Starting phenix.real_space_refine on Sat May 17 16:11:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bze_45065/05_2025/9bze_45065_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bze_45065/05_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_45065/05_2025/9bze_45065.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bze_45065/05_2025/9bze_45065.map" model { file = "/net/cci-nas-00/data/ceres_data/9bze_45065/05_2025/9bze_45065_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bze_45065/05_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 9.02, per 1000 atoms: 0.56 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: 4.08 Conformation dependent library (CDL) restraints added in 2.0 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: 1.67 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: 5.53 Time building geometry restraints manager: 4.78 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: 14.890 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: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 34.890 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.410 ------------------------------------------------------------------------------- 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 : 1.680 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: 0.7878 (tp) REVERT: A 78 LYS cc_start: 0.8855 (tttt) cc_final: 0.8629 (ttmt) 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: 0.9091 (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: 0.8835 (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: 0.8347 (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: 0.8368 (ttmt) REVERT: A 362 ASP cc_start: 0.6076 (m-30) cc_final: 0.5756 (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: 0.7163 (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: 0.7261 (mmm) REVERT: A 435 SER cc_start: 0.9408 (p) cc_final: 0.8801 (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: 0.8128 (mt) REVERT: A 583 SER cc_start: 0.8180 (m) cc_final: 0.7872 (t) REVERT: A 590 SER cc_start: 0.9100 (p) cc_final: 0.8346 (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: 0.9167 (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: 0.8341 (mm) REVERT: B 99 LYS cc_start: 0.9064 (mmtt) cc_final: 0.8420 (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: 0.8224 (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: 0.7218 (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: 0.7955 (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: 0.8488 (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: 0.8667 (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: 0.7853 (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: 0.5353 (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: 0.6042 (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: 0.3960 (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: 0.3082 time to fit residues: 446.2306 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 : 1.675 ------------------------------------------------------------------------------- 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 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 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 127 GLN D 186 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.126430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.090574 restraints weight = 39313.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.093925 restraints weight = 20428.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.096173 restraints weight = 13004.801| |-----------------------------------------------------------------------------| r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3078 r_free = 0.3078 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3078 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16386 Z= 0.188 Angle : 0.625 7.854 22134 Z= 0.333 Chirality : 0.043 0.260 2360 Planarity : 0.004 0.033 2818 Dihedral : 11.390 178.564 2242 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.12 % Allowed : 2.86 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.36 (0.19), residues: 1932 helix: 1.36 (0.15), residues: 1110 sheet: 0.18 (0.42), residues: 126 loop : 0.49 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 124 HIS 0.010 0.001 HIS A 255 PHE 0.033 0.002 PHE C 168 TYR 0.020 0.002 TYR D 142 ARG 0.007 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.04712 ( 871) hydrogen bonds : angle 5.06298 ( 2571) covalent geometry : bond 0.00406 (16386) covalent geometry : angle 0.62466 (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 818 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 816 time to evaluate : 1.876 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: A 8 LYS cc_start: 0.9256 (tptp) cc_final: 0.8888 (tppt) REVERT: A 41 ILE cc_start: 0.9374 (mm) cc_final: 0.9049 (mm) REVERT: A 52 LYS cc_start: 0.9674 (tppt) cc_final: 0.9363 (tppp) REVERT: A 118 TYR cc_start: 0.9388 (t80) cc_final: 0.9139 (t80) REVERT: A 143 LEU cc_start: 0.9332 (tp) cc_final: 0.9122 (tp) REVERT: A 147 GLN cc_start: 0.9454 (mt0) cc_final: 0.8603 (mt0) REVERT: A 158 ASN cc_start: 0.9403 (m110) cc_final: 0.9012 (m-40) REVERT: A 162 LYS cc_start: 0.8797 (ttmm) cc_final: 0.8519 (ttmm) REVERT: A 181 ASP cc_start: 0.8900 (m-30) cc_final: 0.8693 (m-30) REVERT: A 191 GLN cc_start: 0.9122 (mm-40) cc_final: 0.8907 (mm-40) REVERT: A 195 LEU cc_start: 0.9597 (mt) cc_final: 0.9323 (mt) REVERT: A 227 MET cc_start: 0.9342 (mtm) cc_final: 0.9042 (mtm) REVERT: A 238 ASP cc_start: 0.8548 (p0) cc_final: 0.7968 (p0) REVERT: A 252 ASN cc_start: 0.9454 (t0) cc_final: 0.9241 (t0) REVERT: A 255 HIS cc_start: 0.8969 (t-90) cc_final: 0.8082 (t-90) REVERT: A 257 ASP cc_start: 0.9263 (m-30) cc_final: 0.8865 (m-30) REVERT: A 262 LEU cc_start: 0.9834 (mt) cc_final: 0.9591 (mt) REVERT: A 270 ASP cc_start: 0.8929 (t0) cc_final: 0.8676 (t0) REVERT: A 291 LEU cc_start: 0.9697 (mt) cc_final: 0.9479 (mt) REVERT: A 319 MET cc_start: 0.9240 (tpp) cc_final: 0.9010 (tpp) REVERT: A 335 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7623 (mm-30) REVERT: A 344 GLU cc_start: 0.9167 (mt-10) cc_final: 0.8900 (mt-10) REVERT: A 349 LEU cc_start: 0.9648 (mt) cc_final: 0.9376 (mt) REVERT: A 359 MET cc_start: 0.8959 (ttp) cc_final: 0.8704 (ttp) REVERT: A 366 LYS cc_start: 0.9275 (mtmm) cc_final: 0.8846 (mtmm) REVERT: A 375 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8540 (mmtm) REVERT: A 415 ASN cc_start: 0.9305 (t0) cc_final: 0.9070 (t0) REVERT: A 447 ASN cc_start: 0.8152 (m-40) cc_final: 0.7918 (t0) REVERT: A 466 MET cc_start: 0.9141 (ptt) cc_final: 0.8717 (ptt) REVERT: A 493 MET cc_start: 0.9082 (tmm) cc_final: 0.8718 (tmm) REVERT: A 494 MET cc_start: 0.9385 (mtp) cc_final: 0.9145 (mtp) REVERT: A 510 LYS cc_start: 0.8957 (mtpt) cc_final: 0.8611 (mtpt) REVERT: A 528 PHE cc_start: 0.9331 (m-80) cc_final: 0.8976 (m-80) REVERT: A 553 PRO cc_start: 0.9581 (Cg_exo) cc_final: 0.9130 (Cg_endo) REVERT: A 602 GLU cc_start: 0.7727 (pt0) cc_final: 0.7198 (pt0) REVERT: A 636 LYS cc_start: 0.9410 (mptt) cc_final: 0.9173 (mmmt) REVERT: A 645 GLN cc_start: 0.8854 (tp40) cc_final: 0.8601 (tp40) REVERT: A 655 THR cc_start: 0.9424 (m) cc_final: 0.9164 (t) REVERT: A 657 PHE cc_start: 0.8998 (m-80) cc_final: 0.8724 (m-80) REVERT: B 8 LYS cc_start: 0.9474 (tptt) cc_final: 0.9057 (tppt) REVERT: B 41 ILE cc_start: 0.9446 (mm) cc_final: 0.9122 (mt) REVERT: B 119 GLU cc_start: 0.9281 (mp0) cc_final: 0.9065 (mp0) REVERT: B 147 GLN cc_start: 0.8751 (mt0) cc_final: 0.8521 (mt0) REVERT: B 150 GLN cc_start: 0.9394 (tp40) cc_final: 0.9191 (tp-100) REVERT: B 172 LEU cc_start: 0.9172 (mp) cc_final: 0.8941 (mp) REVERT: B 184 ARG cc_start: 0.9414 (tpp80) cc_final: 0.9112 (tpp80) REVERT: B 191 GLN cc_start: 0.9276 (mm-40) cc_final: 0.9057 (mm-40) REVERT: B 202 ASN cc_start: 0.9312 (t0) cc_final: 0.8826 (t0) REVERT: B 211 GLU cc_start: 0.8720 (mm-30) cc_final: 0.8278 (mm-30) REVERT: B 236 TYR cc_start: 0.9324 (t80) cc_final: 0.8919 (t80) REVERT: B 288 PHE cc_start: 0.9409 (t80) cc_final: 0.9131 (t80) REVERT: B 308 LYS cc_start: 0.9423 (mttm) cc_final: 0.9082 (mmmm) REVERT: B 315 ASP cc_start: 0.8864 (p0) cc_final: 0.8349 (p0) REVERT: B 321 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8426 (tm-30) REVERT: B 322 MET cc_start: 0.8839 (mmm) cc_final: 0.8411 (mmm) REVERT: B 348 MET cc_start: 0.9506 (ptm) cc_final: 0.9130 (ptm) REVERT: B 374 SER cc_start: 0.9091 (t) cc_final: 0.8188 (p) REVERT: B 375 LYS cc_start: 0.9169 (mttm) cc_final: 0.8960 (mmmm) REVERT: B 378 PHE cc_start: 0.9191 (p90) cc_final: 0.8939 (p90) REVERT: B 387 GLN cc_start: 0.9218 (mt0) cc_final: 0.9013 (mt0) REVERT: B 390 GLN cc_start: 0.9221 (mt0) cc_final: 0.8981 (mm110) REVERT: B 393 SER cc_start: 0.9371 (m) cc_final: 0.9032 (p) REVERT: B 398 ASP cc_start: 0.8114 (t0) cc_final: 0.7877 (t0) REVERT: B 410 ASN cc_start: 0.8784 (m110) cc_final: 0.8292 (m110) REVERT: B 423 LYS cc_start: 0.9573 (mttt) cc_final: 0.9284 (mppt) REVERT: B 474 GLN cc_start: 0.8777 (mt0) cc_final: 0.8524 (mt0) REVERT: B 493 MET cc_start: 0.9661 (tmm) cc_final: 0.9411 (tmm) REVERT: B 516 GLN cc_start: 0.8798 (tp-100) cc_final: 0.8065 (tp40) REVERT: B 543 ILE cc_start: 0.9721 (mm) cc_final: 0.9424 (mm) REVERT: B 558 TRP cc_start: 0.9315 (m100) cc_final: 0.8577 (m100) REVERT: B 565 VAL cc_start: 0.9812 (t) cc_final: 0.9557 (p) REVERT: B 575 ARG cc_start: 0.8804 (mtm-85) cc_final: 0.8411 (mtm-85) REVERT: B 612 TYR cc_start: 0.9146 (m-80) cc_final: 0.8548 (m-10) REVERT: B 615 MET cc_start: 0.9157 (mmp) cc_final: 0.8714 (mmp) REVERT: B 639 ASP cc_start: 0.9212 (m-30) cc_final: 0.8840 (m-30) REVERT: B 640 MET cc_start: 0.9427 (tpp) cc_final: 0.9088 (tpp) REVERT: B 677 ARG cc_start: 0.9370 (mmm-85) cc_final: 0.9070 (mmm-85) REVERT: C 35 ILE cc_start: 0.7101 (tt) cc_final: 0.6854 (tt) REVERT: C 93 MET cc_start: 0.8719 (ttm) cc_final: 0.8397 (ttp) REVERT: C 101 HIS cc_start: 0.8020 (m170) cc_final: 0.6733 (m170) REVERT: C 123 GLU cc_start: 0.9611 (mm-30) cc_final: 0.9298 (mm-30) REVERT: C 157 MET cc_start: 0.9184 (mtm) cc_final: 0.8739 (mtm) REVERT: C 158 VAL cc_start: 0.9632 (t) cc_final: 0.9101 (t) REVERT: C 162 TYR cc_start: 0.9293 (m-10) cc_final: 0.8570 (m-10) REVERT: C 163 LEU cc_start: 0.9628 (tt) cc_final: 0.9250 (tt) REVERT: C 173 TYR cc_start: 0.7396 (t80) cc_final: 0.6453 (t80) REVERT: C 201 HIS cc_start: 0.9128 (m170) cc_final: 0.8768 (m170) REVERT: C 229 ILE cc_start: 0.6085 (mt) cc_final: 0.5622 (mm) REVERT: C 233 ASN cc_start: 0.9287 (m110) cc_final: 0.8812 (m110) REVERT: C 239 GLU cc_start: 0.9476 (pt0) cc_final: 0.9159 (pt0) REVERT: C 260 ILE cc_start: 0.6878 (pt) cc_final: 0.6470 (pt) REVERT: C 278 GLU cc_start: 0.8468 (mm-30) cc_final: 0.7762 (pm20) REVERT: D 20 MET cc_start: 0.8970 (mtm) cc_final: 0.8722 (mpp) REVERT: D 96 MET cc_start: 0.8991 (mmm) cc_final: 0.8785 (mmt) REVERT: D 139 VAL cc_start: 0.8274 (t) cc_final: 0.7936 (m) REVERT: D 148 ASP cc_start: 0.7459 (m-30) cc_final: 0.7145 (m-30) REVERT: D 184 LEU cc_start: 0.6774 (mt) cc_final: 0.6520 (mt) REVERT: D 186 GLN cc_start: 0.7762 (mm110) cc_final: 0.7389 (mm110) REVERT: D 281 ASP cc_start: 0.8147 (p0) cc_final: 0.7786 (t0) REVERT: D 315 LEU cc_start: 0.9284 (tp) cc_final: 0.8962 (tp) outliers start: 2 outliers final: 0 residues processed: 817 average time/residue: 0.2739 time to fit residues: 328.9956 Evaluate side-chains 658 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 658 time to evaluate : 1.745 ------------------------------------------------------------------------------- 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: 0.9990 chunk 175 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 47 optimal weight: 9.9990 chunk 191 optimal weight: 0.8980 chunk 57 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 chunk 189 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN A 668 ASN B 19 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN 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 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN ** C 238 ASN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.114574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.079929 restraints weight = 41788.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.083019 restraints weight = 21711.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.085115 restraints weight = 13633.029| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.5514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 16386 Z= 0.301 Angle : 0.691 8.648 22134 Z= 0.368 Chirality : 0.045 0.254 2360 Planarity : 0.004 0.038 2818 Dihedral : 11.406 172.661 2242 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.23 % Allowed : 3.55 % Favored : 96.21 % 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: 1.13 (0.19), residues: 1932 helix: 1.13 (0.15), residues: 1145 sheet: 0.24 (0.42), residues: 126 loop : 0.39 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 124 HIS 0.008 0.002 HIS B 675 PHE 0.028 0.003 PHE A 654 TYR 0.040 0.002 TYR B 574 ARG 0.008 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.04366 ( 871) hydrogen bonds : angle 5.06889 ( 2571) covalent geometry : bond 0.00624 (16386) covalent geometry : angle 0.69066 (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 759 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 755 time to evaluate : 1.769 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: 0.9210 (tptp) cc_final: 0.8890 (tppt) REVERT: A 12 LEU cc_start: 0.9669 (mt) cc_final: 0.9397 (mt) REVERT: A 41 ILE cc_start: 0.9578 (mm) cc_final: 0.9373 (mm) REVERT: A 95 MET cc_start: 0.9200 (mmm) cc_final: 0.8851 (tpp) REVERT: A 107 LYS cc_start: 0.9146 (mttm) cc_final: 0.8768 (mtpp) REVERT: A 129 PHE cc_start: 0.9547 (m-10) cc_final: 0.9267 (m-80) REVERT: A 147 GLN cc_start: 0.9426 (mt0) cc_final: 0.8656 (mt0) REVERT: A 149 TYR cc_start: 0.9266 (t80) cc_final: 0.8294 (t80) REVERT: A 157 LEU cc_start: 0.9441 (tp) cc_final: 0.9105 (tp) REVERT: A 158 ASN cc_start: 0.9430 (m110) cc_final: 0.9055 (m-40) REVERT: A 181 ASP cc_start: 0.9013 (m-30) cc_final: 0.8673 (m-30) REVERT: A 195 LEU cc_start: 0.9712 (mt) cc_final: 0.9432 (mt) REVERT: A 214 LYS cc_start: 0.8954 (tppt) cc_final: 0.8733 (tppt) REVERT: A 223 VAL cc_start: 0.9781 (m) cc_final: 0.9252 (p) REVERT: A 227 MET cc_start: 0.9336 (mtm) cc_final: 0.8923 (mtm) REVERT: A 255 HIS cc_start: 0.8895 (t-90) cc_final: 0.8023 (t-90) REVERT: A 257 ASP cc_start: 0.9183 (m-30) cc_final: 0.8944 (m-30) REVERT: A 262 LEU cc_start: 0.9866 (mt) cc_final: 0.9640 (mt) REVERT: A 274 ARG cc_start: 0.8727 (mtp180) cc_final: 0.8453 (ttm110) REVERT: A 314 MET cc_start: 0.9037 (tmm) cc_final: 0.8788 (ppp) REVERT: A 316 GLU cc_start: 0.9055 (tp30) cc_final: 0.8629 (tp30) REVERT: A 317 MET cc_start: 0.8755 (ptp) cc_final: 0.8482 (ptp) REVERT: A 322 MET cc_start: 0.8965 (tpt) cc_final: 0.8329 (tpp) REVERT: A 333 LYS cc_start: 0.9558 (tppt) cc_final: 0.9320 (tppp) REVERT: A 335 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7633 (mm-30) REVERT: A 344 GLU cc_start: 0.9350 (mt-10) cc_final: 0.8826 (mt-10) REVERT: A 349 LEU cc_start: 0.9680 (mt) cc_final: 0.9474 (mt) REVERT: A 359 MET cc_start: 0.8952 (ttp) cc_final: 0.8745 (ttp) REVERT: A 366 LYS cc_start: 0.9256 (mtmm) cc_final: 0.9050 (mtmm) REVERT: A 375 LYS cc_start: 0.9009 (mmtt) cc_final: 0.8584 (mmtm) REVERT: A 378 PHE cc_start: 0.9090 (p90) cc_final: 0.8753 (p90) REVERT: A 415 ASN cc_start: 0.9406 (t0) cc_final: 0.9093 (t0) REVERT: A 459 LYS cc_start: 0.9008 (mttp) cc_final: 0.8629 (mtmt) REVERT: A 493 MET cc_start: 0.8982 (tmm) cc_final: 0.8553 (tmm) REVERT: A 501 GLN cc_start: 0.9362 (tt0) cc_final: 0.8610 (tm-30) REVERT: A 512 GLU cc_start: 0.8533 (pm20) cc_final: 0.8100 (pm20) REVERT: A 515 ASP cc_start: 0.9006 (m-30) cc_final: 0.8719 (m-30) REVERT: A 561 LEU cc_start: 0.9385 (tp) cc_final: 0.8928 (tp) REVERT: A 599 GLU cc_start: 0.9205 (pt0) cc_final: 0.8753 (pt0) REVERT: A 601 ILE cc_start: 0.9537 (mm) cc_final: 0.9262 (mm) REVERT: A 615 MET cc_start: 0.9129 (mmt) cc_final: 0.8850 (mmp) REVERT: A 636 LYS cc_start: 0.9434 (mptt) cc_final: 0.9152 (mmmm) REVERT: A 640 MET cc_start: 0.9283 (tpp) cc_final: 0.8947 (tpp) REVERT: A 645 GLN cc_start: 0.9179 (tp40) cc_final: 0.8857 (tp40) REVERT: A 655 THR cc_start: 0.9501 (m) cc_final: 0.9178 (p) REVERT: A 686 ARG cc_start: 0.8435 (mmm-85) cc_final: 0.7817 (mtm180) REVERT: B 8 LYS cc_start: 0.9433 (tptt) cc_final: 0.9011 (tppt) REVERT: B 55 LEU cc_start: 0.9751 (mt) cc_final: 0.9545 (mt) REVERT: B 58 LEU cc_start: 0.9806 (mt) cc_final: 0.9592 (mt) REVERT: B 99 LYS cc_start: 0.9599 (tppt) cc_final: 0.9390 (tppt) REVERT: B 109 ASN cc_start: 0.9412 (m-40) cc_final: 0.8986 (m-40) REVERT: B 111 LYS cc_start: 0.9680 (mptt) cc_final: 0.9472 (mmtt) REVERT: B 119 GLU cc_start: 0.9407 (mp0) cc_final: 0.9084 (mp0) REVERT: B 129 PHE cc_start: 0.9569 (m-10) cc_final: 0.9335 (m-80) REVERT: B 143 LEU cc_start: 0.9265 (tp) cc_final: 0.8464 (tp) REVERT: B 148 GLU cc_start: 0.9032 (mp0) cc_final: 0.7940 (mp0) REVERT: B 149 TYR cc_start: 0.9223 (t80) cc_final: 0.8603 (t80) REVERT: B 150 GLN cc_start: 0.9449 (tp40) cc_final: 0.9069 (tp-100) REVERT: B 167 LEU cc_start: 0.9274 (mt) cc_final: 0.8723 (mt) REVERT: B 172 LEU cc_start: 0.9406 (mp) cc_final: 0.9141 (mp) REVERT: B 176 ASN cc_start: 0.8841 (t0) cc_final: 0.8631 (t0) REVERT: B 184 ARG cc_start: 0.9444 (tpp80) cc_final: 0.8944 (tpp80) REVERT: B 211 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8535 (mm-30) REVERT: B 239 GLN cc_start: 0.8862 (tm-30) cc_final: 0.8370 (tm-30) REVERT: B 252 ASN cc_start: 0.9295 (t0) cc_final: 0.8968 (t0) REVERT: B 288 PHE cc_start: 0.9592 (t80) cc_final: 0.9349 (t80) REVERT: B 290 GLU cc_start: 0.9459 (tt0) cc_final: 0.9223 (tm-30) REVERT: B 291 LEU cc_start: 0.9670 (mt) cc_final: 0.9444 (mp) REVERT: B 321 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8282 (tm-30) REVERT: B 322 MET cc_start: 0.9079 (mmm) cc_final: 0.8218 (mmm) REVERT: B 335 GLU cc_start: 0.8452 (mm-30) cc_final: 0.8212 (mm-30) REVERT: B 348 MET cc_start: 0.9524 (ptm) cc_final: 0.9304 (ptm) REVERT: B 375 LYS cc_start: 0.9187 (mttm) cc_final: 0.8921 (mtpp) REVERT: B 378 PHE cc_start: 0.9230 (p90) cc_final: 0.8941 (p90) REVERT: B 390 GLN cc_start: 0.9265 (mt0) cc_final: 0.8980 (mm-40) REVERT: B 393 SER cc_start: 0.9324 (m) cc_final: 0.9049 (p) REVERT: B 398 ASP cc_start: 0.8410 (t0) cc_final: 0.8160 (t0) REVERT: B 407 ILE cc_start: 0.9178 (mp) cc_final: 0.8939 (mp) REVERT: B 410 ASN cc_start: 0.9001 (m-40) cc_final: 0.8700 (m-40) REVERT: B 415 ASN cc_start: 0.9504 (t0) cc_final: 0.9216 (t0) REVERT: B 423 LYS cc_start: 0.9555 (mttt) cc_final: 0.9343 (mtpt) REVERT: B 437 THR cc_start: 0.9735 (m) cc_final: 0.9521 (m) REVERT: B 492 PHE cc_start: 0.9678 (m-80) cc_final: 0.9304 (m-10) REVERT: B 522 TYR cc_start: 0.9311 (m-80) cc_final: 0.9089 (m-10) REVERT: B 543 ILE cc_start: 0.9763 (mm) cc_final: 0.9483 (mm) REVERT: B 550 MET cc_start: 0.8154 (mtp) cc_final: 0.7788 (mtm) REVERT: B 588 GLN cc_start: 0.9372 (mm-40) cc_final: 0.8818 (mm-40) REVERT: B 612 TYR cc_start: 0.9292 (m-80) cc_final: 0.8831 (m-10) REVERT: B 615 MET cc_start: 0.9489 (mmp) cc_final: 0.9063 (mmp) REVERT: B 639 ASP cc_start: 0.9208 (m-30) cc_final: 0.8806 (m-30) REVERT: B 640 MET cc_start: 0.9371 (tpp) cc_final: 0.8926 (tpp) REVERT: B 677 ARG cc_start: 0.9464 (mmm-85) cc_final: 0.9239 (mmm-85) REVERT: C 20 MET cc_start: 0.9502 (tmm) cc_final: 0.9191 (tmm) REVERT: C 21 PHE cc_start: 0.9137 (m-10) cc_final: 0.8861 (m-80) REVERT: C 101 HIS cc_start: 0.8361 (m170) cc_final: 0.7150 (m170) REVERT: C 107 ASN cc_start: 0.8736 (m-40) cc_final: 0.8436 (t0) REVERT: C 157 MET cc_start: 0.9246 (mtm) cc_final: 0.8999 (mtm) REVERT: C 158 VAL cc_start: 0.9658 (t) cc_final: 0.9198 (t) REVERT: C 162 TYR cc_start: 0.9356 (m-10) cc_final: 0.8694 (m-10) REVERT: C 163 LEU cc_start: 0.9680 (tt) cc_final: 0.9290 (tt) REVERT: C 168 PHE cc_start: 0.9101 (m-80) cc_final: 0.8745 (m-80) REVERT: C 173 TYR cc_start: 0.7366 (t80) cc_final: 0.6442 (t80) REVERT: C 177 TYR cc_start: 0.9146 (t80) cc_final: 0.8873 (t80) REVERT: C 179 TYR cc_start: 0.8175 (t80) cc_final: 0.7692 (t80) REVERT: C 185 MET cc_start: 0.4905 (mmm) cc_final: 0.3981 (mpp) REVERT: C 201 HIS cc_start: 0.9172 (m170) cc_final: 0.8857 (m170) REVERT: C 252 LEU cc_start: 0.7579 (mt) cc_final: 0.7365 (mt) REVERT: C 271 LEU cc_start: 0.8047 (mt) cc_final: 0.7560 (mt) REVERT: D 20 MET cc_start: 0.9000 (mtm) cc_final: 0.8734 (mpp) REVERT: D 148 ASP cc_start: 0.7225 (m-30) cc_final: 0.6936 (m-30) REVERT: D 176 LEU cc_start: 0.9666 (mt) cc_final: 0.9332 (tp) REVERT: D 186 GLN cc_start: 0.7866 (mm110) cc_final: 0.7248 (mm110) REVERT: D 201 HIS cc_start: 0.8976 (m170) cc_final: 0.8622 (m170) REVERT: D 219 GLU cc_start: 0.9184 (tp30) cc_final: 0.8933 (tp30) REVERT: D 266 LYS cc_start: 0.8856 (mmtp) cc_final: 0.8612 (mmmm) REVERT: D 281 ASP cc_start: 0.8371 (p0) cc_final: 0.7868 (t0) REVERT: D 282 ILE cc_start: 0.6230 (OUTLIER) cc_final: 0.5412 (tp) outliers start: 4 outliers final: 0 residues processed: 756 average time/residue: 0.2712 time to fit residues: 302.8892 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 : 1.677 ------------------------------------------------------------------------------- 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: 6.9990 chunk 99 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 90 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN A 545 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 304 HIS ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN C 238 ASN C 249 GLN D 233 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.116658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.082133 restraints weight = 41030.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.085235 restraints weight = 21693.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.087348 restraints weight = 13742.011| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2977 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2977 r_free = 0.2977 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 = 0.2977 r_free = 0.2977 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2977 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.5880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16386 Z= 0.185 Angle : 0.597 7.602 22134 Z= 0.318 Chirality : 0.043 0.248 2360 Planarity : 0.004 0.047 2818 Dihedral : 11.108 173.595 2242 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.17 % Allowed : 1.63 % Favored : 98.19 % 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: 1.09 (0.19), residues: 1932 helix: 1.20 (0.15), residues: 1129 sheet: 0.13 (0.42), residues: 126 loop : 0.23 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP D 124 HIS 0.007 0.001 HIS D 84 PHE 0.018 0.002 PHE D 320 TYR 0.033 0.002 TYR B 574 ARG 0.007 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.03991 ( 871) hydrogen bonds : angle 4.93613 ( 2571) covalent geometry : bond 0.00403 (16386) covalent geometry : angle 0.59718 (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 743 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 740 time to evaluate : 1.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9230 (tptp) cc_final: 0.8910 (tppt) REVERT: A 30 LYS cc_start: 0.9511 (tptp) cc_final: 0.9280 (tptp) REVERT: A 65 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8306 (mp0) REVERT: A 95 MET cc_start: 0.9035 (mmm) cc_final: 0.8414 (mmm) REVERT: A 107 LYS cc_start: 0.9170 (mttm) cc_final: 0.8794 (mtpp) REVERT: A 129 PHE cc_start: 0.9529 (m-10) cc_final: 0.9263 (m-80) REVERT: A 139 GLU cc_start: 0.8986 (mp0) cc_final: 0.8780 (mm-30) REVERT: A 147 GLN cc_start: 0.9425 (mt0) cc_final: 0.8613 (mt0) REVERT: A 149 TYR cc_start: 0.9253 (t80) cc_final: 0.8513 (t80) REVERT: A 181 ASP cc_start: 0.9012 (m-30) cc_final: 0.8715 (m-30) REVERT: A 195 LEU cc_start: 0.9695 (mt) cc_final: 0.9411 (mt) REVERT: A 214 LYS cc_start: 0.8706 (tppt) cc_final: 0.8290 (mmtt) REVERT: A 223 VAL cc_start: 0.9771 (m) cc_final: 0.9242 (p) REVERT: A 227 MET cc_start: 0.9277 (mtm) cc_final: 0.8898 (mtm) REVERT: A 232 ASN cc_start: 0.8994 (m-40) cc_final: 0.8508 (m-40) REVERT: A 238 ASP cc_start: 0.8299 (p0) cc_final: 0.7962 (p0) REVERT: A 255 HIS cc_start: 0.8844 (t-90) cc_final: 0.7618 (t-90) REVERT: A 257 ASP cc_start: 0.9173 (m-30) cc_final: 0.8804 (m-30) REVERT: A 262 LEU cc_start: 0.9872 (mt) cc_final: 0.9616 (mt) REVERT: A 266 LYS cc_start: 0.8585 (tptp) cc_final: 0.8290 (tptp) REVERT: A 314 MET cc_start: 0.9108 (tmm) cc_final: 0.8851 (ppp) REVERT: A 319 MET cc_start: 0.9286 (tpp) cc_final: 0.9002 (tpp) REVERT: A 321 GLU cc_start: 0.8424 (pp20) cc_final: 0.8040 (pp20) REVERT: A 333 LYS cc_start: 0.9569 (tppt) cc_final: 0.9342 (tppp) REVERT: A 335 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7633 (mm-30) REVERT: A 344 GLU cc_start: 0.9343 (mt-10) cc_final: 0.8744 (mt-10) REVERT: A 345 LYS cc_start: 0.9785 (ttpt) cc_final: 0.9445 (ttmt) REVERT: A 349 LEU cc_start: 0.9701 (mt) cc_final: 0.9427 (mt) REVERT: A 366 LYS cc_start: 0.9346 (mtmm) cc_final: 0.8999 (mtmm) REVERT: A 375 LYS cc_start: 0.8983 (mmtt) cc_final: 0.8603 (mmtm) REVERT: A 415 ASN cc_start: 0.9405 (t0) cc_final: 0.8741 (t0) REVERT: A 418 ASN cc_start: 0.9187 (OUTLIER) cc_final: 0.8981 (m110) REVERT: A 420 MET cc_start: 0.9433 (tpp) cc_final: 0.9165 (mmm) REVERT: A 447 ASN cc_start: 0.8699 (m110) cc_final: 0.8272 (m-40) REVERT: A 459 LYS cc_start: 0.9013 (mttp) cc_final: 0.8533 (mtmt) REVERT: A 466 MET cc_start: 0.9208 (ptt) cc_final: 0.8917 (ptt) REVERT: A 493 MET cc_start: 0.8961 (tmm) cc_final: 0.8492 (tmm) REVERT: A 501 GLN cc_start: 0.9393 (tt0) cc_final: 0.8693 (tm-30) REVERT: A 515 ASP cc_start: 0.8946 (m-30) cc_final: 0.8584 (m-30) REVERT: A 550 MET cc_start: 0.8169 (mtm) cc_final: 0.7391 (mtm) REVERT: A 561 LEU cc_start: 0.9368 (tp) cc_final: 0.8914 (tp) REVERT: A 599 GLU cc_start: 0.9172 (pt0) cc_final: 0.8728 (pt0) REVERT: A 601 ILE cc_start: 0.9534 (mm) cc_final: 0.9325 (mm) REVERT: A 615 MET cc_start: 0.9094 (mmt) cc_final: 0.8807 (mmm) REVERT: A 636 LYS cc_start: 0.9465 (mptt) cc_final: 0.9143 (mmmm) REVERT: A 640 MET cc_start: 0.9310 (tpp) cc_final: 0.8798 (tpp) REVERT: A 645 GLN cc_start: 0.9227 (tp40) cc_final: 0.8959 (tp-100) REVERT: A 655 THR cc_start: 0.9409 (m) cc_final: 0.8890 (p) REVERT: A 657 PHE cc_start: 0.9302 (m-80) cc_final: 0.9093 (m-80) REVERT: A 686 ARG cc_start: 0.8509 (mmm-85) cc_final: 0.7818 (mtm180) REVERT: B 8 LYS cc_start: 0.9411 (tptt) cc_final: 0.8961 (tppt) REVERT: B 55 LEU cc_start: 0.9771 (mt) cc_final: 0.9565 (mt) REVERT: B 119 GLU cc_start: 0.9398 (mp0) cc_final: 0.9081 (mp0) REVERT: B 149 TYR cc_start: 0.9244 (t80) cc_final: 0.8524 (t80) REVERT: B 150 GLN cc_start: 0.9499 (tp40) cc_final: 0.9254 (tp-100) REVERT: B 162 LYS cc_start: 0.9241 (tppt) cc_final: 0.8894 (tppp) REVERT: B 167 LEU cc_start: 0.9317 (mt) cc_final: 0.8777 (mt) REVERT: B 172 LEU cc_start: 0.9376 (mp) cc_final: 0.9117 (mp) REVERT: B 176 ASN cc_start: 0.8775 (t0) cc_final: 0.8555 (t0) REVERT: B 181 ASP cc_start: 0.8716 (m-30) cc_final: 0.8359 (m-30) REVERT: B 184 ARG cc_start: 0.9423 (tpp80) cc_final: 0.9039 (tpp80) REVERT: B 211 GLU cc_start: 0.8887 (mm-30) cc_final: 0.8449 (mm-30) REVERT: B 235 ARG cc_start: 0.9308 (ttm110) cc_final: 0.8557 (ptp-110) REVERT: B 252 ASN cc_start: 0.9376 (t0) cc_final: 0.9109 (t0) REVERT: B 286 ASP cc_start: 0.9047 (m-30) cc_final: 0.8827 (m-30) REVERT: B 288 PHE cc_start: 0.9526 (t80) cc_final: 0.9308 (t80) REVERT: B 291 LEU cc_start: 0.9664 (mt) cc_final: 0.9352 (mt) REVERT: B 321 GLU cc_start: 0.8875 (tm-30) cc_final: 0.8459 (tm-30) REVERT: B 322 MET cc_start: 0.9146 (mmm) cc_final: 0.8566 (mmm) REVERT: B 335 GLU cc_start: 0.8466 (mm-30) cc_final: 0.8179 (mm-30) REVERT: B 348 MET cc_start: 0.9441 (ptm) cc_final: 0.9123 (ptt) REVERT: B 375 LYS cc_start: 0.9193 (mttm) cc_final: 0.8924 (mtpp) REVERT: B 390 GLN cc_start: 0.9228 (mt0) cc_final: 0.8989 (mm-40) REVERT: B 393 SER cc_start: 0.9341 (m) cc_final: 0.9016 (p) REVERT: B 399 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8636 (mp0) REVERT: B 402 GLU cc_start: 0.9068 (tp30) cc_final: 0.8833 (tp30) REVERT: B 407 ILE cc_start: 0.9121 (mp) cc_final: 0.8789 (mp) REVERT: B 410 ASN cc_start: 0.8952 (m-40) cc_final: 0.8722 (m-40) REVERT: B 415 ASN cc_start: 0.9366 (t0) cc_final: 0.9123 (t0) REVERT: B 543 ILE cc_start: 0.9753 (mm) cc_final: 0.9475 (mm) REVERT: B 550 MET cc_start: 0.8081 (mtp) cc_final: 0.7856 (mtm) REVERT: B 570 MET cc_start: 0.8913 (mtp) cc_final: 0.8664 (mtp) REVERT: B 576 LEU cc_start: 0.9503 (mt) cc_final: 0.9225 (mt) REVERT: B 588 GLN cc_start: 0.9433 (mm-40) cc_final: 0.9018 (mm-40) REVERT: B 615 MET cc_start: 0.9495 (mmp) cc_final: 0.9136 (mmp) REVERT: B 639 ASP cc_start: 0.9163 (m-30) cc_final: 0.8916 (m-30) REVERT: B 640 MET cc_start: 0.9205 (tpp) cc_final: 0.8685 (tpp) REVERT: B 677 ARG cc_start: 0.9459 (mmm-85) cc_final: 0.9230 (mmm-85) REVERT: C 20 MET cc_start: 0.9488 (tmm) cc_final: 0.9187 (tmm) REVERT: C 21 PHE cc_start: 0.9103 (m-10) cc_final: 0.8822 (m-80) REVERT: C 37 LEU cc_start: 0.1331 (tp) cc_final: 0.0917 (tp) REVERT: C 90 LEU cc_start: 0.9652 (mt) cc_final: 0.9388 (mt) REVERT: C 93 MET cc_start: 0.8972 (ttp) cc_final: 0.8344 (tmm) REVERT: C 101 HIS cc_start: 0.8303 (m170) cc_final: 0.7162 (m170) REVERT: C 107 ASN cc_start: 0.8782 (m-40) cc_final: 0.8519 (t0) REVERT: C 157 MET cc_start: 0.9236 (mtm) cc_final: 0.8951 (mtm) REVERT: C 168 PHE cc_start: 0.9079 (m-80) cc_final: 0.8809 (m-80) REVERT: C 177 TYR cc_start: 0.9134 (t80) cc_final: 0.8905 (t80) REVERT: C 179 TYR cc_start: 0.8314 (t80) cc_final: 0.8072 (t80) REVERT: C 185 MET cc_start: 0.4834 (mmm) cc_final: 0.4604 (mpp) REVERT: C 201 HIS cc_start: 0.9026 (m170) cc_final: 0.8352 (m170) REVERT: C 208 LEU cc_start: 0.8508 (mm) cc_final: 0.8220 (mm) REVERT: C 233 ASN cc_start: 0.9359 (m110) cc_final: 0.8824 (m110) REVERT: C 237 GLU cc_start: 0.9593 (mm-30) cc_final: 0.9338 (pp20) REVERT: C 252 LEU cc_start: 0.7535 (mt) cc_final: 0.7299 (mt) REVERT: C 270 ASN cc_start: 0.8931 (m110) cc_final: 0.8697 (m110) REVERT: C 281 ASP cc_start: 0.8584 (m-30) cc_final: 0.8347 (m-30) REVERT: D 20 MET cc_start: 0.9047 (mtm) cc_final: 0.8749 (mpp) REVERT: D 139 VAL cc_start: 0.8311 (m) cc_final: 0.8011 (p) REVERT: D 148 ASP cc_start: 0.7224 (m-30) cc_final: 0.6911 (m-30) REVERT: D 176 LEU cc_start: 0.9657 (mt) cc_final: 0.9327 (tp) REVERT: D 219 GLU cc_start: 0.9191 (tp30) cc_final: 0.8948 (tp30) REVERT: D 266 LYS cc_start: 0.8866 (mmtp) cc_final: 0.8646 (mmmm) outliers start: 3 outliers final: 0 residues processed: 740 average time/residue: 0.2660 time to fit residues: 291.2799 Evaluate side-chains 655 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 654 time to evaluate : 1.763 ------------------------------------------------------------------------------- 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: 1.9990 chunk 41 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 175 optimal weight: 8.9990 chunk 182 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 242 GLN A 313 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.115622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.081655 restraints weight = 42628.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.084667 restraints weight = 22058.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.086706 restraints weight = 13780.656| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.6289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16386 Z= 0.205 Angle : 0.619 7.299 22134 Z= 0.328 Chirality : 0.043 0.199 2360 Planarity : 0.004 0.045 2818 Dihedral : 11.028 177.839 2242 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.06 % Allowed : 2.27 % Favored : 97.67 % 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: 1.07 (0.19), residues: 1932 helix: 1.22 (0.15), residues: 1158 sheet: -0.03 (0.41), residues: 130 loop : 0.10 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 124 HIS 0.006 0.001 HIS D 84 PHE 0.028 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 0.03931 ( 871) hydrogen bonds : angle 4.91900 ( 2571) covalent geometry : bond 0.00441 (16386) covalent geometry : angle 0.61866 (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 741 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 740 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9264 (tptp) cc_final: 0.8955 (tppt) REVERT: A 12 LEU cc_start: 0.9656 (mt) cc_final: 0.9443 (mt) REVERT: A 30 LYS cc_start: 0.9513 (tptp) cc_final: 0.9275 (tptp) REVERT: A 65 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8364 (mp0) REVERT: A 107 LYS cc_start: 0.9213 (mttm) cc_final: 0.8861 (mtpp) REVERT: A 117 ARG cc_start: 0.9267 (tpp80) cc_final: 0.9025 (tpp80) REVERT: A 129 PHE cc_start: 0.9559 (m-10) cc_final: 0.9211 (m-80) REVERT: A 139 GLU cc_start: 0.9107 (mp0) cc_final: 0.8867 (mp0) REVERT: A 147 GLN cc_start: 0.9414 (mt0) cc_final: 0.9188 (mt0) REVERT: A 149 TYR cc_start: 0.9245 (t80) cc_final: 0.8565 (t80) REVERT: A 150 GLN cc_start: 0.9553 (tp40) cc_final: 0.9313 (tp40) REVERT: A 172 LEU cc_start: 0.9594 (mp) cc_final: 0.9220 (mp) REVERT: A 174 GLU cc_start: 0.7763 (tp30) cc_final: 0.7366 (tp30) REVERT: A 181 ASP cc_start: 0.8919 (m-30) cc_final: 0.8650 (m-30) REVERT: A 191 GLN cc_start: 0.9094 (OUTLIER) cc_final: 0.8513 (mm-40) REVERT: A 195 LEU cc_start: 0.9692 (mt) cc_final: 0.9413 (mt) REVERT: A 214 LYS cc_start: 0.8707 (tppt) cc_final: 0.8295 (mmtt) REVERT: A 223 VAL cc_start: 0.9775 (m) cc_final: 0.9194 (p) REVERT: A 227 MET cc_start: 0.9306 (mtm) cc_final: 0.8832 (mtm) REVERT: A 231 ASP cc_start: 0.9116 (t0) cc_final: 0.8804 (t0) REVERT: A 232 ASN cc_start: 0.9033 (m-40) cc_final: 0.8509 (m-40) REVERT: A 238 ASP cc_start: 0.8263 (p0) cc_final: 0.7905 (p0) REVERT: A 257 ASP cc_start: 0.9162 (m-30) cc_final: 0.8859 (m-30) REVERT: A 259 ASN cc_start: 0.8866 (p0) cc_final: 0.8660 (p0) REVERT: A 262 LEU cc_start: 0.9883 (mt) cc_final: 0.9642 (mt) REVERT: A 263 ASP cc_start: 0.9297 (m-30) cc_final: 0.8969 (m-30) REVERT: A 301 PHE cc_start: 0.9307 (m-10) cc_final: 0.8849 (m-10) REVERT: A 314 MET cc_start: 0.9110 (tmm) cc_final: 0.8810 (ppp) REVERT: A 316 GLU cc_start: 0.9021 (tp30) cc_final: 0.8669 (tp30) REVERT: A 319 MET cc_start: 0.9274 (tpp) cc_final: 0.8948 (tpp) REVERT: A 333 LYS cc_start: 0.9592 (tppt) cc_final: 0.9329 (tppp) REVERT: A 335 GLU cc_start: 0.8112 (mm-30) cc_final: 0.7670 (mm-30) REVERT: A 344 GLU cc_start: 0.9311 (mt-10) cc_final: 0.8762 (mt-10) REVERT: A 345 LYS cc_start: 0.9804 (ttpt) cc_final: 0.9522 (ttmt) REVERT: A 349 LEU cc_start: 0.9703 (mt) cc_final: 0.9436 (mt) REVERT: A 375 LYS cc_start: 0.9012 (mmtt) cc_final: 0.8734 (mmtm) REVERT: A 393 SER cc_start: 0.9304 (m) cc_final: 0.8647 (m) REVERT: A 399 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8115 (tm-30) REVERT: A 402 GLU cc_start: 0.8153 (mp0) cc_final: 0.7524 (mp0) REVERT: A 407 ILE cc_start: 0.9234 (mt) cc_final: 0.8979 (mt) REVERT: A 415 ASN cc_start: 0.9333 (t0) cc_final: 0.9013 (t0) REVERT: A 420 MET cc_start: 0.9441 (tpp) cc_final: 0.9186 (mmm) REVERT: A 447 ASN cc_start: 0.8670 (m110) cc_final: 0.7928 (m-40) REVERT: A 459 LYS cc_start: 0.9018 (mttp) cc_final: 0.8441 (mtmm) REVERT: A 466 MET cc_start: 0.9196 (ptt) cc_final: 0.8914 (ptt) REVERT: A 491 PHE cc_start: 0.9662 (t80) cc_final: 0.9329 (t80) REVERT: A 493 MET cc_start: 0.8917 (tmm) cc_final: 0.8615 (tmm) REVERT: A 501 GLN cc_start: 0.9380 (tt0) cc_final: 0.8720 (tm-30) REVERT: A 515 ASP cc_start: 0.8990 (m-30) cc_final: 0.8741 (m-30) REVERT: A 550 MET cc_start: 0.8316 (mtm) cc_final: 0.7567 (mtm) REVERT: A 561 LEU cc_start: 0.9410 (tp) cc_final: 0.8974 (tp) REVERT: A 599 GLU cc_start: 0.9179 (pt0) cc_final: 0.8920 (pt0) REVERT: A 636 LYS cc_start: 0.9435 (mptt) cc_final: 0.9105 (mmmm) REVERT: A 640 MET cc_start: 0.9391 (tpp) cc_final: 0.8786 (tpp) REVERT: A 645 GLN cc_start: 0.9217 (tp40) cc_final: 0.8920 (tp-100) REVERT: A 667 LEU cc_start: 0.9396 (tt) cc_final: 0.9191 (tt) REVERT: A 677 ARG cc_start: 0.9136 (tpp80) cc_final: 0.8845 (tpp80) REVERT: A 686 ARG cc_start: 0.8514 (mmm-85) cc_final: 0.7582 (mtm180) REVERT: B 8 LYS cc_start: 0.9411 (tptt) cc_final: 0.9034 (tppt) REVERT: B 12 LEU cc_start: 0.9610 (mt) cc_final: 0.9366 (mt) REVERT: B 21 ASP cc_start: 0.9020 (m-30) cc_final: 0.8804 (t0) REVERT: B 55 LEU cc_start: 0.9777 (mt) cc_final: 0.9567 (mt) REVERT: B 60 GLU cc_start: 0.9373 (mt-10) cc_final: 0.9122 (tm-30) REVERT: B 87 LYS cc_start: 0.9436 (tptt) cc_final: 0.8978 (tttt) REVERT: B 88 LYS cc_start: 0.9355 (mppt) cc_final: 0.9132 (mmtt) REVERT: B 109 ASN cc_start: 0.9437 (m-40) cc_final: 0.9018 (m-40) REVERT: B 111 LYS cc_start: 0.9701 (mptt) cc_final: 0.9470 (mmtt) REVERT: B 119 GLU cc_start: 0.9402 (mp0) cc_final: 0.9042 (mp0) REVERT: B 143 LEU cc_start: 0.9342 (tp) cc_final: 0.8316 (tp) REVERT: B 148 GLU cc_start: 0.9046 (mp0) cc_final: 0.7716 (mp0) REVERT: B 149 TYR cc_start: 0.9410 (t80) cc_final: 0.8476 (t80) REVERT: B 167 LEU cc_start: 0.9332 (mt) cc_final: 0.8972 (mt) REVERT: B 173 LEU cc_start: 0.9375 (mt) cc_final: 0.9007 (mt) REVERT: B 181 ASP cc_start: 0.8636 (m-30) cc_final: 0.8279 (m-30) REVERT: B 184 ARG cc_start: 0.9393 (tpp80) cc_final: 0.8992 (tpp80) REVERT: B 211 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8384 (mm-30) REVERT: B 235 ARG cc_start: 0.9182 (ttm110) cc_final: 0.8811 (mtm-85) REVERT: B 252 ASN cc_start: 0.9381 (t0) cc_final: 0.8949 (t0) REVERT: B 321 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8377 (tm-30) REVERT: B 322 MET cc_start: 0.9147 (mmm) cc_final: 0.8351 (mmm) REVERT: B 335 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8117 (mm-30) REVERT: B 350 ARG cc_start: 0.9474 (mmm-85) cc_final: 0.9135 (mmm-85) REVERT: B 393 SER cc_start: 0.9346 (m) cc_final: 0.9024 (p) REVERT: B 399 GLU cc_start: 0.8974 (mm-30) cc_final: 0.8762 (mp0) REVERT: B 402 GLU cc_start: 0.9063 (tp30) cc_final: 0.8838 (tp30) REVERT: B 407 ILE cc_start: 0.9169 (mp) cc_final: 0.8854 (mp) REVERT: B 415 ASN cc_start: 0.9415 (t0) cc_final: 0.9065 (t0) REVERT: B 437 THR cc_start: 0.9700 (m) cc_final: 0.9478 (p) REVERT: B 494 MET cc_start: 0.9434 (mtp) cc_final: 0.9071 (mmt) REVERT: B 543 ILE cc_start: 0.9744 (mm) cc_final: 0.9458 (mm) REVERT: B 550 MET cc_start: 0.8157 (mtp) cc_final: 0.7778 (mtm) REVERT: B 576 LEU cc_start: 0.9507 (mt) cc_final: 0.9262 (mt) REVERT: B 588 GLN cc_start: 0.9422 (mm-40) cc_final: 0.8994 (mm-40) REVERT: B 612 TYR cc_start: 0.9011 (m-80) cc_final: 0.8595 (m-80) REVERT: B 615 MET cc_start: 0.9484 (mmp) cc_final: 0.9120 (mmp) REVERT: B 639 ASP cc_start: 0.9139 (m-30) cc_final: 0.8852 (m-30) REVERT: B 640 MET cc_start: 0.9125 (tpp) cc_final: 0.8456 (tpp) REVERT: B 667 LEU cc_start: 0.9374 (tp) cc_final: 0.8945 (tp) REVERT: B 677 ARG cc_start: 0.9465 (mmm-85) cc_final: 0.9237 (mmm-85) REVERT: B 680 LYS cc_start: 0.9025 (mttt) cc_final: 0.8817 (mtpt) REVERT: C 89 VAL cc_start: 0.6242 (t) cc_final: 0.6029 (m) REVERT: C 90 LEU cc_start: 0.9677 (mt) cc_final: 0.9277 (mt) REVERT: C 93 MET cc_start: 0.8935 (ttp) cc_final: 0.8312 (tmm) REVERT: C 101 HIS cc_start: 0.8288 (m170) cc_final: 0.7266 (m170) REVERT: C 107 ASN cc_start: 0.8852 (m-40) cc_final: 0.8535 (t0) REVERT: C 150 GLU cc_start: 0.9347 (pm20) cc_final: 0.9067 (tt0) REVERT: C 157 MET cc_start: 0.9226 (mtm) cc_final: 0.8849 (mtm) REVERT: C 162 TYR cc_start: 0.9369 (m-10) cc_final: 0.8779 (m-10) REVERT: C 173 TYR cc_start: 0.7400 (t80) cc_final: 0.6724 (t80) REVERT: C 177 TYR cc_start: 0.9181 (t80) cc_final: 0.8966 (t80) REVERT: C 185 MET cc_start: 0.5730 (mmm) cc_final: 0.4788 (mpp) REVERT: C 201 HIS cc_start: 0.9094 (m170) cc_final: 0.8445 (m170) REVERT: C 208 LEU cc_start: 0.8595 (mm) cc_final: 0.8311 (mt) REVERT: C 233 ASN cc_start: 0.9360 (m110) cc_final: 0.8771 (m110) REVERT: C 252 LEU cc_start: 0.7398 (mt) cc_final: 0.7170 (mt) REVERT: C 281 ASP cc_start: 0.8561 (m-30) cc_final: 0.8289 (m-30) REVERT: D 20 MET cc_start: 0.9019 (mtm) cc_final: 0.8703 (mpp) REVERT: D 30 TRP cc_start: 0.8134 (p-90) cc_final: 0.7710 (p-90) REVERT: D 96 MET cc_start: 0.9014 (mmt) cc_final: 0.8812 (mmm) REVERT: D 148 ASP cc_start: 0.7001 (m-30) cc_final: 0.6718 (m-30) REVERT: D 176 LEU cc_start: 0.9640 (mt) cc_final: 0.9349 (tp) REVERT: D 184 LEU cc_start: 0.7299 (mt) cc_final: 0.7009 (mt) REVERT: D 201 HIS cc_start: 0.9327 (m170) cc_final: 0.8908 (m170) outliers start: 1 outliers final: 0 residues processed: 740 average time/residue: 0.2655 time to fit residues: 292.1525 Evaluate side-chains 641 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 640 time to evaluate : 1.887 ------------------------------------------------------------------------------- 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: 4.9990 chunk 126 optimal weight: 0.5980 chunk 62 optimal weight: 8.9990 chunk 69 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 chunk 21 optimal weight: 7.9990 chunk 115 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 113 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 overall best weight: 2.7184 ------------------------------------------------------------------------------- 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 ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS ** 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 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 28 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN D 233 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.115344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.081497 restraints weight = 42297.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.084516 restraints weight = 22073.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.086621 restraints weight = 13924.134| |-----------------------------------------------------------------------------| r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2956 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2956 r_free = 0.2956 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 = 0.2956 r_free = 0.2956 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2956 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.6604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16386 Z= 0.226 Angle : 0.632 7.457 22134 Z= 0.336 Chirality : 0.044 0.270 2360 Planarity : 0.004 0.049 2818 Dihedral : 11.055 179.945 2242 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.13 (0.15), residues: 1156 sheet: 0.42 (0.45), residues: 110 loop : -0.07 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP D 124 HIS 0.006 0.001 HIS A 438 PHE 0.034 0.002 PHE C 166 TYR 0.040 0.002 TYR D 142 ARG 0.009 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 871) hydrogen bonds : angle 4.93817 ( 2571) covalent geometry : bond 0.00485 (16386) covalent geometry : angle 0.63177 (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 721 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 721 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9231 (tptp) cc_final: 0.8928 (tppt) REVERT: A 12 LEU cc_start: 0.9658 (mt) cc_final: 0.9432 (mt) REVERT: A 30 LYS cc_start: 0.9521 (tptp) cc_final: 0.9299 (tptp) REVERT: A 65 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8353 (mp0) REVERT: A 107 LYS cc_start: 0.9195 (mttm) cc_final: 0.8860 (mtpp) REVERT: A 129 PHE cc_start: 0.9562 (m-10) cc_final: 0.9258 (m-10) REVERT: A 147 GLN cc_start: 0.9438 (mt0) cc_final: 0.8763 (mt0) REVERT: A 149 TYR cc_start: 0.9318 (t80) cc_final: 0.8613 (t80) REVERT: A 172 LEU cc_start: 0.9580 (mp) cc_final: 0.9190 (mp) REVERT: A 181 ASP cc_start: 0.8996 (m-30) cc_final: 0.8711 (m-30) REVERT: A 195 LEU cc_start: 0.9679 (mt) cc_final: 0.9409 (mt) REVERT: A 214 LYS cc_start: 0.8758 (tppt) cc_final: 0.8521 (tppt) REVERT: A 218 ASN cc_start: 0.9579 (t0) cc_final: 0.9372 (t0) REVERT: A 223 VAL cc_start: 0.9786 (m) cc_final: 0.9283 (p) REVERT: A 227 MET cc_start: 0.9270 (mtm) cc_final: 0.8952 (mtm) REVERT: A 255 HIS cc_start: 0.8885 (t-90) cc_final: 0.7837 (t-90) REVERT: A 257 ASP cc_start: 0.9114 (m-30) cc_final: 0.8862 (m-30) REVERT: A 262 LEU cc_start: 0.9887 (mt) cc_final: 0.9647 (mt) REVERT: A 301 PHE cc_start: 0.9270 (m-10) cc_final: 0.8725 (m-10) REVERT: A 314 MET cc_start: 0.9156 (tmm) cc_final: 0.8862 (ppp) REVERT: A 333 LYS cc_start: 0.9588 (tppt) cc_final: 0.9304 (tppp) REVERT: A 335 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7673 (mm-30) REVERT: A 344 GLU cc_start: 0.9324 (mt-10) cc_final: 0.8732 (mt-10) REVERT: A 345 LYS cc_start: 0.9809 (ttpt) cc_final: 0.9518 (ttmt) REVERT: A 349 LEU cc_start: 0.9697 (mt) cc_final: 0.9473 (mt) REVERT: A 366 LYS cc_start: 0.9408 (mtmm) cc_final: 0.9068 (mtmm) REVERT: A 375 LYS cc_start: 0.9161 (mmtt) cc_final: 0.8858 (mmtm) REVERT: A 393 SER cc_start: 0.9227 (m) cc_final: 0.8468 (m) REVERT: A 402 GLU cc_start: 0.8279 (mp0) cc_final: 0.7648 (mp0) REVERT: A 407 ILE cc_start: 0.9288 (mt) cc_final: 0.9040 (mt) REVERT: A 415 ASN cc_start: 0.9288 (t0) cc_final: 0.8911 (t0) REVERT: A 441 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8768 (mt-10) REVERT: A 459 LYS cc_start: 0.9015 (mttp) cc_final: 0.8443 (mtmm) REVERT: A 466 MET cc_start: 0.9237 (ptt) cc_final: 0.9014 (ptt) REVERT: A 493 MET cc_start: 0.8905 (tmm) cc_final: 0.8577 (tmm) REVERT: A 501 GLN cc_start: 0.9377 (tt0) cc_final: 0.8696 (tm-30) REVERT: A 515 ASP cc_start: 0.9002 (m-30) cc_final: 0.8750 (m-30) REVERT: A 561 LEU cc_start: 0.9423 (tp) cc_final: 0.9006 (tp) REVERT: A 598 MET cc_start: 0.8467 (mtp) cc_final: 0.8168 (mtp) REVERT: A 599 GLU cc_start: 0.9154 (pt0) cc_final: 0.8899 (pt0) REVERT: A 615 MET cc_start: 0.9123 (mmt) cc_final: 0.8850 (mmp) REVERT: A 636 LYS cc_start: 0.9386 (mptt) cc_final: 0.9155 (mmmm) REVERT: A 640 MET cc_start: 0.9389 (tpp) cc_final: 0.8779 (tpp) REVERT: A 645 GLN cc_start: 0.9250 (tp40) cc_final: 0.8949 (tp-100) REVERT: A 667 LEU cc_start: 0.9409 (tt) cc_final: 0.9186 (tt) REVERT: A 677 ARG cc_start: 0.9108 (tpp80) cc_final: 0.8841 (tpp80) REVERT: B 8 LYS cc_start: 0.9392 (tptt) cc_final: 0.9037 (tppt) REVERT: B 12 LEU cc_start: 0.9614 (mt) cc_final: 0.9376 (mt) REVERT: B 21 ASP cc_start: 0.8992 (m-30) cc_final: 0.8764 (t0) REVERT: B 55 LEU cc_start: 0.9770 (mt) cc_final: 0.9551 (mt) REVERT: B 58 LEU cc_start: 0.9783 (mt) cc_final: 0.9553 (mt) REVERT: B 60 GLU cc_start: 0.9327 (mt-10) cc_final: 0.9102 (tm-30) REVERT: B 117 ARG cc_start: 0.9446 (mmm-85) cc_final: 0.9058 (mmm-85) REVERT: B 119 GLU cc_start: 0.9418 (mp0) cc_final: 0.9014 (mp0) REVERT: B 143 LEU cc_start: 0.9320 (tp) cc_final: 0.8354 (tp) REVERT: B 148 GLU cc_start: 0.9081 (mp0) cc_final: 0.7858 (mp0) REVERT: B 149 TYR cc_start: 0.9464 (t80) cc_final: 0.8152 (t80) REVERT: B 150 GLN cc_start: 0.9509 (tp-100) cc_final: 0.9138 (tp-100) REVERT: B 167 LEU cc_start: 0.9372 (mt) cc_final: 0.9072 (mt) REVERT: B 172 LEU cc_start: 0.9430 (mp) cc_final: 0.9123 (mp) REVERT: B 173 LEU cc_start: 0.9394 (mt) cc_final: 0.9141 (mt) REVERT: B 181 ASP cc_start: 0.8606 (m-30) cc_final: 0.8251 (m-30) REVERT: B 184 ARG cc_start: 0.9368 (tpp80) cc_final: 0.8871 (tpp80) REVERT: B 211 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8399 (mm-30) REVERT: B 238 ASP cc_start: 0.8368 (t0) cc_final: 0.7829 (t70) REVERT: B 239 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8239 (tm-30) REVERT: B 252 ASN cc_start: 0.9437 (t0) cc_final: 0.8986 (t0) REVERT: B 263 ASP cc_start: 0.9251 (m-30) cc_final: 0.8851 (m-30) REVERT: B 276 LYS cc_start: 0.9133 (ptmm) cc_final: 0.8928 (ptmm) REVERT: B 286 ASP cc_start: 0.9007 (m-30) cc_final: 0.8725 (m-30) REVERT: B 321 GLU cc_start: 0.8816 (tm-30) cc_final: 0.8339 (tm-30) REVERT: B 322 MET cc_start: 0.9165 (mmm) cc_final: 0.8364 (mmm) REVERT: B 335 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8132 (mm-30) REVERT: B 348 MET cc_start: 0.9453 (ptm) cc_final: 0.8935 (ptp) REVERT: B 350 ARG cc_start: 0.9414 (mmm-85) cc_final: 0.9169 (mmm-85) REVERT: B 352 GLU cc_start: 0.8406 (mp0) cc_final: 0.8118 (mm-30) REVERT: B 355 TYR cc_start: 0.8750 (m-10) cc_final: 0.8427 (m-10) REVERT: B 393 SER cc_start: 0.9369 (m) cc_final: 0.9048 (p) REVERT: B 407 ILE cc_start: 0.9197 (mp) cc_final: 0.8951 (mp) REVERT: B 415 ASN cc_start: 0.9395 (t0) cc_final: 0.9088 (t0) REVERT: B 437 THR cc_start: 0.9707 (m) cc_final: 0.9467 (p) REVERT: B 543 ILE cc_start: 0.9741 (mm) cc_final: 0.9435 (mm) REVERT: B 550 MET cc_start: 0.8165 (mtp) cc_final: 0.7630 (mtm) REVERT: B 588 GLN cc_start: 0.9399 (mm-40) cc_final: 0.8890 (mm-40) REVERT: B 612 TYR cc_start: 0.9050 (m-80) cc_final: 0.8630 (m-80) REVERT: B 615 MET cc_start: 0.9490 (mmp) cc_final: 0.9157 (mmp) REVERT: B 639 ASP cc_start: 0.9116 (m-30) cc_final: 0.8858 (m-30) REVERT: B 640 MET cc_start: 0.9026 (tpp) cc_final: 0.8387 (tpp) REVERT: B 677 ARG cc_start: 0.9474 (mmm-85) cc_final: 0.9251 (mmm-85) REVERT: C 17 PHE cc_start: 0.8910 (p90) cc_final: 0.8661 (p90) REVERT: C 107 ASN cc_start: 0.8851 (m-40) cc_final: 0.8538 (t0) REVERT: C 150 GLU cc_start: 0.9399 (pm20) cc_final: 0.9133 (tt0) REVERT: C 153 LEU cc_start: 0.9530 (mt) cc_final: 0.9327 (mt) REVERT: C 157 MET cc_start: 0.9295 (mtm) cc_final: 0.8943 (mtm) REVERT: C 174 TYR cc_start: 0.7722 (t80) cc_final: 0.7166 (t80) REVERT: C 177 TYR cc_start: 0.9143 (t80) cc_final: 0.8922 (t80) REVERT: C 185 MET cc_start: 0.6169 (mmm) cc_final: 0.5004 (mpp) REVERT: C 201 HIS cc_start: 0.9122 (m170) cc_final: 0.8810 (m170) REVERT: C 208 LEU cc_start: 0.8525 (mm) cc_final: 0.8295 (mt) REVERT: C 281 ASP cc_start: 0.8660 (m-30) cc_final: 0.8406 (m-30) REVERT: D 30 TRP cc_start: 0.8271 (p-90) cc_final: 0.7403 (p-90) REVERT: D 96 MET cc_start: 0.9081 (mmt) cc_final: 0.8789 (mmm) REVERT: D 148 ASP cc_start: 0.6985 (m-30) cc_final: 0.6688 (m-30) REVERT: D 176 LEU cc_start: 0.9646 (mt) cc_final: 0.9387 (tp) REVERT: D 185 MET cc_start: 0.7732 (ptp) cc_final: 0.7353 (ptp) REVERT: D 189 GLU cc_start: 0.9046 (tm-30) cc_final: 0.8702 (tm-30) REVERT: D 270 ASN cc_start: 0.8548 (m-40) cc_final: 0.8330 (m-40) outliers start: 0 outliers final: 0 residues processed: 721 average time/residue: 0.2663 time to fit residues: 285.1019 Evaluate side-chains 626 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 626 time to evaluate : 1.898 ------------------------------------------------------------------------------- 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: 5.9990 chunk 85 optimal weight: 2.9990 chunk 161 optimal weight: 20.0000 chunk 23 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 146 optimal weight: 6.9990 chunk 184 optimal weight: 6.9990 chunk 119 optimal weight: 0.9980 chunk 175 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** 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 365 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.118816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.085083 restraints weight = 41306.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.088175 restraints weight = 21197.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.090272 restraints weight = 13244.734| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 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 = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.6798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16386 Z= 0.139 Angle : 0.590 6.949 22134 Z= 0.313 Chirality : 0.043 0.355 2360 Planarity : 0.003 0.046 2818 Dihedral : 10.844 179.704 2242 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.98 (0.19), residues: 1932 helix: 1.20 (0.15), residues: 1148 sheet: -0.15 (0.41), residues: 130 loop : -0.01 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP D 124 HIS 0.009 0.001 HIS C 101 PHE 0.028 0.002 PHE C 166 TYR 0.039 0.001 TYR D 142 ARG 0.009 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.03834 ( 871) hydrogen bonds : angle 4.81875 ( 2571) covalent geometry : bond 0.00308 (16386) covalent geometry : angle 0.59023 (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 739 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 739 time to evaluate : 1.701 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: 0.9208 (tptp) cc_final: 0.8908 (tppt) REVERT: A 12 LEU cc_start: 0.9654 (mt) cc_final: 0.9323 (mt) REVERT: A 30 LYS cc_start: 0.9529 (tptp) cc_final: 0.9298 (tptp) REVERT: A 65 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8437 (mp0) REVERT: A 107 LYS cc_start: 0.9170 (mttm) cc_final: 0.8756 (mtpp) REVERT: A 117 ARG cc_start: 0.9236 (tpp80) cc_final: 0.8878 (tpp80) REVERT: A 129 PHE cc_start: 0.9521 (m-10) cc_final: 0.9213 (m-10) REVERT: A 147 GLN cc_start: 0.9333 (mt0) cc_final: 0.8627 (mt0) REVERT: A 149 TYR cc_start: 0.9369 (t80) cc_final: 0.8594 (t80) REVERT: A 172 LEU cc_start: 0.9535 (mp) cc_final: 0.9190 (mp) REVERT: A 181 ASP cc_start: 0.8909 (m-30) cc_final: 0.8627 (m-30) REVERT: A 195 LEU cc_start: 0.9694 (mt) cc_final: 0.9421 (mt) REVERT: A 214 LYS cc_start: 0.8693 (tppt) cc_final: 0.8436 (tppt) REVERT: A 223 VAL cc_start: 0.9746 (m) cc_final: 0.9084 (p) REVERT: A 227 MET cc_start: 0.9302 (mtm) cc_final: 0.8756 (mtm) REVERT: A 231 ASP cc_start: 0.8404 (t0) cc_final: 0.8128 (p0) REVERT: A 232 ASN cc_start: 0.9079 (m-40) cc_final: 0.8183 (m-40) REVERT: A 255 HIS cc_start: 0.8897 (t-90) cc_final: 0.7896 (t-90) REVERT: A 257 ASP cc_start: 0.9136 (m-30) cc_final: 0.8890 (m-30) REVERT: A 262 LEU cc_start: 0.9877 (mt) cc_final: 0.9590 (mt) REVERT: A 263 ASP cc_start: 0.9253 (m-30) cc_final: 0.9045 (m-30) REVERT: A 301 PHE cc_start: 0.9186 (m-10) cc_final: 0.8675 (m-10) REVERT: A 333 LYS cc_start: 0.9578 (tppt) cc_final: 0.9265 (tppp) REVERT: A 335 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7531 (mm-30) REVERT: A 344 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8648 (mt-10) REVERT: A 349 LEU cc_start: 0.9679 (mt) cc_final: 0.9462 (mt) REVERT: A 366 LYS cc_start: 0.9430 (mtmm) cc_final: 0.9193 (mtmm) REVERT: A 375 LYS cc_start: 0.9071 (mmtt) cc_final: 0.8774 (mmtm) REVERT: A 393 SER cc_start: 0.9197 (m) cc_final: 0.8411 (m) REVERT: A 402 GLU cc_start: 0.8268 (mp0) cc_final: 0.7615 (mp0) REVERT: A 407 ILE cc_start: 0.9255 (mt) cc_final: 0.8992 (mt) REVERT: A 415 ASN cc_start: 0.9244 (t0) cc_final: 0.8928 (t0) REVERT: A 420 MET cc_start: 0.9479 (tpp) cc_final: 0.9243 (mmm) REVERT: A 459 LYS cc_start: 0.9000 (mttp) cc_final: 0.8397 (mtmm) REVERT: A 466 MET cc_start: 0.9234 (ptt) cc_final: 0.9009 (ptt) REVERT: A 493 MET cc_start: 0.8901 (tmm) cc_final: 0.8371 (tmm) REVERT: A 501 GLN cc_start: 0.9396 (tt0) cc_final: 0.8736 (tm-30) REVERT: A 515 ASP cc_start: 0.8940 (m-30) cc_final: 0.8660 (m-30) REVERT: A 561 LEU cc_start: 0.9364 (tp) cc_final: 0.8889 (tp) REVERT: A 595 MET cc_start: 0.8979 (mmp) cc_final: 0.8726 (mmp) REVERT: A 598 MET cc_start: 0.8529 (mtp) cc_final: 0.7535 (mtp) REVERT: A 599 GLU cc_start: 0.9188 (pt0) cc_final: 0.8716 (pt0) REVERT: A 601 ILE cc_start: 0.9542 (mm) cc_final: 0.8987 (mm) REVERT: A 602 GLU cc_start: 0.7952 (pt0) cc_final: 0.7443 (pt0) REVERT: A 615 MET cc_start: 0.9115 (mmt) cc_final: 0.8828 (mmm) REVERT: A 628 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8513 (mm-30) REVERT: A 640 MET cc_start: 0.9342 (tpp) cc_final: 0.8707 (tpp) REVERT: A 645 GLN cc_start: 0.9165 (tp40) cc_final: 0.8861 (tp-100) REVERT: A 646 GLN cc_start: 0.9349 (pt0) cc_final: 0.9089 (pt0) REVERT: A 667 LEU cc_start: 0.9407 (tt) cc_final: 0.9175 (tt) REVERT: A 686 ARG cc_start: 0.8452 (mmm-85) cc_final: 0.7834 (mtm180) REVERT: B 8 LYS cc_start: 0.9392 (tptt) cc_final: 0.9099 (tppt) REVERT: B 12 LEU cc_start: 0.9619 (mt) cc_final: 0.9403 (mt) REVERT: B 55 LEU cc_start: 0.9778 (mt) cc_final: 0.9562 (mt) REVERT: B 58 LEU cc_start: 0.9767 (mt) cc_final: 0.9547 (mt) REVERT: B 60 GLU cc_start: 0.9276 (mt-10) cc_final: 0.9051 (tm-30) REVERT: B 87 LYS cc_start: 0.9300 (tptt) cc_final: 0.8888 (tttt) REVERT: B 117 ARG cc_start: 0.9396 (mmm-85) cc_final: 0.9014 (mmm-85) REVERT: B 119 GLU cc_start: 0.9340 (mp0) cc_final: 0.8968 (mp0) REVERT: B 149 TYR cc_start: 0.9366 (t80) cc_final: 0.8348 (t80) REVERT: B 167 LEU cc_start: 0.9366 (mt) cc_final: 0.9002 (mt) REVERT: B 168 VAL cc_start: 0.9442 (t) cc_final: 0.9197 (m) REVERT: B 171 PHE cc_start: 0.9285 (m-80) cc_final: 0.9058 (m-80) REVERT: B 172 LEU cc_start: 0.9419 (mp) cc_final: 0.9104 (mp) REVERT: B 173 LEU cc_start: 0.9420 (mt) cc_final: 0.9162 (mt) REVERT: B 181 ASP cc_start: 0.8660 (m-30) cc_final: 0.8272 (m-30) REVERT: B 184 ARG cc_start: 0.9453 (tpp80) cc_final: 0.9045 (tpp80) REVERT: B 211 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8422 (mm-30) REVERT: B 238 ASP cc_start: 0.8378 (t0) cc_final: 0.7857 (t70) REVERT: B 239 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8224 (tm-30) REVERT: B 252 ASN cc_start: 0.9434 (t0) cc_final: 0.8965 (t0) REVERT: B 263 ASP cc_start: 0.9210 (m-30) cc_final: 0.8785 (m-30) REVERT: B 286 ASP cc_start: 0.8979 (m-30) cc_final: 0.8553 (m-30) REVERT: B 321 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8343 (tm-30) REVERT: B 322 MET cc_start: 0.9179 (mmm) cc_final: 0.8168 (mmm) REVERT: B 335 GLU cc_start: 0.8479 (mm-30) cc_final: 0.8124 (mm-30) REVERT: B 348 MET cc_start: 0.9463 (ptm) cc_final: 0.9094 (ptp) REVERT: B 350 ARG cc_start: 0.9359 (mmm-85) cc_final: 0.9140 (mmm-85) REVERT: B 355 TYR cc_start: 0.8788 (m-10) cc_final: 0.8333 (m-10) REVERT: B 362 ASP cc_start: 0.8822 (m-30) cc_final: 0.8254 (m-30) REVERT: B 384 GLU cc_start: 0.8826 (pm20) cc_final: 0.8464 (pm20) REVERT: B 393 SER cc_start: 0.9363 (m) cc_final: 0.9103 (p) REVERT: B 402 GLU cc_start: 0.9032 (tp30) cc_final: 0.8821 (tp30) REVERT: B 407 ILE cc_start: 0.9118 (mp) cc_final: 0.8786 (mp) REVERT: B 410 ASN cc_start: 0.8806 (m-40) cc_final: 0.8514 (m-40) REVERT: B 415 ASN cc_start: 0.9317 (t0) cc_final: 0.9087 (t0) REVERT: B 423 LYS cc_start: 0.9536 (mttt) cc_final: 0.9321 (mtmt) REVERT: B 437 THR cc_start: 0.9641 (m) cc_final: 0.9416 (p) REVERT: B 543 ILE cc_start: 0.9720 (mm) cc_final: 0.9409 (mm) REVERT: B 550 MET cc_start: 0.8109 (mtp) cc_final: 0.7790 (mtm) REVERT: B 588 GLN cc_start: 0.9405 (mm-40) cc_final: 0.8893 (mm-40) REVERT: B 612 TYR cc_start: 0.8944 (m-80) cc_final: 0.8581 (m-80) REVERT: B 639 ASP cc_start: 0.9090 (m-30) cc_final: 0.8834 (m-30) REVERT: B 640 MET cc_start: 0.9022 (tpp) cc_final: 0.8425 (tpp) REVERT: C 17 PHE cc_start: 0.8896 (p90) cc_final: 0.8682 (p90) REVERT: C 101 HIS cc_start: 0.8159 (m170) cc_final: 0.7129 (m-70) REVERT: C 107 ASN cc_start: 0.8881 (m-40) cc_final: 0.8614 (t0) REVERT: C 150 GLU cc_start: 0.9366 (pm20) cc_final: 0.9129 (tt0) REVERT: C 153 LEU cc_start: 0.9532 (mt) cc_final: 0.9304 (mt) REVERT: C 157 MET cc_start: 0.9253 (mtm) cc_final: 0.8888 (mtm) REVERT: C 173 TYR cc_start: 0.7449 (t80) cc_final: 0.6499 (t80) REVERT: C 174 TYR cc_start: 0.7801 (t80) cc_final: 0.7211 (t80) REVERT: C 177 TYR cc_start: 0.9112 (t80) cc_final: 0.8847 (t80) REVERT: C 185 MET cc_start: 0.6426 (mmm) cc_final: 0.5091 (mpp) REVERT: C 201 HIS cc_start: 0.9078 (m170) cc_final: 0.8830 (m170) REVERT: C 208 LEU cc_start: 0.8559 (mm) cc_final: 0.8315 (mt) REVERT: C 252 LEU cc_start: 0.7323 (mt) cc_final: 0.6993 (mt) REVERT: C 281 ASP cc_start: 0.8642 (m-30) cc_final: 0.8358 (m-30) REVERT: D 30 TRP cc_start: 0.8158 (p-90) cc_final: 0.7215 (p-90) REVERT: D 66 ASP cc_start: 0.5992 (p0) cc_final: 0.5744 (p0) REVERT: D 96 MET cc_start: 0.9064 (mmt) cc_final: 0.8838 (mmm) REVERT: D 148 ASP cc_start: 0.7127 (m-30) cc_final: 0.6834 (m-30) REVERT: D 176 LEU cc_start: 0.9651 (mt) cc_final: 0.9348 (tp) REVERT: D 189 GLU cc_start: 0.9009 (tm-30) cc_final: 0.8640 (tm-30) REVERT: D 201 HIS cc_start: 0.9298 (m170) cc_final: 0.8963 (m170) outliers start: 0 outliers final: 0 residues processed: 739 average time/residue: 0.2624 time to fit residues: 287.8778 Evaluate side-chains 639 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 639 time to evaluate : 1.678 ------------------------------------------------------------------------------- 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: 0.8980 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 183 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 180 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN A 191 GLN A 320 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 233 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.117862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.084426 restraints weight = 41539.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.087362 restraints weight = 21259.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.089395 restraints weight = 13649.056| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 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 = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.6944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16386 Z= 0.158 Angle : 0.602 7.133 22134 Z= 0.319 Chirality : 0.043 0.346 2360 Planarity : 0.003 0.046 2818 Dihedral : 10.757 177.844 2242 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 14.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % 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: 1.04 (0.19), residues: 1932 helix: 1.23 (0.15), residues: 1150 sheet: -0.41 (0.40), residues: 146 loop : 0.16 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP D 124 HIS 0.007 0.001 HIS C 101 PHE 0.024 0.002 PHE C 166 TYR 0.035 0.001 TYR D 142 ARG 0.010 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.03841 ( 871) hydrogen bonds : angle 4.81717 ( 2571) covalent geometry : bond 0.00347 (16386) covalent geometry : angle 0.60188 (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 720 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 720 time to evaluate : 1.741 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: 0.9230 (tptp) cc_final: 0.8913 (tppt) REVERT: A 12 LEU cc_start: 0.9622 (mt) cc_final: 0.9284 (mt) REVERT: A 30 LYS cc_start: 0.9540 (tptp) cc_final: 0.9301 (tptp) REVERT: A 107 LYS cc_start: 0.9195 (mttm) cc_final: 0.8774 (mtpp) REVERT: A 117 ARG cc_start: 0.9241 (tpp80) cc_final: 0.8888 (tpp80) REVERT: A 129 PHE cc_start: 0.9475 (m-10) cc_final: 0.9169 (m-10) REVERT: A 147 GLN cc_start: 0.9357 (mt0) cc_final: 0.8741 (mt0) REVERT: A 149 TYR cc_start: 0.9254 (t80) cc_final: 0.8329 (t80) REVERT: A 172 LEU cc_start: 0.9559 (mp) cc_final: 0.9263 (mp) REVERT: A 181 ASP cc_start: 0.8961 (m-30) cc_final: 0.8650 (m-30) REVERT: A 195 LEU cc_start: 0.9682 (mt) cc_final: 0.9419 (mt) REVERT: A 214 LYS cc_start: 0.8714 (tppt) cc_final: 0.8474 (tppt) REVERT: A 223 VAL cc_start: 0.9795 (m) cc_final: 0.9236 (p) REVERT: A 227 MET cc_start: 0.9246 (mtm) cc_final: 0.8737 (mtm) REVERT: A 231 ASP cc_start: 0.8379 (t0) cc_final: 0.7996 (p0) REVERT: A 232 ASN cc_start: 0.9047 (m-40) cc_final: 0.8309 (m110) REVERT: A 255 HIS cc_start: 0.8715 (t-90) cc_final: 0.7883 (t-90) REVERT: A 257 ASP cc_start: 0.9077 (m-30) cc_final: 0.8861 (m-30) REVERT: A 262 LEU cc_start: 0.9879 (mt) cc_final: 0.9596 (mt) REVERT: A 263 ASP cc_start: 0.9302 (m-30) cc_final: 0.9024 (m-30) REVERT: A 266 LYS cc_start: 0.8599 (ttpp) cc_final: 0.8070 (tmmt) REVERT: A 284 ILE cc_start: 0.9269 (mm) cc_final: 0.9052 (mm) REVERT: A 301 PHE cc_start: 0.9118 (m-10) cc_final: 0.8656 (m-10) REVERT: A 333 LYS cc_start: 0.9568 (tppt) cc_final: 0.9249 (tppp) REVERT: A 335 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7587 (mm-30) REVERT: A 344 GLU cc_start: 0.9274 (mt-10) cc_final: 0.8644 (mt-10) REVERT: A 345 LYS cc_start: 0.9760 (ttpt) cc_final: 0.9469 (ttmt) REVERT: A 349 LEU cc_start: 0.9688 (mt) cc_final: 0.9469 (mt) REVERT: A 350 ARG cc_start: 0.8966 (mtp-110) cc_final: 0.8552 (mtp180) REVERT: A 366 LYS cc_start: 0.9439 (mtmm) cc_final: 0.9187 (mtmm) REVERT: A 375 LYS cc_start: 0.9059 (mmtt) cc_final: 0.8767 (mmtm) REVERT: A 393 SER cc_start: 0.9193 (m) cc_final: 0.8374 (m) REVERT: A 402 GLU cc_start: 0.8276 (mp0) cc_final: 0.7593 (mp0) REVERT: A 415 ASN cc_start: 0.9261 (t0) cc_final: 0.8910 (t0) REVERT: A 420 MET cc_start: 0.9492 (tpp) cc_final: 0.9225 (mmm) REVERT: A 459 LYS cc_start: 0.8996 (mttp) cc_final: 0.8431 (mtmm) REVERT: A 466 MET cc_start: 0.9162 (ptt) cc_final: 0.8826 (ptt) REVERT: A 493 MET cc_start: 0.8895 (tmm) cc_final: 0.8523 (tmm) REVERT: A 501 GLN cc_start: 0.9363 (tt0) cc_final: 0.8726 (tm-30) REVERT: A 515 ASP cc_start: 0.8950 (m-30) cc_final: 0.8684 (m-30) REVERT: A 561 LEU cc_start: 0.9385 (tp) cc_final: 0.8966 (tp) REVERT: A 595 MET cc_start: 0.9040 (mmp) cc_final: 0.8749 (mmp) REVERT: A 615 MET cc_start: 0.9206 (mmt) cc_final: 0.8927 (mmm) REVERT: A 632 MET cc_start: 0.8572 (mpp) cc_final: 0.8345 (mpp) REVERT: A 640 MET cc_start: 0.9336 (tpp) cc_final: 0.8692 (tpp) REVERT: A 645 GLN cc_start: 0.9211 (tp40) cc_final: 0.8911 (tp-100) REVERT: A 646 GLN cc_start: 0.9335 (pt0) cc_final: 0.9101 (pt0) REVERT: A 667 LEU cc_start: 0.9417 (tt) cc_final: 0.9169 (tt) REVERT: B 8 LYS cc_start: 0.9350 (tptt) cc_final: 0.9052 (tppt) REVERT: B 12 LEU cc_start: 0.9645 (mt) cc_final: 0.9413 (mt) REVERT: B 55 LEU cc_start: 0.9784 (mt) cc_final: 0.9560 (mt) REVERT: B 58 LEU cc_start: 0.9766 (mt) cc_final: 0.9555 (mt) REVERT: B 60 GLU cc_start: 0.9304 (mt-10) cc_final: 0.9104 (tm-30) REVERT: B 87 LYS cc_start: 0.9323 (tptt) cc_final: 0.8891 (tttt) REVERT: B 88 LYS cc_start: 0.8918 (tttm) cc_final: 0.8603 (tttp) REVERT: B 117 ARG cc_start: 0.9394 (mmm-85) cc_final: 0.9039 (mmm-85) REVERT: B 119 GLU cc_start: 0.9326 (mp0) cc_final: 0.8951 (mp0) REVERT: B 149 TYR cc_start: 0.9326 (t80) cc_final: 0.8339 (t80) REVERT: B 150 GLN cc_start: 0.9500 (tp-100) cc_final: 0.9246 (tp-100) REVERT: B 167 LEU cc_start: 0.9348 (mt) cc_final: 0.9147 (mt) REVERT: B 172 LEU cc_start: 0.9449 (mp) cc_final: 0.9167 (mp) REVERT: B 173 LEU cc_start: 0.9424 (mt) cc_final: 0.9176 (mt) REVERT: B 184 ARG cc_start: 0.9399 (tpp80) cc_final: 0.8988 (tpp80) REVERT: B 211 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8428 (mm-30) REVERT: B 238 ASP cc_start: 0.8385 (t0) cc_final: 0.7849 (t70) REVERT: B 239 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8223 (tm-30) REVERT: B 252 ASN cc_start: 0.9429 (t0) cc_final: 0.8937 (t0) REVERT: B 263 ASP cc_start: 0.9227 (m-30) cc_final: 0.8790 (m-30) REVERT: B 274 ARG cc_start: 0.8803 (tpp80) cc_final: 0.8534 (tpp80) REVERT: B 321 GLU cc_start: 0.8880 (tm-30) cc_final: 0.8370 (tm-30) REVERT: B 322 MET cc_start: 0.9206 (mmm) cc_final: 0.8394 (mmm) REVERT: B 335 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8117 (mm-30) REVERT: B 350 ARG cc_start: 0.9308 (mmm-85) cc_final: 0.9084 (mmm-85) REVERT: B 355 TYR cc_start: 0.8748 (m-10) cc_final: 0.8499 (m-10) REVERT: B 362 ASP cc_start: 0.8878 (m-30) cc_final: 0.8645 (m-30) REVERT: B 384 GLU cc_start: 0.8838 (pm20) cc_final: 0.8440 (pm20) REVERT: B 387 GLN cc_start: 0.8897 (mt0) cc_final: 0.8657 (mp10) REVERT: B 393 SER cc_start: 0.9323 (m) cc_final: 0.9041 (p) REVERT: B 402 GLU cc_start: 0.9036 (tp30) cc_final: 0.8793 (tp30) REVERT: B 407 ILE cc_start: 0.9170 (mp) cc_final: 0.8667 (mp) REVERT: B 410 ASN cc_start: 0.8761 (m-40) cc_final: 0.8498 (m-40) REVERT: B 415 ASN cc_start: 0.9335 (t0) cc_final: 0.9040 (t0) REVERT: B 426 GLU cc_start: 0.8989 (pm20) cc_final: 0.8733 (pm20) REVERT: B 427 LYS cc_start: 0.9477 (ttmm) cc_final: 0.9225 (ttmm) REVERT: B 437 THR cc_start: 0.9648 (m) cc_final: 0.9414 (p) REVERT: B 543 ILE cc_start: 0.9720 (mm) cc_final: 0.9427 (mm) REVERT: B 588 GLN cc_start: 0.9309 (mm-40) cc_final: 0.8872 (mm-40) REVERT: B 612 TYR cc_start: 0.8950 (m-80) cc_final: 0.8669 (m-80) REVERT: B 615 MET cc_start: 0.9437 (mmp) cc_final: 0.9143 (mmp) REVERT: B 639 ASP cc_start: 0.9114 (m-30) cc_final: 0.8692 (m-30) REVERT: B 640 MET cc_start: 0.9060 (tpp) cc_final: 0.8487 (tpp) REVERT: C 17 PHE cc_start: 0.8943 (p90) cc_final: 0.8701 (p90) REVERT: C 101 HIS cc_start: 0.7623 (m170) cc_final: 0.7062 (m-70) REVERT: C 105 TYR cc_start: 0.8273 (m-80) cc_final: 0.7996 (m-80) REVERT: C 107 ASN cc_start: 0.8900 (m-40) cc_final: 0.8642 (t0) REVERT: C 150 GLU cc_start: 0.9373 (pm20) cc_final: 0.9132 (tt0) REVERT: C 153 LEU cc_start: 0.9504 (mt) cc_final: 0.9303 (mt) REVERT: C 157 MET cc_start: 0.9214 (mtm) cc_final: 0.8823 (mtm) REVERT: C 173 TYR cc_start: 0.7599 (t80) cc_final: 0.6667 (t80) REVERT: C 174 TYR cc_start: 0.7598 (t80) cc_final: 0.6991 (t80) REVERT: C 177 TYR cc_start: 0.9113 (t80) cc_final: 0.8814 (t80) REVERT: C 185 MET cc_start: 0.6355 (mmm) cc_final: 0.5252 (mpp) REVERT: C 201 HIS cc_start: 0.9115 (m170) cc_final: 0.8873 (m170) REVERT: C 208 LEU cc_start: 0.8934 (mm) cc_final: 0.8618 (mt) REVERT: C 229 ILE cc_start: 0.6929 (mt) cc_final: 0.6354 (mt) REVERT: C 233 ASN cc_start: 0.9388 (m110) cc_final: 0.8826 (m110) REVERT: C 237 GLU cc_start: 0.9586 (mm-30) cc_final: 0.9365 (pp20) REVERT: C 252 LEU cc_start: 0.7377 (mt) cc_final: 0.7075 (mt) REVERT: C 281 ASP cc_start: 0.8742 (m-30) cc_final: 0.8472 (m-30) REVERT: D 30 TRP cc_start: 0.8223 (p-90) cc_final: 0.7269 (p-90) REVERT: D 66 ASP cc_start: 0.6157 (p0) cc_final: 0.5929 (p0) REVERT: D 96 MET cc_start: 0.9073 (mmt) cc_final: 0.8846 (mmm) REVERT: D 148 ASP cc_start: 0.7115 (m-30) cc_final: 0.6843 (m-30) REVERT: D 176 LEU cc_start: 0.9647 (mt) cc_final: 0.9368 (tp) REVERT: D 189 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8674 (tm-30) REVERT: D 270 ASN cc_start: 0.8664 (m110) cc_final: 0.8450 (m110) outliers start: 0 outliers final: 0 residues processed: 720 average time/residue: 0.2606 time to fit residues: 280.5174 Evaluate side-chains 621 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 621 time to evaluate : 1.713 ------------------------------------------------------------------------------- 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: 0.8980 chunk 102 optimal weight: 0.7980 chunk 182 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 115 optimal weight: 0.0970 chunk 127 optimal weight: 0.0060 chunk 188 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN A 365 ASN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 180 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 365 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.120946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.087284 restraints weight = 41012.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.090464 restraints weight = 21125.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.092555 restraints weight = 13132.756| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3062 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3062 r_free = 0.3062 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3062 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.7129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16386 Z= 0.125 Angle : 0.616 7.518 22134 Z= 0.325 Chirality : 0.043 0.272 2360 Planarity : 0.003 0.043 2818 Dihedral : 10.557 177.339 2242 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 13.69 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: 0.89 (0.19), residues: 1932 helix: 1.04 (0.15), residues: 1157 sheet: -0.26 (0.41), residues: 134 loop : 0.16 (0.24), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 124 HIS 0.008 0.001 HIS D 201 PHE 0.024 0.002 PHE B 128 TYR 0.035 0.001 TYR D 142 ARG 0.011 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 871) hydrogen bonds : angle 4.86557 ( 2571) covalent geometry : bond 0.00276 (16386) covalent geometry : angle 0.61559 (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 725 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 725 time to evaluate : 1.730 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: 0.9197 (tptp) cc_final: 0.8860 (tppt) REVERT: A 12 LEU cc_start: 0.9624 (mt) cc_final: 0.8985 (mt) REVERT: A 15 GLU cc_start: 0.8781 (mt-10) cc_final: 0.8495 (mt-10) REVERT: A 107 LYS cc_start: 0.9185 (mttm) cc_final: 0.8741 (mtpp) REVERT: A 129 PHE cc_start: 0.9497 (m-10) cc_final: 0.9197 (m-10) REVERT: A 147 GLN cc_start: 0.9304 (mt0) cc_final: 0.8990 (mt0) REVERT: A 149 TYR cc_start: 0.9511 (t80) cc_final: 0.8442 (t80) REVERT: A 162 LYS cc_start: 0.9015 (ttmt) cc_final: 0.8630 (ttmt) REVERT: A 172 LEU cc_start: 0.9544 (mp) cc_final: 0.9200 (mp) REVERT: A 181 ASP cc_start: 0.8958 (m-30) cc_final: 0.8677 (m-30) REVERT: A 195 LEU cc_start: 0.9701 (mt) cc_final: 0.9456 (mt) REVERT: A 214 LYS cc_start: 0.8674 (tppt) cc_final: 0.8430 (tppt) REVERT: A 227 MET cc_start: 0.9260 (mtm) cc_final: 0.8755 (mtm) REVERT: A 231 ASP cc_start: 0.8232 (t0) cc_final: 0.7786 (p0) REVERT: A 232 ASN cc_start: 0.8997 (m-40) cc_final: 0.8198 (m110) REVERT: A 235 ARG cc_start: 0.9110 (ttm110) cc_final: 0.8489 (ttm-80) REVERT: A 236 TYR cc_start: 0.9109 (t80) cc_final: 0.8713 (t80) REVERT: A 257 ASP cc_start: 0.9096 (m-30) cc_final: 0.8816 (m-30) REVERT: A 262 LEU cc_start: 0.9869 (mt) cc_final: 0.9574 (mt) REVERT: A 263 ASP cc_start: 0.9282 (m-30) cc_final: 0.8981 (m-30) REVERT: A 266 LYS cc_start: 0.8673 (ttpp) cc_final: 0.8143 (tmmt) REVERT: A 301 PHE cc_start: 0.9114 (m-10) cc_final: 0.8748 (m-10) REVERT: A 319 MET cc_start: 0.9076 (tpp) cc_final: 0.8445 (tpp) REVERT: A 333 LYS cc_start: 0.9578 (tppt) cc_final: 0.9263 (tppp) REVERT: A 335 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7717 (mm-30) REVERT: A 344 GLU cc_start: 0.9249 (mt-10) cc_final: 0.8588 (mt-10) REVERT: A 345 LYS cc_start: 0.9741 (ttpt) cc_final: 0.9427 (ttmt) REVERT: A 349 LEU cc_start: 0.9669 (mt) cc_final: 0.9453 (mt) REVERT: A 366 LYS cc_start: 0.9451 (mtmm) cc_final: 0.9187 (mtmm) REVERT: A 375 LYS cc_start: 0.9005 (mmtt) cc_final: 0.8798 (mmtm) REVERT: A 393 SER cc_start: 0.9209 (m) cc_final: 0.8407 (m) REVERT: A 402 GLU cc_start: 0.8360 (mp0) cc_final: 0.7750 (mp0) REVERT: A 407 ILE cc_start: 0.9262 (mt) cc_final: 0.8996 (mt) REVERT: A 415 ASN cc_start: 0.9283 (t0) cc_final: 0.9052 (t0) REVERT: A 459 LYS cc_start: 0.8976 (mttp) cc_final: 0.8370 (mtmm) REVERT: A 466 MET cc_start: 0.9178 (ptt) cc_final: 0.8872 (ptt) REVERT: A 471 TYR cc_start: 0.9085 (t80) cc_final: 0.8845 (t80) REVERT: A 474 GLN cc_start: 0.9292 (mt0) cc_final: 0.8924 (mm-40) REVERT: A 493 MET cc_start: 0.8859 (tmm) cc_final: 0.8482 (tmm) REVERT: A 501 GLN cc_start: 0.9362 (tt0) cc_final: 0.8734 (tm-30) REVERT: A 515 ASP cc_start: 0.8904 (m-30) cc_final: 0.8628 (m-30) REVERT: A 550 MET cc_start: 0.8513 (mtt) cc_final: 0.7599 (mtt) REVERT: A 561 LEU cc_start: 0.9341 (tp) cc_final: 0.8914 (tp) REVERT: A 595 MET cc_start: 0.8952 (mmp) cc_final: 0.8748 (mmp) REVERT: A 599 GLU cc_start: 0.9219 (pm20) cc_final: 0.8984 (pm20) REVERT: A 615 MET cc_start: 0.9170 (mmt) cc_final: 0.8920 (mmm) REVERT: A 628 GLU cc_start: 0.8826 (mm-30) cc_final: 0.8556 (mm-30) REVERT: A 640 MET cc_start: 0.9366 (tpp) cc_final: 0.8687 (tpp) REVERT: A 645 GLN cc_start: 0.9191 (tp40) cc_final: 0.8898 (tp-100) REVERT: A 667 LEU cc_start: 0.9418 (tt) cc_final: 0.9177 (tt) REVERT: B 8 LYS cc_start: 0.9373 (tptt) cc_final: 0.9062 (tppt) REVERT: B 12 LEU cc_start: 0.9641 (mt) cc_final: 0.9395 (mt) REVERT: B 21 ASP cc_start: 0.8698 (t70) cc_final: 0.8494 (t0) REVERT: B 55 LEU cc_start: 0.9779 (mt) cc_final: 0.9559 (mt) REVERT: B 58 LEU cc_start: 0.9757 (mt) cc_final: 0.9552 (mt) REVERT: B 87 LYS cc_start: 0.9282 (tptt) cc_final: 0.8905 (tttt) REVERT: B 88 LYS cc_start: 0.8961 (tttm) cc_final: 0.8638 (tttp) REVERT: B 98 PHE cc_start: 0.9412 (t80) cc_final: 0.9105 (t80) REVERT: B 117 ARG cc_start: 0.9398 (mmm-85) cc_final: 0.9019 (mmm-85) REVERT: B 119 GLU cc_start: 0.9317 (mp0) cc_final: 0.8992 (mp0) REVERT: B 139 GLU cc_start: 0.9152 (mp0) cc_final: 0.8753 (mp0) REVERT: B 149 TYR cc_start: 0.9327 (t80) cc_final: 0.8394 (t80) REVERT: B 162 LYS cc_start: 0.9303 (tppt) cc_final: 0.9061 (tppt) REVERT: B 167 LEU cc_start: 0.9396 (mt) cc_final: 0.8990 (mt) REVERT: B 172 LEU cc_start: 0.9344 (mp) cc_final: 0.9103 (mp) REVERT: B 173 LEU cc_start: 0.9417 (mt) cc_final: 0.9176 (mt) REVERT: B 211 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8463 (mm-30) REVERT: B 221 LYS cc_start: 0.8909 (mmmm) cc_final: 0.8453 (mttp) REVERT: B 228 LYS cc_start: 0.9467 (mmmm) cc_final: 0.9241 (tppt) REVERT: B 238 ASP cc_start: 0.8395 (t0) cc_final: 0.7756 (t70) REVERT: B 239 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8324 (tm-30) REVERT: B 252 ASN cc_start: 0.9419 (t0) cc_final: 0.8815 (t0) REVERT: B 263 ASP cc_start: 0.9169 (m-30) cc_final: 0.8719 (m-30) REVERT: B 321 GLU cc_start: 0.8870 (tm-30) cc_final: 0.8332 (tm-30) REVERT: B 322 MET cc_start: 0.9204 (mmm) cc_final: 0.8392 (mmm) REVERT: B 335 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8037 (mm-30) REVERT: B 350 ARG cc_start: 0.9234 (mmm-85) cc_final: 0.8955 (mmm-85) REVERT: B 355 TYR cc_start: 0.8890 (m-10) cc_final: 0.8329 (m-10) REVERT: B 358 ILE cc_start: 0.9745 (mm) cc_final: 0.9492 (mm) REVERT: B 374 SER cc_start: 0.9333 (t) cc_final: 0.8796 (p) REVERT: B 384 GLU cc_start: 0.8736 (pm20) cc_final: 0.8411 (pm20) REVERT: B 387 GLN cc_start: 0.8926 (mt0) cc_final: 0.8695 (mp10) REVERT: B 402 GLU cc_start: 0.9038 (tp30) cc_final: 0.8779 (tp30) REVERT: B 403 ILE cc_start: 0.8992 (tp) cc_final: 0.8673 (tp) REVERT: B 407 ILE cc_start: 0.9020 (mp) cc_final: 0.8534 (mp) REVERT: B 410 ASN cc_start: 0.8956 (m-40) cc_final: 0.8697 (m-40) REVERT: B 415 ASN cc_start: 0.9313 (t0) cc_final: 0.9084 (t0) REVERT: B 437 THR cc_start: 0.9639 (m) cc_final: 0.9405 (p) REVERT: B 477 ILE cc_start: 0.9468 (mp) cc_final: 0.9049 (tt) REVERT: B 493 MET cc_start: 0.9387 (tmm) cc_final: 0.9154 (tmm) REVERT: B 494 MET cc_start: 0.9377 (mmt) cc_final: 0.8970 (mmt) REVERT: B 515 ASP cc_start: 0.8990 (m-30) cc_final: 0.8786 (m-30) REVERT: B 543 ILE cc_start: 0.9723 (mm) cc_final: 0.9442 (mm) REVERT: B 550 MET cc_start: 0.8530 (mtm) cc_final: 0.8260 (mtt) REVERT: B 570 MET cc_start: 0.8780 (mtp) cc_final: 0.8398 (mtp) REVERT: B 602 GLU cc_start: 0.8369 (pp20) cc_final: 0.8150 (pp20) REVERT: B 612 TYR cc_start: 0.8914 (m-80) cc_final: 0.8713 (m-80) REVERT: B 634 MET cc_start: 0.9372 (mmm) cc_final: 0.9058 (mpp) REVERT: B 639 ASP cc_start: 0.9084 (m-30) cc_final: 0.8689 (m-30) REVERT: B 640 MET cc_start: 0.9095 (tpp) cc_final: 0.8537 (tpp) REVERT: B 664 THR cc_start: 0.9041 (p) cc_final: 0.8219 (p) REVERT: B 671 ASP cc_start: 0.8963 (m-30) cc_final: 0.8755 (m-30) REVERT: C 17 PHE cc_start: 0.8924 (p90) cc_final: 0.8692 (p90) REVERT: C 37 LEU cc_start: 0.1786 (tp) cc_final: 0.1585 (tp) REVERT: C 74 MET cc_start: 0.8031 (mpp) cc_final: 0.7677 (mpp) REVERT: C 90 LEU cc_start: 0.9577 (mt) cc_final: 0.9300 (mt) REVERT: C 101 HIS cc_start: 0.7496 (m170) cc_final: 0.6873 (m90) REVERT: C 105 TYR cc_start: 0.8366 (m-80) cc_final: 0.8093 (m-80) REVERT: C 107 ASN cc_start: 0.8854 (m-40) cc_final: 0.8579 (t0) REVERT: C 150 GLU cc_start: 0.9365 (pm20) cc_final: 0.9072 (tt0) REVERT: C 153 LEU cc_start: 0.9523 (mt) cc_final: 0.9301 (mt) REVERT: C 157 MET cc_start: 0.9236 (mtm) cc_final: 0.8881 (mtm) REVERT: C 173 TYR cc_start: 0.7567 (t80) cc_final: 0.6660 (t80) REVERT: C 174 TYR cc_start: 0.7648 (t80) cc_final: 0.6934 (t80) REVERT: C 177 TYR cc_start: 0.9111 (t80) cc_final: 0.8763 (t80) REVERT: C 185 MET cc_start: 0.6487 (mmm) cc_final: 0.5606 (mpp) REVERT: C 208 LEU cc_start: 0.8917 (mm) cc_final: 0.8545 (mt) REVERT: C 229 ILE cc_start: 0.6878 (mt) cc_final: 0.6547 (mm) REVERT: C 233 ASN cc_start: 0.9412 (m110) cc_final: 0.8861 (m110) REVERT: C 252 LEU cc_start: 0.7346 (mt) cc_final: 0.7038 (mt) REVERT: C 281 ASP cc_start: 0.8733 (m-30) cc_final: 0.8472 (m-30) REVERT: D 30 TRP cc_start: 0.8203 (p-90) cc_final: 0.7296 (p-90) REVERT: D 66 ASP cc_start: 0.5980 (p0) cc_final: 0.5710 (p0) REVERT: D 96 MET cc_start: 0.9035 (mmt) cc_final: 0.8798 (mmm) REVERT: D 148 ASP cc_start: 0.7183 (m-30) cc_final: 0.6915 (m-30) REVERT: D 176 LEU cc_start: 0.9641 (mt) cc_final: 0.9356 (tp) REVERT: D 189 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8625 (tm-30) REVERT: D 201 HIS cc_start: 0.9325 (m170) cc_final: 0.9033 (m170) REVERT: D 270 ASN cc_start: 0.8818 (m110) cc_final: 0.8578 (m110) outliers start: 0 outliers final: 0 residues processed: 725 average time/residue: 0.2721 time to fit residues: 293.1595 Evaluate side-chains 639 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 639 time to evaluate : 1.764 ------------------------------------------------------------------------------- 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: 5.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 160 optimal weight: 6.9990 chunk 106 optimal weight: 0.2980 chunk 120 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 127 optimal weight: 0.0060 chunk 68 optimal weight: 8.9990 chunk 70 optimal weight: 8.9990 overall best weight: 2.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN D 132 GLN D 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.117553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.084117 restraints weight = 42285.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.087100 restraints weight = 21760.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.089197 restraints weight = 13817.223| |-----------------------------------------------------------------------------| r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 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 = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.7235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16386 Z= 0.186 Angle : 0.643 7.175 22134 Z= 0.341 Chirality : 0.043 0.280 2360 Planarity : 0.004 0.044 2818 Dihedral : 10.682 179.694 2242 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.86 (0.19), residues: 1932 helix: 1.00 (0.15), residues: 1155 sheet: -0.41 (0.40), residues: 146 loop : 0.24 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 124 HIS 0.012 0.001 HIS C 201 PHE 0.022 0.002 PHE C 227 TYR 0.039 0.002 TYR D 142 ARG 0.007 0.001 ARG B 164 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 871) hydrogen bonds : angle 4.96640 ( 2571) covalent geometry : bond 0.00406 (16386) covalent geometry : angle 0.64287 (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: 0 poor density : 718 time to evaluate : 1.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9190 (tptp) cc_final: 0.8898 (tppt) REVERT: A 12 LEU cc_start: 0.9618 (mt) cc_final: 0.9277 (mt) REVERT: A 65 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8373 (mp0) REVERT: A 71 LEU cc_start: 0.9646 (mt) cc_final: 0.9443 (mt) REVERT: A 107 LYS cc_start: 0.9268 (mttm) cc_final: 0.8845 (mtpp) REVERT: A 129 PHE cc_start: 0.9518 (m-10) cc_final: 0.9258 (m-10) REVERT: A 143 LEU cc_start: 0.9443 (tp) cc_final: 0.9226 (tp) REVERT: A 147 GLN cc_start: 0.9374 (mt0) cc_final: 0.8548 (mt0) REVERT: A 149 TYR cc_start: 0.9507 (t80) cc_final: 0.8252 (t80) REVERT: A 172 LEU cc_start: 0.9560 (mp) cc_final: 0.9262 (mp) REVERT: A 181 ASP cc_start: 0.8966 (m-30) cc_final: 0.8638 (m-30) REVERT: A 195 LEU cc_start: 0.9697 (mt) cc_final: 0.9441 (mt) REVERT: A 214 LYS cc_start: 0.8706 (tppt) cc_final: 0.8447 (tppt) REVERT: A 218 ASN cc_start: 0.9520 (t0) cc_final: 0.9272 (t0) REVERT: A 223 VAL cc_start: 0.9786 (m) cc_final: 0.9226 (p) REVERT: A 227 MET cc_start: 0.9206 (mtm) cc_final: 0.8815 (mtm) REVERT: A 231 ASP cc_start: 0.8418 (t0) cc_final: 0.7853 (p0) REVERT: A 232 ASN cc_start: 0.8940 (m-40) cc_final: 0.8192 (m110) REVERT: A 238 ASP cc_start: 0.8248 (p0) cc_final: 0.7871 (p0) REVERT: A 255 HIS cc_start: 0.8710 (t-90) cc_final: 0.8014 (t-90) REVERT: A 262 LEU cc_start: 0.9870 (mt) cc_final: 0.9576 (mt) REVERT: A 263 ASP cc_start: 0.9286 (m-30) cc_final: 0.8986 (m-30) REVERT: A 266 LYS cc_start: 0.8725 (ttpp) cc_final: 0.8177 (tmmt) REVERT: A 301 PHE cc_start: 0.9137 (m-10) cc_final: 0.8732 (m-10) REVERT: A 319 MET cc_start: 0.9112 (tpp) cc_final: 0.8775 (tpp) REVERT: A 333 LYS cc_start: 0.9564 (tppt) cc_final: 0.9255 (tppp) REVERT: A 335 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7601 (mm-30) REVERT: A 344 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8664 (mt-10) REVERT: A 345 LYS cc_start: 0.9743 (ttpt) cc_final: 0.9426 (ttmt) REVERT: A 349 LEU cc_start: 0.9697 (mt) cc_final: 0.9455 (mt) REVERT: A 350 ARG cc_start: 0.8995 (mtp-110) cc_final: 0.8558 (mtp180) REVERT: A 365 ASN cc_start: 0.9214 (m110) cc_final: 0.8853 (m110) REVERT: A 366 LYS cc_start: 0.9432 (mtmm) cc_final: 0.9222 (mtmm) REVERT: A 393 SER cc_start: 0.9209 (m) cc_final: 0.8436 (m) REVERT: A 402 GLU cc_start: 0.8369 (mp0) cc_final: 0.7728 (mp0) REVERT: A 407 ILE cc_start: 0.9318 (mt) cc_final: 0.9080 (mt) REVERT: A 415 ASN cc_start: 0.9328 (t0) cc_final: 0.8599 (t0) REVERT: A 418 ASN cc_start: 0.9209 (m110) cc_final: 0.8773 (m-40) REVERT: A 459 LYS cc_start: 0.9023 (mttp) cc_final: 0.8463 (mtmm) REVERT: A 466 MET cc_start: 0.9234 (ptt) cc_final: 0.8928 (ptt) REVERT: A 474 GLN cc_start: 0.9327 (mt0) cc_final: 0.8984 (mm-40) REVERT: A 493 MET cc_start: 0.8836 (tmm) cc_final: 0.8474 (tmm) REVERT: A 501 GLN cc_start: 0.9375 (tt0) cc_final: 0.8761 (tm-30) REVERT: A 515 ASP cc_start: 0.8995 (m-30) cc_final: 0.8761 (m-30) REVERT: A 550 MET cc_start: 0.8405 (mtt) cc_final: 0.8023 (mtt) REVERT: A 561 LEU cc_start: 0.9390 (tp) cc_final: 0.8983 (tp) REVERT: A 615 MET cc_start: 0.9233 (mmt) cc_final: 0.8905 (mmm) REVERT: A 628 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8603 (mm-30) REVERT: A 632 MET cc_start: 0.8465 (mpp) cc_final: 0.8236 (mpp) REVERT: A 640 MET cc_start: 0.9358 (tpp) cc_final: 0.8726 (tpp) REVERT: A 645 GLN cc_start: 0.9212 (tp40) cc_final: 0.8929 (tp40) REVERT: A 667 LEU cc_start: 0.9477 (tt) cc_final: 0.9187 (tt) REVERT: B 8 LYS cc_start: 0.9357 (tptt) cc_final: 0.9056 (tppt) REVERT: B 12 LEU cc_start: 0.9640 (mt) cc_final: 0.9407 (mt) REVERT: B 55 LEU cc_start: 0.9780 (mt) cc_final: 0.9552 (mt) REVERT: B 87 LYS cc_start: 0.9334 (tptt) cc_final: 0.8924 (tttt) REVERT: B 88 LYS cc_start: 0.8983 (tttm) cc_final: 0.8695 (tttp) REVERT: B 98 PHE cc_start: 0.9305 (t80) cc_final: 0.8931 (t80) REVERT: B 117 ARG cc_start: 0.9404 (mmm-85) cc_final: 0.9033 (mmm-85) REVERT: B 119 GLU cc_start: 0.9314 (mp0) cc_final: 0.9011 (mp0) REVERT: B 143 LEU cc_start: 0.9184 (tp) cc_final: 0.8359 (tp) REVERT: B 148 GLU cc_start: 0.8954 (mp0) cc_final: 0.7838 (mp0) REVERT: B 149 TYR cc_start: 0.9415 (t80) cc_final: 0.8326 (t80) REVERT: B 162 LYS cc_start: 0.9347 (tppt) cc_final: 0.9086 (tppt) REVERT: B 167 LEU cc_start: 0.9420 (mt) cc_final: 0.9150 (mt) REVERT: B 172 LEU cc_start: 0.9390 (mp) cc_final: 0.9167 (mp) REVERT: B 173 LEU cc_start: 0.9400 (mt) cc_final: 0.9155 (mt) REVERT: B 211 GLU cc_start: 0.8802 (mm-30) cc_final: 0.8310 (mm-30) REVERT: B 235 ARG cc_start: 0.9149 (ttm110) cc_final: 0.8615 (mtm-85) REVERT: B 238 ASP cc_start: 0.8565 (t0) cc_final: 0.7963 (t70) REVERT: B 239 GLN cc_start: 0.9004 (tm-30) cc_final: 0.8347 (tm-30) REVERT: B 252 ASN cc_start: 0.9415 (t0) cc_final: 0.9133 (t0) REVERT: B 263 ASP cc_start: 0.9202 (m-30) cc_final: 0.8772 (m-30) REVERT: B 321 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8378 (tm-30) REVERT: B 322 MET cc_start: 0.9203 (mmm) cc_final: 0.8133 (mmm) REVERT: B 335 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8126 (mm-30) REVERT: B 355 TYR cc_start: 0.8851 (m-10) cc_final: 0.8524 (m-10) REVERT: B 374 SER cc_start: 0.9244 (t) cc_final: 0.8713 (p) REVERT: B 384 GLU cc_start: 0.8788 (pm20) cc_final: 0.8456 (pm20) REVERT: B 407 ILE cc_start: 0.9102 (mp) cc_final: 0.8773 (mp) REVERT: B 410 ASN cc_start: 0.8949 (m-40) cc_final: 0.8662 (m-40) REVERT: B 415 ASN cc_start: 0.9385 (t0) cc_final: 0.9099 (t0) REVERT: B 426 GLU cc_start: 0.9011 (pm20) cc_final: 0.8744 (pm20) REVERT: B 427 LYS cc_start: 0.9479 (ttmm) cc_final: 0.9209 (ttmm) REVERT: B 437 THR cc_start: 0.9652 (m) cc_final: 0.9403 (p) REVERT: B 505 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8477 (mt-10) REVERT: B 522 TYR cc_start: 0.9319 (m-80) cc_final: 0.9060 (m-10) REVERT: B 543 ILE cc_start: 0.9734 (mm) cc_final: 0.9516 (mm) REVERT: B 550 MET cc_start: 0.8706 (mtm) cc_final: 0.8481 (mtt) REVERT: B 612 TYR cc_start: 0.8945 (m-80) cc_final: 0.8703 (m-80) REVERT: B 634 MET cc_start: 0.9410 (mmm) cc_final: 0.9045 (mpp) REVERT: B 640 MET cc_start: 0.9054 (tpp) cc_final: 0.8496 (tpp) REVERT: B 664 THR cc_start: 0.8950 (p) cc_final: 0.8301 (p) REVERT: B 668 ASN cc_start: 0.9209 (m-40) cc_final: 0.8923 (m-40) REVERT: B 671 ASP cc_start: 0.9031 (m-30) cc_final: 0.8816 (m-30) REVERT: B 680 LYS cc_start: 0.8879 (mttt) cc_final: 0.8602 (mtpt) REVERT: C 17 PHE cc_start: 0.9030 (p90) cc_final: 0.8755 (p90) REVERT: C 74 MET cc_start: 0.7935 (mpp) cc_final: 0.7704 (mpp) REVERT: C 101 HIS cc_start: 0.7730 (m170) cc_final: 0.7234 (m170) REVERT: C 105 TYR cc_start: 0.8350 (m-80) cc_final: 0.8018 (m-80) REVERT: C 107 ASN cc_start: 0.8920 (m-40) cc_final: 0.8633 (t0) REVERT: C 143 LYS cc_start: 0.9026 (tptp) cc_final: 0.8552 (pptt) REVERT: C 150 GLU cc_start: 0.9395 (pm20) cc_final: 0.9127 (tt0) REVERT: C 153 LEU cc_start: 0.9515 (mt) cc_final: 0.9310 (mt) REVERT: C 157 MET cc_start: 0.9239 (mtm) cc_final: 0.8935 (mtm) REVERT: C 173 TYR cc_start: 0.7508 (t80) cc_final: 0.6669 (t80) REVERT: C 174 TYR cc_start: 0.7699 (t80) cc_final: 0.6993 (t80) REVERT: C 177 TYR cc_start: 0.9119 (t80) cc_final: 0.8815 (t80) REVERT: C 179 TYR cc_start: 0.8869 (t80) cc_final: 0.8553 (t80) REVERT: C 185 MET cc_start: 0.6414 (mmm) cc_final: 0.5283 (mpp) REVERT: C 208 LEU cc_start: 0.8999 (mm) cc_final: 0.8614 (mt) REVERT: C 229 ILE cc_start: 0.6968 (mt) cc_final: 0.6425 (mt) REVERT: C 233 ASN cc_start: 0.9382 (m110) cc_final: 0.8690 (m110) REVERT: C 252 LEU cc_start: 0.7365 (mt) cc_final: 0.7043 (mt) REVERT: C 281 ASP cc_start: 0.8804 (m-30) cc_final: 0.8535 (m-30) REVERT: D 30 TRP cc_start: 0.8279 (p-90) cc_final: 0.7251 (p-90) REVERT: D 54 THR cc_start: 0.6989 (m) cc_final: 0.6778 (p) REVERT: D 96 MET cc_start: 0.9035 (mmt) cc_final: 0.8823 (mmm) REVERT: D 148 ASP cc_start: 0.7191 (m-30) cc_final: 0.6949 (m-30) REVERT: D 176 LEU cc_start: 0.9635 (mt) cc_final: 0.9386 (tp) REVERT: D 189 GLU cc_start: 0.9080 (tm-30) cc_final: 0.8761 (tm-30) REVERT: D 229 ILE cc_start: 0.8912 (mp) cc_final: 0.8666 (tp) REVERT: D 270 ASN cc_start: 0.8738 (m110) cc_final: 0.8493 (m110) outliers start: 0 outliers final: 0 residues processed: 718 average time/residue: 0.2628 time to fit residues: 282.5607 Evaluate side-chains 639 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 639 time to evaluate : 1.736 ------------------------------------------------------------------------------- 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: 0.7980 chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 105 optimal weight: 0.2980 chunk 179 optimal weight: 9.9990 chunk 190 optimal weight: 4.9990 chunk 58 optimal weight: 0.0770 chunk 180 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS A 447 ASN ** A 668 ASN ** 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 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.121958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.088124 restraints weight = 41465.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.091267 restraints weight = 21715.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.093441 restraints weight = 13614.663| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.7449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16386 Z= 0.130 Angle : 0.642 9.319 22134 Z= 0.339 Chirality : 0.043 0.228 2360 Planarity : 0.003 0.042 2818 Dihedral : 10.476 179.309 2242 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: 0.78 (0.19), residues: 1932 helix: 0.97 (0.15), residues: 1151 sheet: -0.30 (0.42), residues: 138 loop : 0.10 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 124 HIS 0.010 0.001 HIS C 201 PHE 0.025 0.002 PHE B 128 TYR 0.037 0.001 TYR D 142 ARG 0.007 0.001 ARG B 164 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 871) hydrogen bonds : angle 4.91042 ( 2571) covalent geometry : bond 0.00291 (16386) covalent geometry : angle 0.64248 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6640.97 seconds wall clock time: 116 minutes 58.74 seconds (7018.74 seconds total)