERT: A 459 LYS cc_start: 0.9026 (mttp) cc_final: 0.8342 (mtmm) REVERT: A 493 MET cc_start: 0.8952 (tmm) cc_final: 0.8591 (tmm) REVERT: A 501 GLN cc_start: 0.9358 (tt0) cc_final: 0.8757 (tm-30) REVERT: A 515 ASP cc_start: 0.8969 (m-30) cc_final: 0.8729 (m-30) REVERT: A 561 LEU cc_start: 0.9434 (tp) cc_final: 0.8978 (tp) REVERT: A 571 TYR cc_start: 0.8824 (t80) cc_final: 0.8233 (t80) REVERT: A 595 MET cc_start: 0.9093 (mmp) cc_final: 0.8456 (mmp) REVERT: A 601 ILE cc_start: 0.9575 (mm) cc_final: 0.9348 (tp) REVERT: A 615 MET cc_start: 0.9207 (mmt) cc_final: 0.8876 (mmm) REVERT: A 628 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8454 (mm-30) REVERT: A 632 MET cc_start: 0.8390 (mpp) cc_final: 0.8169 (mpp) REVERT: A 640 MET cc_start: 0.9325 (tpp) cc_final: 0.8730 (tpp) REVERT: A 645 GLN cc_start: 0.9229 (tp40) cc_final: 0.8889 (tp-100) REVERT: A 654 PHE cc_start: 0.9222 (t80) cc_final: 0.8843 (t80) REVERT: A 657 PHE cc_start: 0.9080 (m-80) cc_final: 0.8676 (m-80) REVERT: A 667 LEU cc_start: 0.9395 (tt) cc_final: 0.9121 (tt) REVERT: A 686 ARG cc_start: 0.8444 (mmm-85) cc_final: 0.7697 (mtm180) REVERT: B 8 LYS cc_start: 0.9386 (tptt) cc_final: 0.9056 (tppt) REVERT: B 12 LEU cc_start: 0.9617 (mt) cc_final: 0.9397 (mt) REVERT: B 20 LYS cc_start: 0.9670 (tmtt) cc_final: 0.9462 (tptp) REVERT: B 21 ASP cc_start: 0.8738 (t70) cc_final: 0.8420 (t0) REVERT: B 41 ILE cc_start: 0.9472 (mm) cc_final: 0.9205 (mt) REVERT: B 55 LEU cc_start: 0.9787 (mt) cc_final: 0.9561 (mt) REVERT: B 87 LYS cc_start: 0.9333 (tptt) cc_final: 0.8927 (tttt) REVERT: B 88 LYS cc_start: 0.9007 (tttm) cc_final: 0.8724 (tttp) REVERT: B 99 LYS cc_start: 0.9541 (tppt) cc_final: 0.9088 (mmmm) REVERT: B 111 LYS cc_start: 0.9677 (mptt) cc_final: 0.9398 (mmtt) REVERT: B 117 ARG cc_start: 0.9366 (mmm-85) cc_final: 0.8973 (mmm-85) REVERT: B 119 GLU cc_start: 0.9346 (mp0) cc_final: 0.9098 (mp0) REVERT: B 139 GLU cc_start: 0.9301 (mm-30) cc_final: 0.8980 (mp0) REVERT: B 143 LEU cc_start: 0.9192 (tp) cc_final: 0.8305 (tp) REVERT: B 148 GLU cc_start: 0.9108 (mp0) cc_final: 0.7932 (mp0) REVERT: B 149 TYR cc_start: 0.9283 (t80) cc_final: 0.8484 (t80) REVERT: B 150 GLN cc_start: 0.9497 (tp-100) cc_final: 0.9172 (tp-100) REVERT: B 167 LEU cc_start: 0.9364 (mt) cc_final: 0.9046 (mt) REVERT: B 172 LEU cc_start: 0.9383 (mp) cc_final: 0.9095 (mp) REVERT: B 181 ASP cc_start: 0.8706 (m-30) cc_final: 0.8316 (m-30) REVERT: B 184 ARG cc_start: 0.9400 (tpp80) cc_final: 0.9094 (tpp80) REVERT: B 211 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8389 (mm-30) REVERT: B 238 ASP cc_start: 0.8554 (t0) cc_final: 0.8006 (t70) REVERT: B 239 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8313 (tm-30) REVERT: B 252 ASN cc_start: 0.9482 (t0) cc_final: 0.9033 (t0) REVERT: B 263 ASP cc_start: 0.9254 (m-30) cc_final: 0.8808 (m-30) REVERT: B 319 MET cc_start: 0.9244 (tpp) cc_final: 0.8937 (mmm) REVERT: B 321 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8447 (tm-30) REVERT: B 322 MET cc_start: 0.9198 (mmm) cc_final: 0.8286 (mmm) REVERT: B 335 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8104 (mm-30) REVERT: B 355 TYR cc_start: 0.8761 (m-10) cc_final: 0.8555 (m-10) REVERT: B 374 SER cc_start: 0.9441 (t) cc_final: 0.8950 (p) REVERT: B 375 LYS cc_start: 0.8916 (mmtp) cc_final: 0.8711 (mmmm) REVERT: B 384 GLU cc_start: 0.8871 (pm20) cc_final: 0.8374 (pm20) REVERT: B 403 ILE cc_start: 0.9098 (tp) cc_final: 0.8797 (tp) REVERT: B 410 ASN cc_start: 0.8746 (m-40) cc_final: 0.8327 (m-40) REVERT: B 415 ASN cc_start: 0.9367 (t0) cc_final: 0.9037 (t0) REVERT: B 447 ASN cc_start: 0.9193 (m-40) cc_final: 0.8488 (m110) REVERT: B 491 PHE cc_start: 0.9639 (t80) cc_final: 0.9294 (t80) REVERT: B 543 ILE cc_start: 0.9736 (mm) cc_final: 0.9530 (mm) REVERT: B 575 ARG cc_start: 0.8991 (mtm-85) cc_final: 0.8764 (mtm-85) REVERT: B 576 LEU cc_start: 0.9459 (mt) cc_final: 0.9231 (mt) REVERT: B 588 GLN cc_start: 0.9287 (mm-40) cc_final: 0.8916 (mm-40) REVERT: B 615 MET cc_start: 0.9428 (mmp) cc_final: 0.9093 (mmp) REVERT: B 640 MET cc_start: 0.9097 (tpp) cc_final: 0.8505 (tpp) REVERT: B 671 ASP cc_start: 0.8995 (m-30) cc_final: 0.8741 (m-30) REVERT: B 680 LYS cc_start: 0.9092 (mttt) cc_final: 0.8824 (mtpt) REVERT: C 17 PHE cc_start: 0.8997 (p90) cc_final: 0.8383 (p90) REVERT: C 21 PHE cc_start: 0.9367 (m-80) cc_final: 0.8702 (m-80) REVERT: C 79 GLU cc_start: 0.6893 (tm-30) cc_final: 0.6221 (pt0) REVERT: C 101 HIS cc_start: 0.8110 (m170) cc_final: 0.7618 (m170) REVERT: C 123 GLU cc_start: 0.9607 (mm-30) cc_final: 0.9374 (mm-30) REVERT: C 157 MET cc_start: 0.9268 (mtm) cc_final: 0.8971 (mtm) REVERT: C 173 TYR cc_start: 0.7463 (t80) cc_final: 0.6613 (t80) REVERT: C 174 TYR cc_start: 0.7613 (t80) cc_final: 0.7028 (t80) REVERT: C 176 LEU cc_start: 0.9252 (mt) cc_final: 0.9040 (mt) REVERT: C 177 TYR cc_start: 0.9114 (t80) cc_final: 0.8764 (t80) REVERT: C 185 MET cc_start: 0.6464 (mmm) cc_final: 0.5443 (mpp) REVERT: C 201 HIS cc_start: 0.9194 (m170) cc_final: 0.8923 (m170) REVERT: C 208 LEU cc_start: 0.9032 (mm) cc_final: 0.8750 (mt) REVERT: C 231 LEU cc_start: 0.9138 (mt) cc_final: 0.8807 (pp) REVERT: C 233 ASN cc_start: 0.9440 (m110) cc_final: 0.8899 (m110) REVERT: C 252 LEU cc_start: 0.7299 (mt) cc_final: 0.6989 (mt) REVERT: C 278 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8425 (pm20) REVERT: C 281 ASP cc_start: 0.8725 (m-30) cc_final: 0.8478 (m-30) REVERT: C 313 GLU cc_start: 0.9049 (tt0) cc_final: 0.8474 (tp30) REVERT: D 30 TRP cc_start: 0.8192 (p-90) cc_final: 0.7092 (p-90) REVERT: D 66 ASP cc_start: 0.6507 (p0) cc_final: 0.6002 (p0) REVERT: D 96 MET cc_start: 0.9073 (mmm) cc_final: 0.8840 (mmm) REVERT: D 109 PHE cc_start: 0.8382 (m-80) cc_final: 0.7618 (m-80) REVERT: D 148 ASP cc_start: 0.7140 (m-30) cc_final: 0.6894 (m-30) REVERT: D 176 LEU cc_start: 0.9592 (mt) cc_final: 0.9346 (tp) REVERT: D 185 MET cc_start: 0.7436 (ptp) cc_final: 0.6619 (mmp) REVERT: D 240 LEU cc_start: 0.8123 (mt) cc_final: 0.7799 (mt) REVERT: D 270 ASN cc_start: 0.8671 (m110) cc_final: 0.8449 (m110) outliers start: 1 outliers final: 0 residues processed: 718 average time/residue: 0.2719 time to fit residues: 292.8078 Evaluate side-chains 625 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 625 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 81 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 190 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN A 180 ASN ** A 410 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 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN ** B 650 GLN ** 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** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.122740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.089515 restraints weight = 41593.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.092690 restraints weight = 21496.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.094863 restraints weight = 13390.133| |-----------------------------------------------------------------------------| r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.7409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16386 Z= 0.134 Angle : 0.636 13.170 22134 Z= 0.329 Chirality : 0.043 0.230 2360 Planarity : 0.003 0.041 2818 Dihedral : 10.017 169.244 2242 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.19), residues: 1932 helix: 1.04 (0.15), residues: 1148 sheet: -0.30 (0.41), residues: 134 loop : -0.03 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP D 124 HIS 0.008 0.001 HIS D 201 PHE 0.030 0.002 PHE D 109 TYR 0.030 0.001 TYR D 142 ARG 0.009 0.001 ARG B 686 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 871) hydrogen bonds : angle 4.82279 ( 2571) covalent geometry : bond 0.00302 (16386) covalent geometry : angle 0.63634 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7020.27 seconds wall clock time: 122 minutes 5.32 seconds (7325.32 seconds total)