Starting phenix.real_space_refine on Sat May 17 17:03:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byw_45046/05_2025/9byw_45046_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byw_45046/05_2025/9byw_45046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9byw_45046/05_2025/9byw_45046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byw_45046/05_2025/9byw_45046.map" model { file = "/net/cci-nas-00/data/ceres_data/9byw_45046/05_2025/9byw_45046_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byw_45046/05_2025/9byw_45046_neut.cif" } resolution = 4.64 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): 0.05s 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: 10.17, per 1000 atoms: 0.63 Number of scatterers: 16038 At special positions: 0 Unit cell: (96.615, 125.091, 132.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.98 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: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.095A 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: 3.948A 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: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.676A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.730A 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: 5.119A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.067A 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: 3.669A 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: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.360A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.394A 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: 7.501A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.478A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.185A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.382A 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: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.593A 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: 5.23 Time building geometry restraints manager: 4.66 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: 4896 1.34 - 1.46: 2984 1.46 - 1.58: 8324 1.58 - 1.70: 26 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.600 -0.060 1.25e-02 6.40e+03 2.31e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.038 1.20e-02 6.94e+03 1.01e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.033 1.08e-02 8.57e+03 9.33e+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 7.16e+00 bond pdb=" CA ILE C 35 " pdb=" CB ILE C 35 " ideal model delta sigma weight residual 1.537 1.569 -0.032 1.21e-02 6.83e+03 7.12e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21575 2.09 - 4.19: 517 4.19 - 6.28: 37 6.28 - 8.37: 1 8.37 - 10.47: 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 110.54 116.65 -6.11 1.36e+00 5.41e-01 2.02e+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 113.50 117.83 -4.33 1.23e+00 6.61e-01 1.24e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.70 -3.99 1.15e+00 7.56e-01 1.21e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.58 3.61 1.06e+00 8.90e-01 1.16e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 9469 35.79 - 71.59: 338 71.59 - 107.38: 37 107.38 - 143.17: 3 143.17 - 178.97: 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 -58.32 120.65 -178.97 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 301.68 151.18 150.51 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 31.86 148.12 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: 2144 0.093 - 0.186: 182 0.186 - 0.279: 29 0.279 - 0.372: 3 0.372 - 0.465: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.40e+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 4.61e+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 2.95e+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 4.15e-02 2.75e+00 pdb=" N PRO D 75 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " 0.017 2.00e-02 2.50e+03 1.12e-02 2.20e+00 pdb=" CG PHE D 92 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.001 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 C 169 " 0.017 2.00e-02 2.50e+03 9.90e-03 1.96e+00 pdb=" CG TYR C 169 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 169 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 169 " 0.008 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 129 2.51 - 3.11: 11553 3.11 - 3.70: 27038 3.70 - 4.30: 41546 4.30 - 4.90: 65401 Nonbonded interactions: 145667 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.961 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.964 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 145662 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: 0.010 Normalize map: mean=0, sd=1: 0.680 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: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 38.420 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5821 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 0.060 16386 Z= 0.315 Angle : 0.740 10.466 22134 Z= 0.463 Chirality : 0.057 0.465 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.953 178.965 6154 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.34 % Allowed : 15.38 % Favored : 83.28 % 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: 0.55 (0.18), residues: 1932 helix: 0.58 (0.14), residues: 1151 sheet: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE D 92 TYR 0.020 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 6.51765 ( 2571) covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74048 (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 802 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 779 time to evaluate : 2.103 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 58 LEU cc_start: 0.9137 (mt) cc_final: 0.6570 (mt) REVERT: A 95 MET cc_start: 0.8221 (tpp) cc_final: 0.7885 (mmm) REVERT: A 136 LYS cc_start: 0.8134 (tptt) cc_final: 0.7406 (tttt) REVERT: A 143 LEU cc_start: 0.9004 (tp) cc_final: 0.8631 (tp) REVERT: A 147 GLN cc_start: 0.8415 (mt0) cc_final: 0.7924 (mt0) REVERT: A 155 THR cc_start: 0.9063 (m) cc_final: 0.8760 (m) REVERT: A 158 ASN cc_start: 0.8072 (m-40) cc_final: 0.7862 (m-40) REVERT: A 166 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8442 (mm-30) REVERT: A 172 LEU cc_start: 0.8583 (mp) cc_final: 0.8358 (mp) REVERT: A 173 LEU cc_start: 0.7045 (mt) cc_final: 0.6693 (mt) REVERT: A 181 ASP cc_start: 0.7470 (m-30) cc_final: 0.6983 (m-30) REVERT: A 190 MET cc_start: 0.7882 (mtt) cc_final: 0.7646 (mtt) REVERT: A 205 LYS cc_start: 0.7012 (mttp) cc_final: 0.6684 (mttt) REVERT: A 220 THR cc_start: 0.8504 (m) cc_final: 0.8301 (p) REVERT: A 344 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7828 (mt-10) REVERT: A 367 VAL cc_start: 0.8759 (m) cc_final: 0.8384 (m) REVERT: A 550 MET cc_start: 0.6875 (mtm) cc_final: 0.6158 (mtp) REVERT: A 597 ILE cc_start: 0.8618 (pt) cc_final: 0.8416 (pt) REVERT: A 634 MET cc_start: 0.8480 (mmp) cc_final: 0.8013 (mmm) REVERT: A 637 VAL cc_start: 0.8973 (t) cc_final: 0.8593 (p) REVERT: A 645 GLN cc_start: 0.6999 (tp40) cc_final: 0.6696 (tp-100) REVERT: A 650 GLN cc_start: 0.6815 (mt0) cc_final: 0.6426 (mt0) REVERT: A 655 THR cc_start: 0.7160 (m) cc_final: 0.6460 (m) REVERT: A 658 LEU cc_start: 0.8182 (mt) cc_final: 0.7635 (mt) REVERT: A 667 LEU cc_start: 0.8626 (tt) cc_final: 0.8258 (tp) REVERT: B 62 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8326 (mp10) REVERT: B 89 PHE cc_start: 0.7137 (t80) cc_final: 0.6771 (t80) REVERT: B 96 SER cc_start: 0.9284 (m) cc_final: 0.8892 (p) REVERT: B 125 VAL cc_start: 0.9206 (t) cc_final: 0.8983 (t) REVERT: B 143 LEU cc_start: 0.9058 (tp) cc_final: 0.8846 (tp) REVERT: B 179 LEU cc_start: 0.8385 (tp) cc_final: 0.8156 (tp) REVERT: B 191 GLN cc_start: 0.8594 (mm-40) cc_final: 0.8217 (mm-40) REVERT: B 193 SER cc_start: 0.8165 (m) cc_final: 0.7927 (p) REVERT: B 200 SER cc_start: 0.8143 (t) cc_final: 0.7870 (m) REVERT: B 213 ILE cc_start: 0.8627 (mt) cc_final: 0.8265 (mp) REVERT: B 216 VAL cc_start: 0.8357 (OUTLIER) cc_final: 0.7776 (m) REVERT: B 232 ASN cc_start: 0.7484 (OUTLIER) cc_final: 0.7265 (t0) REVERT: B 265 LYS cc_start: 0.7847 (mmtt) cc_final: 0.7594 (mmmm) REVERT: B 282 VAL cc_start: 0.8804 (t) cc_final: 0.8492 (m) REVERT: B 288 PHE cc_start: 0.7210 (t80) cc_final: 0.6440 (t80) REVERT: B 319 MET cc_start: 0.7580 (tpp) cc_final: 0.6817 (tpp) REVERT: B 358 ILE cc_start: 0.8730 (mm) cc_final: 0.8316 (mm) REVERT: B 362 ASP cc_start: 0.5782 (m-30) cc_final: 0.4508 (m-30) REVERT: B 373 ILE cc_start: 0.9091 (mt) cc_final: 0.7999 (mt) REVERT: B 384 GLU cc_start: 0.6657 (pm20) cc_final: 0.6297 (pm20) REVERT: B 391 VAL cc_start: 0.9072 (p) cc_final: 0.8869 (p) REVERT: B 410 ASN cc_start: 0.8614 (OUTLIER) cc_final: 0.8114 (m-40) REVERT: B 411 LEU cc_start: 0.7568 (mp) cc_final: 0.7153 (mp) REVERT: B 417 LEU cc_start: 0.8670 (tp) cc_final: 0.7464 (tt) REVERT: B 445 ILE cc_start: 0.8671 (mt) cc_final: 0.8454 (mm) REVERT: B 471 TYR cc_start: 0.6004 (t80) cc_final: 0.5294 (t80) REVERT: B 474 GLN cc_start: 0.8332 (mt0) cc_final: 0.8115 (mt0) REVERT: B 565 VAL cc_start: 0.9400 (t) cc_final: 0.9123 (p) REVERT: B 585 SER cc_start: 0.9134 (p) cc_final: 0.8464 (t) REVERT: B 589 SER cc_start: 0.8091 (m) cc_final: 0.7521 (t) REVERT: B 613 TYR cc_start: 0.7322 (t80) cc_final: 0.6630 (t80) REVERT: B 634 MET cc_start: 0.8149 (mmp) cc_final: 0.7809 (mmm) REVERT: B 656 LEU cc_start: 0.8616 (mt) cc_final: 0.8214 (mt) REVERT: C 90 LEU cc_start: 0.5687 (mt) cc_final: 0.4379 (mt) REVERT: C 151 ILE cc_start: 0.6601 (mm) cc_final: 0.6167 (mm) REVERT: C 208 LEU cc_start: 0.6294 (mt) cc_final: 0.5683 (mt) REVERT: D 126 LYS cc_start: 0.2375 (OUTLIER) cc_final: 0.2038 (tptp) REVERT: D 174 TYR cc_start: 0.1481 (t80) cc_final: 0.0307 (t80) REVERT: D 195 LEU cc_start: 0.8036 (tt) cc_final: 0.7738 (tt) REVERT: D 282 ILE cc_start: -0.1245 (OUTLIER) cc_final: -0.1516 (tp) outliers start: 23 outliers final: 4 residues processed: 799 average time/residue: 0.3031 time to fit residues: 344.3847 Evaluate side-chains 529 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 520 time to evaluate : 1.835 ------------------------------------------------------------------------------- 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: 3.9990 chunk 145 optimal weight: 5.9990 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 150 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 112 optimal weight: 0.9980 chunk 174 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN A 239 GLN A 320 ASN A 365 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 304 HIS ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN C 24 GLN C 28 GLN C 38 ASN C 119 ASN D 25 ASN D 80 HIS D 136 GLN ** D 265 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.131835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.091515 restraints weight = 43648.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.093545 restraints weight = 27773.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.096627 restraints weight = 20594.889| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3386 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3386 r_free = 0.3386 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3383 r_free = 0.3383 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3383 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16386 Z= 0.218 Angle : 0.657 7.140 22134 Z= 0.351 Chirality : 0.044 0.240 2360 Planarity : 0.004 0.061 2818 Dihedral : 11.633 175.652 2242 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 14.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.41 % Allowed : 3.73 % Favored : 95.86 % 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: 1.41 (0.19), residues: 1932 helix: 1.38 (0.15), residues: 1116 sheet: -0.17 (0.40), residues: 152 loop : 0.66 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 558 HIS 0.008 0.002 HIS B 572 PHE 0.035 0.002 PHE D 178 TYR 0.028 0.002 TYR A 140 ARG 0.005 0.001 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.04729 ( 871) hydrogen bonds : angle 5.14712 ( 2571) covalent geometry : bond 0.00465 (16386) covalent geometry : angle 0.65672 (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 590 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 583 time to evaluate : 1.894 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 128 PHE cc_start: 0.9223 (t80) cc_final: 0.8741 (t80) REVERT: A 143 LEU cc_start: 0.9130 (tp) cc_final: 0.8927 (tp) REVERT: A 147 GLN cc_start: 0.9083 (mt0) cc_final: 0.8635 (mt0) REVERT: A 168 VAL cc_start: 0.8550 (t) cc_final: 0.8270 (t) REVERT: A 172 LEU cc_start: 0.8947 (mp) cc_final: 0.8500 (mp) REVERT: A 173 LEU cc_start: 0.9135 (mt) cc_final: 0.8883 (mt) REVERT: A 205 LYS cc_start: 0.7253 (mttp) cc_final: 0.6983 (mttt) REVERT: A 214 LYS cc_start: 0.9269 (mmmt) cc_final: 0.8888 (mmtt) REVERT: A 220 THR cc_start: 0.7817 (m) cc_final: 0.7568 (p) REVERT: A 239 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: A 270 ASP cc_start: 0.8748 (m-30) cc_final: 0.8119 (t70) REVERT: A 286 ASP cc_start: 0.8792 (m-30) cc_final: 0.8460 (m-30) REVERT: A 291 LEU cc_start: 0.8803 (mt) cc_final: 0.8452 (mt) REVERT: A 322 MET cc_start: 0.8766 (mmm) cc_final: 0.7898 (mmm) REVERT: A 349 LEU cc_start: 0.8488 (tp) cc_final: 0.8237 (tp) REVERT: A 359 MET cc_start: 0.7997 (ttt) cc_final: 0.7772 (ttt) REVERT: A 375 LYS cc_start: 0.9087 (mmtm) cc_final: 0.8620 (mmtm) REVERT: A 406 ASP cc_start: 0.8273 (m-30) cc_final: 0.7977 (m-30) REVERT: A 407 ILE cc_start: 0.8905 (mt) cc_final: 0.8565 (mt) REVERT: A 425 ILE cc_start: 0.9389 (mt) cc_final: 0.9176 (mt) REVERT: A 498 TYR cc_start: 0.8798 (m-80) cc_final: 0.8377 (m-80) REVERT: A 512 GLU cc_start: 0.8492 (pm20) cc_final: 0.8002 (pm20) REVERT: A 546 LEU cc_start: 0.9409 (mt) cc_final: 0.9171 (mt) REVERT: A 550 MET cc_start: 0.7317 (mtm) cc_final: 0.6386 (mtp) REVERT: A 598 MET cc_start: 0.8951 (mtm) cc_final: 0.8545 (mtt) REVERT: A 599 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7209 (mm-30) REVERT: A 601 ILE cc_start: 0.8826 (tt) cc_final: 0.8563 (tt) REVERT: A 602 GLU cc_start: 0.8263 (pm20) cc_final: 0.6535 (mp0) REVERT: A 645 GLN cc_start: 0.8392 (tp40) cc_final: 0.8027 (tp-100) REVERT: A 650 GLN cc_start: 0.7745 (mt0) cc_final: 0.7131 (mt0) REVERT: A 655 THR cc_start: 0.7764 (m) cc_final: 0.7001 (m) REVERT: A 659 LYS cc_start: 0.8674 (mttt) cc_final: 0.8442 (mmmt) REVERT: B 8 LYS cc_start: 0.9445 (tttm) cc_final: 0.9192 (tppt) REVERT: B 12 LEU cc_start: 0.9584 (mt) cc_final: 0.9355 (mt) REVERT: B 95 MET cc_start: 0.9022 (tpp) cc_final: 0.7703 (tpp) REVERT: B 99 LYS cc_start: 0.9582 (mmmt) cc_final: 0.8834 (mmmt) REVERT: B 115 LEU cc_start: 0.8582 (mp) cc_final: 0.8300 (mp) REVERT: B 229 LEU cc_start: 0.7967 (mp) cc_final: 0.7721 (mt) REVERT: B 288 PHE cc_start: 0.9367 (t80) cc_final: 0.8927 (t80) REVERT: B 322 MET cc_start: 0.8533 (mmm) cc_final: 0.8219 (mmt) REVERT: B 326 PHE cc_start: 0.9320 (m-80) cc_final: 0.8606 (m-80) REVERT: B 350 ARG cc_start: 0.7872 (mtm-85) cc_final: 0.7644 (mtm110) REVERT: B 358 ILE cc_start: 0.8480 (mm) cc_final: 0.8232 (mm) REVERT: B 413 SER cc_start: 0.9228 (m) cc_final: 0.8454 (t) REVERT: B 417 LEU cc_start: 0.9366 (tt) cc_final: 0.8961 (tt) REVERT: B 425 ILE cc_start: 0.9069 (mt) cc_final: 0.8697 (mt) REVERT: B 458 MET cc_start: 0.9317 (mmm) cc_final: 0.8944 (mmm) REVERT: B 479 TYR cc_start: 0.8350 (t80) cc_final: 0.7917 (t80) REVERT: B 493 MET cc_start: 0.9221 (tmm) cc_final: 0.8988 (tmm) REVERT: B 494 MET cc_start: 0.9498 (mtp) cc_final: 0.9123 (mtp) REVERT: B 512 GLU cc_start: 0.8620 (pm20) cc_final: 0.8356 (pm20) REVERT: B 584 ILE cc_start: 0.8689 (tp) cc_final: 0.8234 (mt) REVERT: B 586 TYR cc_start: 0.9458 (m-80) cc_final: 0.9024 (m-80) REVERT: B 588 GLN cc_start: 0.9042 (mm-40) cc_final: 0.8836 (mm-40) REVERT: B 602 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8310 (pp20) REVERT: B 645 GLN cc_start: 0.8912 (tp40) cc_final: 0.8661 (tp-100) REVERT: C 38 ASN cc_start: 0.7121 (m-40) cc_final: 0.6192 (p0) REVERT: C 93 MET cc_start: 0.8825 (mtm) cc_final: 0.8560 (mmt) REVERT: C 95 MET cc_start: 0.8332 (tmm) cc_final: 0.7913 (tmm) REVERT: C 96 MET cc_start: 0.8590 (mmm) cc_final: 0.8062 (mmm) REVERT: C 141 LEU cc_start: 0.6816 (mp) cc_final: 0.6606 (pp) REVERT: C 227 PHE cc_start: 0.7915 (t80) cc_final: 0.7592 (t80) REVERT: D 55 TYR cc_start: 0.8236 (t80) cc_final: 0.8007 (t80) REVERT: D 119 ASN cc_start: 0.7724 (m110) cc_final: 0.7378 (m110) REVERT: D 154 PHE cc_start: 0.8145 (t80) cc_final: 0.7857 (t80) REVERT: D 169 TYR cc_start: 0.7644 (m-80) cc_final: 0.6813 (m-80) REVERT: D 174 TYR cc_start: 0.1991 (t80) cc_final: 0.1354 (t80) REVERT: D 178 PHE cc_start: 0.7911 (m-80) cc_final: 0.7625 (m-80) REVERT: D 201 HIS cc_start: 0.8322 (m90) cc_final: 0.7902 (m90) REVERT: D 263 ASN cc_start: 0.6974 (p0) cc_final: 0.6616 (p0) outliers start: 7 outliers final: 0 residues processed: 586 average time/residue: 0.2777 time to fit residues: 238.4023 Evaluate side-chains 475 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 473 time to evaluate : 1.929 ------------------------------------------------------------------------------- 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: 8.9990 chunk 168 optimal weight: 6.9990 chunk 175 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 191 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 171 optimal weight: 0.8980 chunk 189 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 218 ASN B 232 ASN B 475 ASN ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 HIS C 24 GLN C 132 GLN C 201 HIS D 71 ASN D 186 GLN D 265 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.125834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.085601 restraints weight = 50494.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.088729 restraints weight = 31657.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.090921 restraints weight = 22161.051| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.5073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 16386 Z= 0.218 Angle : 0.629 7.642 22134 Z= 0.336 Chirality : 0.043 0.183 2360 Planarity : 0.004 0.041 2818 Dihedral : 11.629 173.100 2242 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.23 % Allowed : 3.21 % Favored : 96.56 % 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: 1.24 (0.19), residues: 1932 helix: 1.29 (0.15), residues: 1130 sheet: -0.56 (0.39), residues: 164 loop : 0.61 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 558 HIS 0.008 0.001 HIS D 201 PHE 0.037 0.002 PHE D 166 TYR 0.020 0.002 TYR B 626 ARG 0.005 0.001 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.04319 ( 871) hydrogen bonds : angle 4.92801 ( 2571) covalent geometry : bond 0.00458 (16386) covalent geometry : angle 0.62939 (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 548 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 544 time to evaluate : 1.867 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 67 GLU cc_start: 0.9311 (tp30) cc_final: 0.8851 (tp30) REVERT: A 71 LEU cc_start: 0.9377 (mt) cc_final: 0.9021 (mt) REVERT: A 99 LYS cc_start: 0.9273 (mmtp) cc_final: 0.8709 (mttt) REVERT: A 108 THR cc_start: 0.9294 (OUTLIER) cc_final: 0.8941 (p) REVERT: A 117 ARG cc_start: 0.9114 (mmt90) cc_final: 0.8763 (mtp85) REVERT: A 119 GLU cc_start: 0.8734 (mp0) cc_final: 0.8374 (tm-30) REVERT: A 128 PHE cc_start: 0.9252 (t80) cc_final: 0.8870 (t80) REVERT: A 136 LYS cc_start: 0.9369 (tptt) cc_final: 0.8936 (ttpp) REVERT: A 143 LEU cc_start: 0.9101 (tp) cc_final: 0.8599 (tp) REVERT: A 147 GLN cc_start: 0.9164 (mt0) cc_final: 0.8763 (mt0) REVERT: A 148 GLU cc_start: 0.8284 (mp0) cc_final: 0.7601 (mp0) REVERT: A 158 ASN cc_start: 0.8820 (m110) cc_final: 0.8571 (m110) REVERT: A 168 VAL cc_start: 0.8353 (t) cc_final: 0.8019 (p) REVERT: A 172 LEU cc_start: 0.8899 (mp) cc_final: 0.8368 (mp) REVERT: A 173 LEU cc_start: 0.9124 (mt) cc_final: 0.8900 (mt) REVERT: A 214 LYS cc_start: 0.9354 (mmmt) cc_final: 0.9071 (mmtt) REVERT: A 220 THR cc_start: 0.7868 (m) cc_final: 0.7410 (p) REVERT: A 260 ASP cc_start: 0.9221 (m-30) cc_final: 0.8887 (p0) REVERT: A 270 ASP cc_start: 0.8695 (m-30) cc_final: 0.8055 (t70) REVERT: A 322 MET cc_start: 0.8717 (mmm) cc_final: 0.8118 (tpp) REVERT: A 345 LYS cc_start: 0.9099 (mttp) cc_final: 0.8764 (mttm) REVERT: A 375 LYS cc_start: 0.9098 (mmtm) cc_final: 0.8643 (mmtm) REVERT: A 385 VAL cc_start: 0.8656 (t) cc_final: 0.8390 (p) REVERT: A 402 GLU cc_start: 0.8843 (mp0) cc_final: 0.8592 (mp0) REVERT: A 406 ASP cc_start: 0.8303 (m-30) cc_final: 0.8063 (m-30) REVERT: A 407 ILE cc_start: 0.8968 (mt) cc_final: 0.8537 (mt) REVERT: A 446 ARG cc_start: 0.8679 (mmm-85) cc_final: 0.8372 (mmp80) REVERT: A 456 LYS cc_start: 0.8791 (mmtm) cc_final: 0.8225 (mmtm) REVERT: A 466 MET cc_start: 0.9295 (ptt) cc_final: 0.9062 (ptp) REVERT: A 468 LEU cc_start: 0.9478 (tp) cc_final: 0.9270 (tp) REVERT: A 479 TYR cc_start: 0.8652 (t80) cc_final: 0.8383 (t80) REVERT: A 498 TYR cc_start: 0.8905 (m-80) cc_final: 0.8495 (m-80) REVERT: A 550 MET cc_start: 0.7737 (mtm) cc_final: 0.7056 (mtm) REVERT: A 598 MET cc_start: 0.8897 (mtm) cc_final: 0.8506 (mtm) REVERT: A 599 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7448 (mm-30) REVERT: A 602 GLU cc_start: 0.9043 (pm20) cc_final: 0.8226 (pm20) REVERT: A 611 THR cc_start: 0.8735 (t) cc_final: 0.8300 (t) REVERT: A 615 MET cc_start: 0.8327 (mmp) cc_final: 0.7965 (mmp) REVERT: A 650 GLN cc_start: 0.7853 (mt0) cc_final: 0.7460 (mt0) REVERT: A 659 LYS cc_start: 0.8588 (mttt) cc_final: 0.8278 (mmmt) REVERT: B 8 LYS cc_start: 0.9495 (tttm) cc_final: 0.9198 (tppt) REVERT: B 12 LEU cc_start: 0.9585 (mt) cc_final: 0.9324 (mt) REVERT: B 24 PHE cc_start: 0.8862 (m-80) cc_final: 0.8575 (m-80) REVERT: B 40 TYR cc_start: 0.9254 (t80) cc_final: 0.8939 (t80) REVERT: B 95 MET cc_start: 0.9087 (tpp) cc_final: 0.7672 (tpp) REVERT: B 99 LYS cc_start: 0.9622 (mmmt) cc_final: 0.8818 (mmmt) REVERT: B 115 LEU cc_start: 0.8764 (mp) cc_final: 0.8481 (mp) REVERT: B 184 ARG cc_start: 0.8108 (tpt170) cc_final: 0.7843 (mmm-85) REVERT: B 200 SER cc_start: 0.7259 (m) cc_final: 0.6916 (p) REVERT: B 228 LYS cc_start: 0.7950 (mmmm) cc_final: 0.7652 (tppt) REVERT: B 288 PHE cc_start: 0.9418 (t80) cc_final: 0.9018 (t80) REVERT: B 307 TYR cc_start: 0.9268 (t80) cc_final: 0.8858 (t80) REVERT: B 319 MET cc_start: 0.8928 (tpp) cc_final: 0.8681 (tpp) REVERT: B 326 PHE cc_start: 0.9389 (m-80) cc_final: 0.8558 (m-80) REVERT: B 379 SER cc_start: 0.8369 (t) cc_final: 0.8045 (t) REVERT: B 392 SER cc_start: 0.9192 (m) cc_final: 0.8901 (t) REVERT: B 413 SER cc_start: 0.9178 (m) cc_final: 0.8547 (t) REVERT: B 444 ASP cc_start: 0.9158 (t0) cc_final: 0.8954 (t70) REVERT: B 458 MET cc_start: 0.9289 (mmm) cc_final: 0.9041 (mmm) REVERT: B 472 LEU cc_start: 0.9180 (mm) cc_final: 0.8912 (mm) REVERT: B 492 PHE cc_start: 0.9265 (m-80) cc_final: 0.8584 (m-80) REVERT: B 493 MET cc_start: 0.9332 (tmm) cc_final: 0.8819 (tmm) REVERT: B 494 MET cc_start: 0.9482 (mtp) cc_final: 0.8887 (mtp) REVERT: B 506 ILE cc_start: 0.9653 (mm) cc_final: 0.9330 (mm) REVERT: B 509 GLU cc_start: 0.9055 (pt0) cc_final: 0.8738 (pp20) REVERT: B 510 LYS cc_start: 0.9556 (mmtp) cc_final: 0.9273 (mmmm) REVERT: B 570 MET cc_start: 0.8565 (mtp) cc_final: 0.8015 (mmt) REVERT: B 586 TYR cc_start: 0.9389 (m-80) cc_final: 0.9098 (m-80) REVERT: B 597 ILE cc_start: 0.8989 (pt) cc_final: 0.8701 (pt) REVERT: B 615 MET cc_start: 0.9144 (mmp) cc_final: 0.8774 (mmm) REVERT: B 645 GLN cc_start: 0.9116 (tp40) cc_final: 0.8855 (tp-100) REVERT: B 648 ILE cc_start: 0.9151 (mm) cc_final: 0.8949 (mm) REVERT: C 74 MET cc_start: 0.7649 (ttm) cc_final: 0.6862 (ptm) REVERT: C 93 MET cc_start: 0.8640 (mtm) cc_final: 0.8348 (mmt) REVERT: C 95 MET cc_start: 0.8440 (tmm) cc_final: 0.7948 (tmm) REVERT: C 96 MET cc_start: 0.8563 (mmm) cc_final: 0.8086 (mmm) REVERT: C 137 MET cc_start: 0.6707 (mpp) cc_final: 0.5971 (ptp) REVERT: C 141 LEU cc_start: 0.7057 (mp) cc_final: 0.6812 (pp) REVERT: C 151 ILE cc_start: 0.8305 (mm) cc_final: 0.7875 (tp) REVERT: C 227 PHE cc_start: 0.7867 (t80) cc_final: 0.7442 (t80) REVERT: C 259 PHE cc_start: 0.6497 (t80) cc_final: 0.5653 (t80) REVERT: C 276 TYR cc_start: 0.8143 (t80) cc_final: 0.7831 (t80) REVERT: D 178 PHE cc_start: 0.8323 (m-80) cc_final: 0.7970 (m-80) REVERT: D 249 GLN cc_start: 0.7678 (pt0) cc_final: 0.7148 (pm20) outliers start: 4 outliers final: 1 residues processed: 546 average time/residue: 0.2733 time to fit residues: 220.7372 Evaluate side-chains 453 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 451 time to evaluate : 1.849 ------------------------------------------------------------------------------- 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: 9.9990 chunk 99 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 39 optimal weight: 0.0040 chunk 50 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 148 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 0.2980 overall best weight: 1.0396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.131652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.092827 restraints weight = 50526.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.095955 restraints weight = 32407.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.098040 restraints weight = 23043.619| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3353 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3353 r_free = 0.3353 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3353 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.5386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16386 Z= 0.131 Angle : 0.575 8.302 22134 Z= 0.305 Chirality : 0.042 0.175 2360 Planarity : 0.003 0.042 2818 Dihedral : 11.038 164.263 2242 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.12 % Allowed : 2.80 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.19), residues: 1932 helix: 1.26 (0.15), residues: 1137 sheet: -0.44 (0.41), residues: 150 loop : 0.53 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 558 HIS 0.017 0.001 HIS C 201 PHE 0.029 0.002 PHE B 81 TYR 0.017 0.001 TYR D 242 ARG 0.009 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03958 ( 871) hydrogen bonds : angle 4.86454 ( 2571) covalent geometry : bond 0.00285 (16386) covalent geometry : angle 0.57453 (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 558 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 556 time to evaluate : 1.838 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 65 GLU cc_start: 0.8354 (mp0) cc_final: 0.8135 (mp0) REVERT: A 67 GLU cc_start: 0.9231 (tp30) cc_final: 0.8710 (tp30) REVERT: A 71 LEU cc_start: 0.9424 (mt) cc_final: 0.8892 (mt) REVERT: A 99 LYS cc_start: 0.9299 (mmtp) cc_final: 0.8868 (mttt) REVERT: A 117 ARG cc_start: 0.9149 (mmt90) cc_final: 0.8720 (mtp85) REVERT: A 147 GLN cc_start: 0.9129 (mt0) cc_final: 0.8636 (mt0) REVERT: A 172 LEU cc_start: 0.8824 (mp) cc_final: 0.8358 (mp) REVERT: A 202 ASN cc_start: 0.8520 (t0) cc_final: 0.8296 (t0) REVERT: A 205 LYS cc_start: 0.6996 (mttt) cc_final: 0.6796 (mttt) REVERT: A 214 LYS cc_start: 0.9266 (mmmt) cc_final: 0.9000 (mmtt) REVERT: A 220 THR cc_start: 0.7791 (m) cc_final: 0.7299 (p) REVERT: A 263 ASP cc_start: 0.8996 (t0) cc_final: 0.8541 (m-30) REVERT: A 312 GLN cc_start: 0.8665 (tp-100) cc_final: 0.7982 (tp-100) REVERT: A 345 LYS cc_start: 0.9129 (mttp) cc_final: 0.8852 (mttm) REVERT: A 349 LEU cc_start: 0.8446 (tp) cc_final: 0.8244 (tp) REVERT: A 373 ILE cc_start: 0.9540 (mt) cc_final: 0.9081 (mt) REVERT: A 375 LYS cc_start: 0.9113 (mmtm) cc_final: 0.8686 (mmtm) REVERT: A 402 GLU cc_start: 0.8876 (mp0) cc_final: 0.8621 (mp0) REVERT: A 407 ILE cc_start: 0.8845 (mt) cc_final: 0.8446 (mt) REVERT: A 425 ILE cc_start: 0.9399 (mm) cc_final: 0.9064 (mm) REVERT: A 456 LYS cc_start: 0.8787 (mmtm) cc_final: 0.8287 (mmtm) REVERT: A 466 MET cc_start: 0.9264 (ptt) cc_final: 0.8934 (ptp) REVERT: A 479 TYR cc_start: 0.8400 (t80) cc_final: 0.8081 (t80) REVERT: A 494 MET cc_start: 0.9508 (mmm) cc_final: 0.9273 (mmm) REVERT: A 498 TYR cc_start: 0.8935 (m-80) cc_final: 0.8543 (m-80) REVERT: A 501 GLN cc_start: 0.9305 (tp-100) cc_final: 0.8957 (tp-100) REVERT: A 510 LYS cc_start: 0.9549 (mttm) cc_final: 0.9334 (mtpp) REVERT: A 516 GLN cc_start: 0.9575 (mt0) cc_final: 0.9243 (tt0) REVERT: A 550 MET cc_start: 0.7676 (mtm) cc_final: 0.6662 (mtm) REVERT: A 571 TYR cc_start: 0.8782 (t80) cc_final: 0.8481 (t80) REVERT: A 598 MET cc_start: 0.8897 (mtm) cc_final: 0.8460 (ttm) REVERT: A 599 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7361 (mm-30) REVERT: A 602 GLU cc_start: 0.9031 (pm20) cc_final: 0.8443 (pm20) REVERT: A 611 THR cc_start: 0.8773 (t) cc_final: 0.8500 (t) REVERT: A 640 MET cc_start: 0.9354 (tpt) cc_final: 0.9111 (tpp) REVERT: A 645 GLN cc_start: 0.8434 (tp40) cc_final: 0.8184 (tp-100) REVERT: A 650 GLN cc_start: 0.7756 (mt0) cc_final: 0.7206 (mt0) REVERT: A 659 LYS cc_start: 0.8812 (mttt) cc_final: 0.8478 (mmmt) REVERT: B 8 LYS cc_start: 0.9469 (tttm) cc_final: 0.9178 (tppt) REVERT: B 12 LEU cc_start: 0.9568 (mt) cc_final: 0.9307 (mt) REVERT: B 17 MET cc_start: 0.9152 (mmm) cc_final: 0.8690 (mmp) REVERT: B 67 GLU cc_start: 0.8779 (mp0) cc_final: 0.8438 (mp0) REVERT: B 95 MET cc_start: 0.9019 (tpp) cc_final: 0.7608 (tpp) REVERT: B 98 PHE cc_start: 0.9600 (t80) cc_final: 0.8999 (t80) REVERT: B 99 LYS cc_start: 0.9636 (mmmt) cc_final: 0.8890 (mmmt) REVERT: B 115 LEU cc_start: 0.8708 (mp) cc_final: 0.8500 (mp) REVERT: B 122 ILE cc_start: 0.9270 (mt) cc_final: 0.8928 (mt) REVERT: B 162 LYS cc_start: 0.8956 (tppt) cc_final: 0.8634 (ttmm) REVERT: B 184 ARG cc_start: 0.8052 (tpt170) cc_final: 0.7510 (mmm-85) REVERT: B 288 PHE cc_start: 0.9395 (t80) cc_final: 0.9057 (t80) REVERT: B 315 ASP cc_start: 0.8490 (p0) cc_final: 0.8082 (p0) REVERT: B 319 MET cc_start: 0.9035 (tpp) cc_final: 0.8750 (tpp) REVERT: B 326 PHE cc_start: 0.9405 (m-80) cc_final: 0.8626 (m-80) REVERT: B 350 ARG cc_start: 0.7692 (mtm110) cc_final: 0.7394 (mtm-85) REVERT: B 370 ASN cc_start: 0.9433 (m-40) cc_final: 0.8789 (t0) REVERT: B 373 ILE cc_start: 0.9551 (mt) cc_final: 0.9164 (mt) REVERT: B 376 VAL cc_start: 0.8621 (t) cc_final: 0.7747 (t) REVERT: B 392 SER cc_start: 0.8958 (m) cc_final: 0.8740 (t) REVERT: B 403 ILE cc_start: 0.8721 (mp) cc_final: 0.8503 (mp) REVERT: B 413 SER cc_start: 0.9182 (m) cc_final: 0.8624 (t) REVERT: B 444 ASP cc_start: 0.9118 (t0) cc_final: 0.8844 (t70) REVERT: B 446 ARG cc_start: 0.8981 (mpp80) cc_final: 0.8705 (mpp80) REVERT: B 453 ARG cc_start: 0.9006 (ttt-90) cc_final: 0.8478 (ttt-90) REVERT: B 458 MET cc_start: 0.9310 (mmm) cc_final: 0.9030 (mmm) REVERT: B 459 LYS cc_start: 0.8595 (mttt) cc_final: 0.8226 (mtmm) REVERT: B 466 MET cc_start: 0.8698 (ptp) cc_final: 0.8427 (ptp) REVERT: B 472 LEU cc_start: 0.9221 (mm) cc_final: 0.8894 (mm) REVERT: B 492 PHE cc_start: 0.9190 (m-80) cc_final: 0.8463 (m-80) REVERT: B 493 MET cc_start: 0.9231 (tmm) cc_final: 0.8790 (tmm) REVERT: B 494 MET cc_start: 0.9254 (mtp) cc_final: 0.8678 (mtp) REVERT: B 506 ILE cc_start: 0.9597 (mm) cc_final: 0.9349 (mm) REVERT: B 509 GLU cc_start: 0.9036 (pt0) cc_final: 0.8661 (pp20) REVERT: B 510 LYS cc_start: 0.9552 (mmtp) cc_final: 0.9106 (mmmm) REVERT: B 585 SER cc_start: 0.8790 (p) cc_final: 0.8436 (t) REVERT: B 586 TYR cc_start: 0.9508 (m-80) cc_final: 0.8948 (m-80) REVERT: B 597 ILE cc_start: 0.8953 (pt) cc_final: 0.8691 (pt) REVERT: B 615 MET cc_start: 0.8930 (mmp) cc_final: 0.8639 (mmm) REVERT: B 645 GLN cc_start: 0.9034 (tp40) cc_final: 0.8804 (tp-100) REVERT: B 648 ILE cc_start: 0.8949 (mm) cc_final: 0.8724 (mm) REVERT: B 667 LEU cc_start: 0.8261 (mp) cc_final: 0.7993 (tp) REVERT: B 675 HIS cc_start: 0.8845 (t-90) cc_final: 0.8442 (t-90) REVERT: C 74 MET cc_start: 0.7576 (ttm) cc_final: 0.6730 (ptm) REVERT: C 95 MET cc_start: 0.8055 (tmm) cc_final: 0.7660 (tmm) REVERT: C 96 MET cc_start: 0.8459 (mmm) cc_final: 0.8022 (mmm) REVERT: C 149 ASP cc_start: 0.8199 (t0) cc_final: 0.7957 (t0) REVERT: C 151 ILE cc_start: 0.8227 (mm) cc_final: 0.7948 (mm) REVERT: C 227 PHE cc_start: 0.7783 (t80) cc_final: 0.7514 (t80) REVERT: C 259 PHE cc_start: 0.6318 (t80) cc_final: 0.5445 (t80) REVERT: C 276 TYR cc_start: 0.8257 (t80) cc_final: 0.7954 (t80) REVERT: D 169 TYR cc_start: 0.8073 (m-80) cc_final: 0.7210 (m-80) REVERT: D 178 PHE cc_start: 0.8365 (m-80) cc_final: 0.7946 (m-80) outliers start: 2 outliers final: 0 residues processed: 556 average time/residue: 0.2762 time to fit residues: 225.4512 Evaluate side-chains 458 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 458 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 67 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 57 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 175 optimal weight: 9.9990 chunk 182 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 86 optimal weight: 0.9980 chunk 18 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 overall best weight: 3.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN B 150 GLN B 218 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 28 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.124360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.084576 restraints weight = 51215.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.087494 restraints weight = 31917.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.089809 restraints weight = 22354.154| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 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 = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.5850 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= 0.205 Angle : 0.629 7.696 22134 Z= 0.333 Chirality : 0.043 0.164 2360 Planarity : 0.004 0.041 2818 Dihedral : 11.167 165.191 2242 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.12 % Allowed : 1.81 % 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: 1.10 (0.19), residues: 1932 helix: 1.19 (0.15), residues: 1125 sheet: -0.70 (0.40), residues: 154 loop : 0.52 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 558 HIS 0.016 0.002 HIS C 201 PHE 0.029 0.002 PHE B 81 TYR 0.017 0.002 TYR B 101 ARG 0.006 0.001 ARG A 452 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 871) hydrogen bonds : angle 5.05085 ( 2571) covalent geometry : bond 0.00433 (16386) covalent geometry : angle 0.62855 (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 534 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 532 time to evaluate : 1.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.9224 (tp30) cc_final: 0.8765 (tp30) REVERT: A 71 LEU cc_start: 0.9417 (mt) cc_final: 0.9106 (mt) REVERT: A 99 LYS cc_start: 0.9411 (mmtp) cc_final: 0.8894 (mttt) REVERT: A 117 ARG cc_start: 0.9140 (mmt90) cc_final: 0.8783 (mtp85) REVERT: A 136 LYS cc_start: 0.8995 (ttpp) cc_final: 0.8633 (tttm) REVERT: A 147 GLN cc_start: 0.9189 (mt0) cc_final: 0.8741 (mt0) REVERT: A 214 LYS cc_start: 0.9343 (mmmt) cc_final: 0.9048 (mmtt) REVERT: A 220 THR cc_start: 0.7977 (m) cc_final: 0.7538 (p) REVERT: A 263 ASP cc_start: 0.8970 (t0) cc_final: 0.8496 (m-30) REVERT: A 312 GLN cc_start: 0.8622 (tp-100) cc_final: 0.8004 (tp-100) REVERT: A 322 MET cc_start: 0.8728 (mmm) cc_final: 0.8106 (tpp) REVERT: A 345 LYS cc_start: 0.9115 (mttp) cc_final: 0.8773 (mttm) REVERT: A 361 GLN cc_start: 0.8960 (tp40) cc_final: 0.8750 (tp-100) REVERT: A 373 ILE cc_start: 0.9558 (mt) cc_final: 0.9117 (mt) REVERT: A 375 LYS cc_start: 0.9099 (mmtm) cc_final: 0.8663 (mmtm) REVERT: A 402 GLU cc_start: 0.8867 (mp0) cc_final: 0.8609 (mp0) REVERT: A 407 ILE cc_start: 0.9062 (mt) cc_final: 0.8650 (mt) REVERT: A 425 ILE cc_start: 0.9414 (mm) cc_final: 0.8969 (mm) REVERT: A 444 ASP cc_start: 0.7988 (t0) cc_final: 0.7272 (t0) REVERT: A 456 LYS cc_start: 0.8805 (mmtm) cc_final: 0.8066 (mmtm) REVERT: A 468 LEU cc_start: 0.9442 (tp) cc_final: 0.9166 (tp) REVERT: A 479 TYR cc_start: 0.8448 (t80) cc_final: 0.7881 (t80) REVERT: A 493 MET cc_start: 0.9032 (tmm) cc_final: 0.8657 (tmm) REVERT: A 494 MET cc_start: 0.9605 (mmm) cc_final: 0.9207 (mmm) REVERT: A 498 TYR cc_start: 0.8972 (m-80) cc_final: 0.8579 (m-80) REVERT: A 501 GLN cc_start: 0.9315 (tp-100) cc_final: 0.8991 (tp-100) REVERT: A 516 GLN cc_start: 0.9550 (mt0) cc_final: 0.9235 (tt0) REVERT: A 550 MET cc_start: 0.7724 (mtm) cc_final: 0.6919 (mtm) REVERT: A 598 MET cc_start: 0.8788 (mtm) cc_final: 0.8496 (ttm) REVERT: A 615 MET cc_start: 0.8071 (mmp) cc_final: 0.7542 (mmm) REVERT: A 640 MET cc_start: 0.9463 (tpt) cc_final: 0.9172 (tpp) REVERT: A 645 GLN cc_start: 0.8534 (tp40) cc_final: 0.8106 (tp40) REVERT: A 657 PHE cc_start: 0.7239 (m-80) cc_final: 0.6649 (m-80) REVERT: A 658 LEU cc_start: 0.9334 (mt) cc_final: 0.9094 (mt) REVERT: A 659 LYS cc_start: 0.8788 (mttt) cc_final: 0.8449 (mmmt) REVERT: A 687 THR cc_start: 0.8768 (m) cc_final: 0.8392 (t) REVERT: B 8 LYS cc_start: 0.9467 (tttm) cc_final: 0.9185 (tppt) REVERT: B 12 LEU cc_start: 0.9592 (mt) cc_final: 0.9341 (mt) REVERT: B 17 MET cc_start: 0.8973 (mmm) cc_final: 0.8434 (mmt) REVERT: B 24 PHE cc_start: 0.8824 (m-80) cc_final: 0.8066 (m-80) REVERT: B 95 MET cc_start: 0.9157 (tpp) cc_final: 0.7805 (tpp) REVERT: B 98 PHE cc_start: 0.9614 (t80) cc_final: 0.8704 (t80) REVERT: B 99 LYS cc_start: 0.9686 (mmmt) cc_final: 0.8921 (mmmt) REVERT: B 124 ILE cc_start: 0.9211 (tp) cc_final: 0.8807 (tp) REVERT: B 184 ARG cc_start: 0.8077 (tpt170) cc_final: 0.7554 (mmm-85) REVERT: B 288 PHE cc_start: 0.9373 (t80) cc_final: 0.9163 (t80) REVERT: B 307 TYR cc_start: 0.9230 (t80) cc_final: 0.8822 (t80) REVERT: B 319 MET cc_start: 0.9003 (tpp) cc_final: 0.8719 (tpp) REVERT: B 326 PHE cc_start: 0.9203 (m-10) cc_final: 0.8561 (m-80) REVERT: B 350 ARG cc_start: 0.7655 (mtm110) cc_final: 0.7422 (mtm-85) REVERT: B 359 MET cc_start: 0.8418 (ttm) cc_final: 0.6965 (tmm) REVERT: B 361 GLN cc_start: 0.8406 (tp40) cc_final: 0.8166 (tp40) REVERT: B 379 SER cc_start: 0.8450 (t) cc_final: 0.7983 (t) REVERT: B 392 SER cc_start: 0.9096 (m) cc_final: 0.8872 (t) REVERT: B 417 LEU cc_start: 0.9380 (tt) cc_final: 0.8948 (tt) REVERT: B 444 ASP cc_start: 0.9098 (t0) cc_final: 0.8881 (t70) REVERT: B 459 LYS cc_start: 0.8742 (mttt) cc_final: 0.8330 (mtmt) REVERT: B 472 LEU cc_start: 0.9234 (mm) cc_final: 0.9023 (mm) REVERT: B 492 PHE cc_start: 0.9194 (m-80) cc_final: 0.8488 (m-80) REVERT: B 493 MET cc_start: 0.9192 (tmm) cc_final: 0.8751 (tmm) REVERT: B 494 MET cc_start: 0.9313 (mtp) cc_final: 0.8685 (mtp) REVERT: B 586 TYR cc_start: 0.9475 (m-80) cc_final: 0.8983 (m-80) REVERT: B 597 ILE cc_start: 0.8907 (pt) cc_final: 0.8697 (pt) REVERT: B 613 TYR cc_start: 0.8448 (t80) cc_final: 0.7933 (t80) REVERT: B 615 MET cc_start: 0.8907 (mmp) cc_final: 0.8700 (mmm) REVERT: B 645 GLN cc_start: 0.9042 (tp40) cc_final: 0.8763 (tp-100) REVERT: B 648 ILE cc_start: 0.9141 (mm) cc_final: 0.8867 (mm) REVERT: B 667 LEU cc_start: 0.8273 (mp) cc_final: 0.7998 (tp) REVERT: B 675 HIS cc_start: 0.8751 (t-90) cc_final: 0.8410 (t-90) REVERT: C 74 MET cc_start: 0.7379 (ttm) cc_final: 0.6579 (ptm) REVERT: C 90 LEU cc_start: 0.8404 (mt) cc_final: 0.8028 (mp) REVERT: C 95 MET cc_start: 0.8250 (tmm) cc_final: 0.7830 (tmm) REVERT: C 96 MET cc_start: 0.8512 (mmm) cc_final: 0.8156 (mmm) REVERT: C 137 MET cc_start: 0.7312 (mpp) cc_final: 0.6293 (tpt) REVERT: C 149 ASP cc_start: 0.8045 (t0) cc_final: 0.7626 (t0) REVERT: C 151 ILE cc_start: 0.8286 (mm) cc_final: 0.7848 (tp) REVERT: C 227 PHE cc_start: 0.7971 (t80) cc_final: 0.7671 (t80) REVERT: C 259 PHE cc_start: 0.6434 (t80) cc_final: 0.5571 (t80) REVERT: C 276 TYR cc_start: 0.8230 (t80) cc_final: 0.7736 (t80) REVERT: D 96 MET cc_start: 0.4719 (tpt) cc_final: 0.3984 (mmm) REVERT: D 169 TYR cc_start: 0.7951 (m-80) cc_final: 0.7024 (m-80) REVERT: D 178 PHE cc_start: 0.8236 (m-80) cc_final: 0.8027 (m-80) REVERT: D 208 LEU cc_start: 0.9195 (mt) cc_final: 0.8981 (mt) outliers start: 2 outliers final: 1 residues processed: 533 average time/residue: 0.2798 time to fit residues: 219.3230 Evaluate side-chains 437 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 436 time to evaluate : 1.844 ------------------------------------------------------------------------------- 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: 0.9980 chunk 126 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 69 optimal weight: 5.9990 chunk 156 optimal weight: 20.0000 chunk 21 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 chunk 169 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.126580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.084963 restraints weight = 51573.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.088194 restraints weight = 31706.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.090339 restraints weight = 22164.096| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.6197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16386 Z= 0.187 Angle : 0.629 9.622 22134 Z= 0.333 Chirality : 0.043 0.184 2360 Planarity : 0.004 0.040 2818 Dihedral : 10.999 161.964 2242 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.06 % Allowed : 1.69 % Favored : 98.25 % 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: 1.11 (0.15), residues: 1129 sheet: -0.46 (0.42), residues: 136 loop : 0.30 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 558 HIS 0.011 0.001 HIS C 201 PHE 0.026 0.002 PHE A 657 TYR 0.019 0.002 TYR B 527 ARG 0.010 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 871) hydrogen bonds : angle 5.04030 ( 2571) covalent geometry : bond 0.00406 (16386) covalent geometry : angle 0.62894 (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 521 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 520 time to evaluate : 1.759 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 67 GLU cc_start: 0.9290 (tp30) cc_final: 0.8873 (tp30) REVERT: A 71 LEU cc_start: 0.9404 (mt) cc_final: 0.9108 (mt) REVERT: A 99 LYS cc_start: 0.9408 (mmtp) cc_final: 0.8892 (mttt) REVERT: A 117 ARG cc_start: 0.9136 (mmt90) cc_final: 0.8825 (mtp85) REVERT: A 147 GLN cc_start: 0.9128 (mt0) cc_final: 0.8708 (mt0) REVERT: A 202 ASN cc_start: 0.8742 (t0) cc_final: 0.8520 (t0) REVERT: A 214 LYS cc_start: 0.9341 (mmmt) cc_final: 0.9045 (mmtt) REVERT: A 220 THR cc_start: 0.8002 (m) cc_final: 0.7594 (p) REVERT: A 259 ASN cc_start: 0.8447 (p0) cc_final: 0.7984 (p0) REVERT: A 263 ASP cc_start: 0.9017 (t0) cc_final: 0.8583 (m-30) REVERT: A 270 ASP cc_start: 0.8730 (m-30) cc_final: 0.8023 (t0) REVERT: A 314 MET cc_start: 0.8432 (ppp) cc_final: 0.8147 (ppp) REVERT: A 349 LEU cc_start: 0.8580 (tp) cc_final: 0.8324 (tp) REVERT: A 361 GLN cc_start: 0.9034 (tp40) cc_final: 0.8806 (tp-100) REVERT: A 375 LYS cc_start: 0.9051 (mmtm) cc_final: 0.8577 (mmtm) REVERT: A 386 LEU cc_start: 0.9066 (mt) cc_final: 0.8862 (mt) REVERT: A 387 GLN cc_start: 0.8191 (mt0) cc_final: 0.7939 (mt0) REVERT: A 402 GLU cc_start: 0.8825 (mp0) cc_final: 0.8555 (mp0) REVERT: A 407 ILE cc_start: 0.8979 (mt) cc_final: 0.8165 (mt) REVERT: A 425 ILE cc_start: 0.9324 (mm) cc_final: 0.8789 (mm) REVERT: A 456 LYS cc_start: 0.8786 (mmtm) cc_final: 0.8166 (mmtm) REVERT: A 479 TYR cc_start: 0.7998 (t80) cc_final: 0.7355 (t80) REVERT: A 494 MET cc_start: 0.9573 (mmm) cc_final: 0.9273 (mmm) REVERT: A 498 TYR cc_start: 0.9139 (m-80) cc_final: 0.8765 (m-80) REVERT: A 501 GLN cc_start: 0.9051 (tp40) cc_final: 0.8714 (tp-100) REVERT: A 550 MET cc_start: 0.7674 (mtm) cc_final: 0.6968 (mtm) REVERT: A 571 TYR cc_start: 0.8729 (t80) cc_final: 0.8362 (t80) REVERT: A 598 MET cc_start: 0.8765 (mtm) cc_final: 0.8475 (ttm) REVERT: A 599 GLU cc_start: 0.7638 (mm-30) cc_final: 0.7354 (mm-30) REVERT: A 615 MET cc_start: 0.8189 (mmp) cc_final: 0.7870 (mmp) REVERT: A 640 MET cc_start: 0.9428 (tpt) cc_final: 0.9141 (tpp) REVERT: B 8 LYS cc_start: 0.9481 (tttm) cc_final: 0.9171 (tppt) REVERT: B 12 LEU cc_start: 0.9558 (mt) cc_final: 0.9330 (mt) REVERT: B 24 PHE cc_start: 0.8842 (m-80) cc_final: 0.8484 (m-80) REVERT: B 41 ILE cc_start: 0.9459 (mm) cc_final: 0.9258 (mm) REVERT: B 95 MET cc_start: 0.9187 (tpp) cc_final: 0.7896 (tpp) REVERT: B 98 PHE cc_start: 0.9610 (t80) cc_final: 0.8829 (t80) REVERT: B 99 LYS cc_start: 0.9668 (mmmt) cc_final: 0.8922 (mmmt) REVERT: B 124 ILE cc_start: 0.9265 (tp) cc_final: 0.8810 (tp) REVERT: B 235 ARG cc_start: 0.7642 (mmm-85) cc_final: 0.7010 (mmt90) REVERT: B 259 ASN cc_start: 0.8847 (m-40) cc_final: 0.8592 (p0) REVERT: B 307 TYR cc_start: 0.9253 (t80) cc_final: 0.8815 (t80) REVERT: B 319 MET cc_start: 0.9013 (tpp) cc_final: 0.8667 (tpp) REVERT: B 326 PHE cc_start: 0.9214 (m-10) cc_final: 0.8539 (m-80) REVERT: B 333 LYS cc_start: 0.8630 (ttpt) cc_final: 0.8395 (tttt) REVERT: B 444 ASP cc_start: 0.9143 (t0) cc_final: 0.8872 (t0) REVERT: B 445 ILE cc_start: 0.8512 (mm) cc_final: 0.8293 (mm) REVERT: B 459 LYS cc_start: 0.8767 (mttt) cc_final: 0.8355 (mtmm) REVERT: B 466 MET cc_start: 0.8650 (ptp) cc_final: 0.8124 (ptp) REVERT: B 472 LEU cc_start: 0.9264 (mm) cc_final: 0.8906 (mm) REVERT: B 492 PHE cc_start: 0.9251 (m-80) cc_final: 0.8596 (m-80) REVERT: B 493 MET cc_start: 0.9228 (tmm) cc_final: 0.8876 (tmm) REVERT: B 494 MET cc_start: 0.9293 (mtp) cc_final: 0.8936 (mtp) REVERT: B 584 ILE cc_start: 0.8910 (tp) cc_final: 0.8702 (tp) REVERT: B 588 GLN cc_start: 0.9326 (mm110) cc_final: 0.9125 (mm110) REVERT: B 613 TYR cc_start: 0.8403 (t80) cc_final: 0.8156 (t80) REVERT: B 615 MET cc_start: 0.8844 (mmp) cc_final: 0.8606 (mmm) REVERT: B 675 HIS cc_start: 0.8757 (t-90) cc_final: 0.8348 (t-90) REVERT: C 74 MET cc_start: 0.7494 (ttm) cc_final: 0.6765 (ptp) REVERT: C 95 MET cc_start: 0.8358 (tmm) cc_final: 0.7961 (tmm) REVERT: C 96 MET cc_start: 0.8475 (mmm) cc_final: 0.8217 (mmm) REVERT: C 137 MET cc_start: 0.7571 (mpp) cc_final: 0.7109 (ptp) REVERT: C 149 ASP cc_start: 0.8044 (t0) cc_final: 0.7670 (t0) REVERT: C 151 ILE cc_start: 0.8344 (mm) cc_final: 0.7960 (tp) REVERT: C 227 PHE cc_start: 0.7984 (t80) cc_final: 0.7697 (t80) REVERT: C 276 TYR cc_start: 0.8306 (t80) cc_final: 0.7848 (t80) REVERT: D 96 MET cc_start: 0.4677 (tpt) cc_final: 0.4097 (tpp) REVERT: D 157 MET cc_start: 0.6897 (tmm) cc_final: 0.6639 (tmm) REVERT: D 169 TYR cc_start: 0.8174 (m-80) cc_final: 0.7332 (m-80) REVERT: D 201 HIS cc_start: 0.8008 (m90) cc_final: 0.7730 (m90) outliers start: 1 outliers final: 1 residues processed: 521 average time/residue: 0.2699 time to fit residues: 208.4161 Evaluate side-chains 430 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 429 time to evaluate : 1.732 ------------------------------------------------------------------------------- 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: 4.9990 chunk 85 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 146 optimal weight: 9.9990 chunk 184 optimal weight: 7.9990 chunk 119 optimal weight: 0.8980 chunk 175 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 ASN A 232 ASN ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.125928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.087532 restraints weight = 50982.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.090499 restraints weight = 32328.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.092418 restraints weight = 23037.482| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3276 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3276 r_free = 0.3276 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 = 0.3276 r_free = 0.3276 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3276 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.6410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16386 Z= 0.172 Angle : 0.626 11.788 22134 Z= 0.332 Chirality : 0.043 0.164 2360 Planarity : 0.004 0.046 2818 Dihedral : 10.803 158.608 2242 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.06 % Allowed : 1.86 % 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: 0.92 (0.19), residues: 1932 helix: 1.08 (0.15), residues: 1135 sheet: -0.47 (0.42), residues: 136 loop : 0.24 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 558 HIS 0.012 0.001 HIS C 201 PHE 0.046 0.002 PHE D 178 TYR 0.022 0.002 TYR D 174 ARG 0.011 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03991 ( 871) hydrogen bonds : angle 5.10219 ( 2571) covalent geometry : bond 0.00376 (16386) covalent geometry : angle 0.62645 (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 509 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 508 time to evaluate : 1.949 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 65 GLU cc_start: 0.8634 (mp0) cc_final: 0.7929 (mp0) REVERT: A 67 GLU cc_start: 0.9246 (tp30) cc_final: 0.8833 (tp30) REVERT: A 71 LEU cc_start: 0.9403 (mt) cc_final: 0.9123 (mt) REVERT: A 99 LYS cc_start: 0.9461 (mmtp) cc_final: 0.8917 (mttt) REVERT: A 117 ARG cc_start: 0.9134 (mmt90) cc_final: 0.8876 (mtp85) REVERT: A 147 GLN cc_start: 0.9108 (mt0) cc_final: 0.8680 (mt0) REVERT: A 214 LYS cc_start: 0.9361 (mmmt) cc_final: 0.9087 (mmtt) REVERT: A 220 THR cc_start: 0.8124 (m) cc_final: 0.7693 (p) REVERT: A 236 TYR cc_start: 0.7648 (t80) cc_final: 0.7296 (t80) REVERT: A 263 ASP cc_start: 0.9136 (t0) cc_final: 0.8635 (m-30) REVERT: A 270 ASP cc_start: 0.8687 (m-30) cc_final: 0.8047 (t0) REVERT: A 312 GLN cc_start: 0.8662 (tp-100) cc_final: 0.8041 (tp-100) REVERT: A 314 MET cc_start: 0.8401 (ppp) cc_final: 0.8102 (ppp) REVERT: A 345 LYS cc_start: 0.9300 (mttp) cc_final: 0.9041 (mttt) REVERT: A 349 LEU cc_start: 0.8576 (tp) cc_final: 0.8356 (tp) REVERT: A 361 GLN cc_start: 0.9033 (tp40) cc_final: 0.8748 (tp40) REVERT: A 375 LYS cc_start: 0.9034 (mmtm) cc_final: 0.8546 (mmtm) REVERT: A 402 GLU cc_start: 0.8861 (mp0) cc_final: 0.8580 (mp0) REVERT: A 407 ILE cc_start: 0.9030 (mt) cc_final: 0.8654 (mt) REVERT: A 455 ASN cc_start: 0.8993 (t0) cc_final: 0.8757 (t0) REVERT: A 456 LYS cc_start: 0.8887 (mmtm) cc_final: 0.8314 (mmtm) REVERT: A 466 MET cc_start: 0.8373 (ptp) cc_final: 0.7709 (pmm) REVERT: A 493 MET cc_start: 0.9018 (tmm) cc_final: 0.8563 (tmm) REVERT: A 494 MET cc_start: 0.9516 (mmm) cc_final: 0.9115 (mmm) REVERT: A 498 TYR cc_start: 0.9126 (m-80) cc_final: 0.8768 (m-80) REVERT: A 501 GLN cc_start: 0.9239 (tp40) cc_final: 0.8793 (tp-100) REVERT: A 550 MET cc_start: 0.7886 (mtm) cc_final: 0.7471 (mtm) REVERT: A 598 MET cc_start: 0.8721 (mtm) cc_final: 0.8478 (ttm) REVERT: A 615 MET cc_start: 0.8179 (mmp) cc_final: 0.7959 (mmp) REVERT: A 640 MET cc_start: 0.9417 (tpt) cc_final: 0.9116 (tpp) REVERT: A 645 GLN cc_start: 0.8511 (tp40) cc_final: 0.8207 (tp-100) REVERT: A 650 GLN cc_start: 0.6796 (mm-40) cc_final: 0.6301 (mm-40) REVERT: B 8 LYS cc_start: 0.9418 (tttm) cc_final: 0.9113 (tppt) REVERT: B 12 LEU cc_start: 0.9591 (mt) cc_final: 0.9307 (mt) REVERT: B 17 MET cc_start: 0.9322 (mtp) cc_final: 0.8972 (mmt) REVERT: B 24 PHE cc_start: 0.8943 (m-80) cc_final: 0.8196 (m-80) REVERT: B 41 ILE cc_start: 0.9351 (mm) cc_final: 0.8969 (mm) REVERT: B 95 MET cc_start: 0.9106 (tpp) cc_final: 0.7855 (tpp) REVERT: B 98 PHE cc_start: 0.9571 (t80) cc_final: 0.8854 (t80) REVERT: B 99 LYS cc_start: 0.9690 (mmmt) cc_final: 0.8988 (mmmt) REVERT: B 124 ILE cc_start: 0.9209 (tp) cc_final: 0.8649 (tp) REVERT: B 235 ARG cc_start: 0.7684 (mmm-85) cc_final: 0.6895 (mmt180) REVERT: B 259 ASN cc_start: 0.8826 (m-40) cc_final: 0.8575 (p0) REVERT: B 288 PHE cc_start: 0.9357 (t80) cc_final: 0.9126 (t80) REVERT: B 307 TYR cc_start: 0.9223 (t80) cc_final: 0.8728 (t80) REVERT: B 319 MET cc_start: 0.9065 (tpp) cc_final: 0.8752 (tpp) REVERT: B 322 MET cc_start: 0.8464 (mmm) cc_final: 0.8246 (mmt) REVERT: B 326 PHE cc_start: 0.9248 (m-10) cc_final: 0.8509 (m-80) REVERT: B 359 MET cc_start: 0.8416 (ttm) cc_final: 0.6938 (tmm) REVERT: B 375 LYS cc_start: 0.9224 (mptt) cc_final: 0.8759 (mptt) REVERT: B 379 SER cc_start: 0.8411 (t) cc_final: 0.7946 (t) REVERT: B 396 ASP cc_start: 0.8740 (m-30) cc_final: 0.8484 (m-30) REVERT: B 403 ILE cc_start: 0.9011 (mp) cc_final: 0.8612 (tp) REVERT: B 444 ASP cc_start: 0.9136 (t0) cc_final: 0.8682 (t0) REVERT: B 445 ILE cc_start: 0.8541 (mm) cc_final: 0.8318 (mm) REVERT: B 459 LYS cc_start: 0.8794 (mttt) cc_final: 0.8380 (mtmm) REVERT: B 472 LEU cc_start: 0.9260 (mm) cc_final: 0.8929 (mt) REVERT: B 492 PHE cc_start: 0.9237 (m-80) cc_final: 0.8581 (m-80) REVERT: B 493 MET cc_start: 0.9177 (tmm) cc_final: 0.8825 (tmm) REVERT: B 494 MET cc_start: 0.9262 (mtp) cc_final: 0.8896 (mtp) REVERT: B 584 ILE cc_start: 0.8950 (tp) cc_final: 0.8730 (tp) REVERT: B 631 ASP cc_start: 0.9146 (t70) cc_final: 0.8823 (t0) REVERT: B 645 GLN cc_start: 0.8951 (tp40) cc_final: 0.8749 (tp-100) REVERT: B 675 HIS cc_start: 0.8727 (t-90) cc_final: 0.8399 (t-90) REVERT: C 95 MET cc_start: 0.8356 (tmm) cc_final: 0.7920 (tmm) REVERT: C 96 MET cc_start: 0.8644 (mmm) cc_final: 0.8252 (mmm) REVERT: C 137 MET cc_start: 0.7747 (mpp) cc_final: 0.6929 (tpt) REVERT: C 149 ASP cc_start: 0.8089 (t0) cc_final: 0.7794 (t0) REVERT: C 151 ILE cc_start: 0.8277 (mm) cc_final: 0.7861 (tp) REVERT: C 227 PHE cc_start: 0.7966 (t80) cc_final: 0.7710 (t80) REVERT: C 276 TYR cc_start: 0.8268 (t80) cc_final: 0.7803 (t80) REVERT: D 96 MET cc_start: 0.4381 (tpt) cc_final: 0.3706 (tpp) REVERT: D 157 MET cc_start: 0.6770 (tmm) cc_final: 0.6537 (tmm) REVERT: D 169 TYR cc_start: 0.8415 (m-80) cc_final: 0.7664 (m-80) REVERT: D 201 HIS cc_start: 0.7972 (m90) cc_final: 0.7634 (m90) outliers start: 1 outliers final: 0 residues processed: 509 average time/residue: 0.2689 time to fit residues: 203.3470 Evaluate side-chains 425 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 1.849 ------------------------------------------------------------------------------- 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: 9.9990 chunk 30 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 chunk 159 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN C 238 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.127691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.086200 restraints weight = 50586.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.089403 restraints weight = 31221.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.091215 restraints weight = 21820.425| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.6645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 16386 Z= 0.160 Angle : 0.636 11.380 22134 Z= 0.335 Chirality : 0.043 0.216 2360 Planarity : 0.004 0.049 2818 Dihedral : 10.619 154.662 2242 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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: 0.83 (0.19), residues: 1932 helix: 1.04 (0.15), residues: 1137 sheet: -0.66 (0.41), residues: 144 loop : 0.18 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 9 HIS 0.014 0.001 HIS C 201 PHE 0.027 0.002 PHE D 178 TYR 0.027 0.002 TYR D 174 ARG 0.014 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 871) hydrogen bonds : angle 5.11593 ( 2571) covalent geometry : bond 0.00348 (16386) covalent geometry : angle 0.63611 (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 496 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 496 time to evaluate : 1.778 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 67 GLU cc_start: 0.9292 (tp30) cc_final: 0.9006 (tp30) REVERT: A 99 LYS cc_start: 0.9448 (mmtp) cc_final: 0.8936 (mttt) REVERT: A 117 ARG cc_start: 0.9167 (mmt90) cc_final: 0.8865 (mtp85) REVERT: A 139 GLU cc_start: 0.9237 (mp0) cc_final: 0.9037 (pm20) REVERT: A 147 GLN cc_start: 0.9117 (mt0) cc_final: 0.8655 (mt0) REVERT: A 158 ASN cc_start: 0.8996 (m110) cc_final: 0.8724 (m110) REVERT: A 202 ASN cc_start: 0.8642 (t0) cc_final: 0.8410 (t0) REVERT: A 214 LYS cc_start: 0.9347 (mmmt) cc_final: 0.9044 (mmtt) REVERT: A 220 THR cc_start: 0.7973 (m) cc_final: 0.7642 (p) REVERT: A 259 ASN cc_start: 0.8456 (p0) cc_final: 0.7908 (p0) REVERT: A 263 ASP cc_start: 0.9122 (t0) cc_final: 0.8623 (m-30) REVERT: A 270 ASP cc_start: 0.8695 (m-30) cc_final: 0.7924 (t0) REVERT: A 312 GLN cc_start: 0.8711 (tp-100) cc_final: 0.8114 (tp-100) REVERT: A 314 MET cc_start: 0.8466 (ppp) cc_final: 0.8195 (ppp) REVERT: A 345 LYS cc_start: 0.9239 (mttp) cc_final: 0.8953 (mttt) REVERT: A 375 LYS cc_start: 0.9073 (mmtm) cc_final: 0.8613 (mmtm) REVERT: A 402 GLU cc_start: 0.8840 (mp0) cc_final: 0.8578 (mp0) REVERT: A 407 ILE cc_start: 0.9015 (mt) cc_final: 0.8643 (mt) REVERT: A 425 ILE cc_start: 0.9320 (mm) cc_final: 0.8714 (mm) REVERT: A 455 ASN cc_start: 0.8936 (t0) cc_final: 0.8725 (t0) REVERT: A 456 LYS cc_start: 0.8907 (mmtm) cc_final: 0.8316 (mmtm) REVERT: A 493 MET cc_start: 0.8985 (tmm) cc_final: 0.8436 (tmm) REVERT: A 494 MET cc_start: 0.9531 (mmm) cc_final: 0.9033 (mmm) REVERT: A 498 TYR cc_start: 0.9160 (m-80) cc_final: 0.8776 (m-80) REVERT: A 501 GLN cc_start: 0.9307 (tp40) cc_final: 0.8865 (tp-100) REVERT: A 550 MET cc_start: 0.7604 (mtm) cc_final: 0.7035 (mtm) REVERT: A 599 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7255 (mm-30) REVERT: A 611 THR cc_start: 0.8869 (t) cc_final: 0.8397 (t) REVERT: A 640 MET cc_start: 0.9402 (tpt) cc_final: 0.9106 (tpp) REVERT: A 645 GLN cc_start: 0.8592 (tp40) cc_final: 0.8329 (tp40) REVERT: A 646 GLN cc_start: 0.9161 (pt0) cc_final: 0.8948 (pm20) REVERT: A 650 GLN cc_start: 0.7006 (mm-40) cc_final: 0.6404 (mm-40) REVERT: B 8 LYS cc_start: 0.9480 (tttm) cc_final: 0.9159 (tppt) REVERT: B 12 LEU cc_start: 0.9597 (mt) cc_final: 0.9333 (mt) REVERT: B 17 MET cc_start: 0.9410 (mtp) cc_final: 0.8990 (mmt) REVERT: B 24 PHE cc_start: 0.9088 (m-80) cc_final: 0.8289 (m-80) REVERT: B 95 MET cc_start: 0.9204 (tpp) cc_final: 0.8000 (tpp) REVERT: B 98 PHE cc_start: 0.9554 (t80) cc_final: 0.8942 (t80) REVERT: B 99 LYS cc_start: 0.9694 (mmmt) cc_final: 0.9031 (mmmt) REVERT: B 124 ILE cc_start: 0.9204 (tp) cc_final: 0.8664 (tp) REVERT: B 235 ARG cc_start: 0.7842 (mmm-85) cc_final: 0.7120 (mmt90) REVERT: B 259 ASN cc_start: 0.8809 (m-40) cc_final: 0.8514 (p0) REVERT: B 288 PHE cc_start: 0.9396 (t80) cc_final: 0.9151 (t80) REVERT: B 307 TYR cc_start: 0.9262 (t80) cc_final: 0.8792 (t80) REVERT: B 319 MET cc_start: 0.9073 (tpp) cc_final: 0.8710 (tpp) REVERT: B 322 MET cc_start: 0.8529 (mmm) cc_final: 0.8328 (mmt) REVERT: B 326 PHE cc_start: 0.9280 (m-10) cc_final: 0.8526 (m-80) REVERT: B 358 ILE cc_start: 0.8644 (mm) cc_final: 0.8439 (mm) REVERT: B 375 LYS cc_start: 0.9257 (mptt) cc_final: 0.8787 (mptt) REVERT: B 396 ASP cc_start: 0.8842 (m-30) cc_final: 0.8566 (m-30) REVERT: B 403 ILE cc_start: 0.9006 (mp) cc_final: 0.8590 (tp) REVERT: B 444 ASP cc_start: 0.9161 (t0) cc_final: 0.8696 (t0) REVERT: B 445 ILE cc_start: 0.8525 (mm) cc_final: 0.8306 (mm) REVERT: B 459 LYS cc_start: 0.8882 (mttt) cc_final: 0.8577 (mtmm) REVERT: B 466 MET cc_start: 0.8597 (ptp) cc_final: 0.8125 (ptp) REVERT: B 472 LEU cc_start: 0.9263 (mm) cc_final: 0.8983 (mm) REVERT: B 492 PHE cc_start: 0.9220 (m-80) cc_final: 0.8579 (m-80) REVERT: B 493 MET cc_start: 0.9193 (tmm) cc_final: 0.8841 (tmm) REVERT: B 494 MET cc_start: 0.9319 (mtp) cc_final: 0.8959 (mtp) REVERT: B 615 MET cc_start: 0.8735 (mmp) cc_final: 0.8415 (mmm) REVERT: B 640 MET cc_start: 0.8992 (ttm) cc_final: 0.8715 (ttm) REVERT: B 645 GLN cc_start: 0.9067 (tp40) cc_final: 0.8857 (tp-100) REVERT: B 675 HIS cc_start: 0.8769 (t-90) cc_final: 0.8435 (t-90) REVERT: C 95 MET cc_start: 0.8099 (tmm) cc_final: 0.7584 (tmm) REVERT: C 96 MET cc_start: 0.8592 (mmm) cc_final: 0.8281 (mmm) REVERT: C 137 MET cc_start: 0.7484 (mpp) cc_final: 0.6518 (tpt) REVERT: C 149 ASP cc_start: 0.8149 (t0) cc_final: 0.7829 (t0) REVERT: C 151 ILE cc_start: 0.8336 (mm) cc_final: 0.7931 (tp) REVERT: C 276 TYR cc_start: 0.8290 (t80) cc_final: 0.7977 (t80) REVERT: D 96 MET cc_start: 0.4813 (tpt) cc_final: 0.4328 (tpt) REVERT: D 157 MET cc_start: 0.6807 (tmm) cc_final: 0.6600 (tmm) REVERT: D 169 TYR cc_start: 0.8528 (m-80) cc_final: 0.7870 (m-80) outliers start: 0 outliers final: 0 residues processed: 496 average time/residue: 0.2702 time to fit residues: 199.4610 Evaluate side-chains 428 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 428 time to evaluate : 1.948 ------------------------------------------------------------------------------- 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: 9.9990 chunk 102 optimal weight: 4.9990 chunk 182 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 77 optimal weight: 0.7980 chunk 96 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 50 optimal weight: 2.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.121412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.083608 restraints weight = 53692.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.086422 restraints weight = 34467.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.088254 restraints weight = 24190.510| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.7000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 16386 Z= 0.255 Angle : 0.716 10.082 22134 Z= 0.379 Chirality : 0.045 0.170 2360 Planarity : 0.004 0.042 2818 Dihedral : 10.877 153.756 2242 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 19.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.50 (0.19), residues: 1932 helix: 0.79 (0.15), residues: 1124 sheet: -0.92 (0.41), residues: 146 loop : 0.08 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 558 HIS 0.013 0.002 HIS C 201 PHE 0.023 0.002 PHE D 178 TYR 0.028 0.002 TYR D 174 ARG 0.013 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04405 ( 871) hydrogen bonds : angle 5.27251 ( 2571) covalent geometry : bond 0.00542 (16386) covalent geometry : angle 0.71562 (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 480 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 1.774 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 67 GLU cc_start: 0.9307 (tp30) cc_final: 0.9036 (tp30) REVERT: A 117 ARG cc_start: 0.9139 (mmt90) cc_final: 0.8804 (mmt180) REVERT: A 147 GLN cc_start: 0.9182 (mt0) cc_final: 0.8931 (mt0) REVERT: A 158 ASN cc_start: 0.8933 (m110) cc_final: 0.8551 (m110) REVERT: A 214 LYS cc_start: 0.9435 (mmmt) cc_final: 0.9125 (mmtt) REVERT: A 220 THR cc_start: 0.8087 (m) cc_final: 0.7774 (p) REVERT: A 259 ASN cc_start: 0.8375 (p0) cc_final: 0.7895 (p0) REVERT: A 263 ASP cc_start: 0.9112 (t0) cc_final: 0.8650 (m-30) REVERT: A 270 ASP cc_start: 0.8618 (m-30) cc_final: 0.8190 (t0) REVERT: A 314 MET cc_start: 0.8398 (ppp) cc_final: 0.8151 (ppp) REVERT: A 322 MET cc_start: 0.8304 (mmm) cc_final: 0.8066 (mmt) REVERT: A 359 MET cc_start: 0.7889 (ttt) cc_final: 0.7660 (ttt) REVERT: A 370 ASN cc_start: 0.9368 (m-40) cc_final: 0.9123 (m110) REVERT: A 375 LYS cc_start: 0.8987 (mmtm) cc_final: 0.8514 (mmtm) REVERT: A 390 GLN cc_start: 0.8212 (tm-30) cc_final: 0.8000 (tm-30) REVERT: A 402 GLU cc_start: 0.8896 (mp0) cc_final: 0.8635 (mp0) REVERT: A 407 ILE cc_start: 0.9051 (mt) cc_final: 0.8604 (mt) REVERT: A 455 ASN cc_start: 0.8997 (t0) cc_final: 0.8751 (t0) REVERT: A 456 LYS cc_start: 0.8888 (mmtm) cc_final: 0.8254 (mmtm) REVERT: A 493 MET cc_start: 0.8997 (tmm) cc_final: 0.8501 (tmm) REVERT: A 494 MET cc_start: 0.9506 (mmm) cc_final: 0.9048 (mmm) REVERT: A 498 TYR cc_start: 0.9234 (m-80) cc_final: 0.8860 (m-80) REVERT: A 501 GLN cc_start: 0.9360 (tp40) cc_final: 0.8880 (tp-100) REVERT: A 550 MET cc_start: 0.8264 (mtm) cc_final: 0.7614 (mtm) REVERT: A 604 ARG cc_start: 0.8633 (mmm-85) cc_final: 0.8395 (tpp80) REVERT: A 606 TYR cc_start: 0.8536 (m-80) cc_final: 0.8140 (m-80) REVERT: A 640 MET cc_start: 0.9513 (tpt) cc_final: 0.9049 (tpp) REVERT: A 650 GLN cc_start: 0.7116 (mm-40) cc_final: 0.6493 (mm-40) REVERT: B 8 LYS cc_start: 0.9484 (tttm) cc_final: 0.9157 (tppt) REVERT: B 12 LEU cc_start: 0.9608 (mt) cc_final: 0.9345 (mt) REVERT: B 17 MET cc_start: 0.9428 (mtp) cc_final: 0.9037 (mmm) REVERT: B 24 PHE cc_start: 0.9053 (m-80) cc_final: 0.8402 (m-80) REVERT: B 65 GLU cc_start: 0.8573 (mm-30) cc_final: 0.8359 (mm-30) REVERT: B 95 MET cc_start: 0.9032 (tpp) cc_final: 0.7906 (tpp) REVERT: B 98 PHE cc_start: 0.9512 (t80) cc_final: 0.8746 (t80) REVERT: B 99 LYS cc_start: 0.9707 (mmmt) cc_final: 0.9009 (mmmt) REVERT: B 259 ASN cc_start: 0.8839 (m-40) cc_final: 0.8531 (p0) REVERT: B 307 TYR cc_start: 0.9254 (t80) cc_final: 0.8746 (t80) REVERT: B 316 GLU cc_start: 0.9023 (mm-30) cc_final: 0.8615 (mm-30) REVERT: B 319 MET cc_start: 0.9061 (tpp) cc_final: 0.8478 (mmm) REVERT: B 322 MET cc_start: 0.8537 (mmm) cc_final: 0.8331 (mmt) REVERT: B 326 PHE cc_start: 0.9247 (m-10) cc_final: 0.8596 (m-80) REVERT: B 359 MET cc_start: 0.8506 (ttm) cc_final: 0.7041 (tmm) REVERT: B 375 LYS cc_start: 0.9234 (mptt) cc_final: 0.8794 (mptt) REVERT: B 379 SER cc_start: 0.8267 (t) cc_final: 0.7749 (t) REVERT: B 444 ASP cc_start: 0.9123 (t0) cc_final: 0.8596 (t0) REVERT: B 458 MET cc_start: 0.9365 (mmm) cc_final: 0.8897 (mmm) REVERT: B 459 LYS cc_start: 0.8783 (mttt) cc_final: 0.8346 (mtmm) REVERT: B 472 LEU cc_start: 0.9238 (mm) cc_final: 0.8971 (mm) REVERT: B 493 MET cc_start: 0.9254 (tmm) cc_final: 0.8902 (tmm) REVERT: B 494 MET cc_start: 0.9350 (mtp) cc_final: 0.8972 (mtp) REVERT: B 584 ILE cc_start: 0.8981 (tp) cc_final: 0.8717 (tp) REVERT: B 586 TYR cc_start: 0.9415 (m-80) cc_final: 0.9067 (m-80) REVERT: B 588 GLN cc_start: 0.9373 (mm110) cc_final: 0.9069 (mm110) REVERT: B 613 TYR cc_start: 0.8483 (t80) cc_final: 0.8083 (t80) REVERT: B 640 MET cc_start: 0.8988 (ttm) cc_final: 0.8762 (ttm) REVERT: B 657 PHE cc_start: 0.8709 (m-80) cc_final: 0.8404 (m-80) REVERT: B 662 MET cc_start: 0.9303 (ttp) cc_final: 0.8868 (tmm) REVERT: B 675 HIS cc_start: 0.8753 (t-90) cc_final: 0.8460 (t-90) REVERT: C 95 MET cc_start: 0.8453 (tmm) cc_final: 0.7853 (tmm) REVERT: C 137 MET cc_start: 0.7742 (mpp) cc_final: 0.6729 (tpp) REVERT: C 138 ILE cc_start: 0.9096 (mm) cc_final: 0.8805 (pt) REVERT: C 149 ASP cc_start: 0.7993 (t0) cc_final: 0.7708 (t0) REVERT: C 151 ILE cc_start: 0.8324 (mm) cc_final: 0.7923 (tp) REVERT: C 249 GLN cc_start: 0.8309 (pt0) cc_final: 0.8055 (pm20) REVERT: C 276 TYR cc_start: 0.8268 (t80) cc_final: 0.7995 (t80) REVERT: D 96 MET cc_start: 0.5927 (tpt) cc_final: 0.5556 (tpp) REVERT: D 169 TYR cc_start: 0.8450 (m-80) cc_final: 0.7707 (m-80) outliers start: 0 outliers final: 0 residues processed: 480 average time/residue: 0.2631 time to fit residues: 189.5847 Evaluate side-chains 408 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 1.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 137 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 0.9990 chunk 160 optimal weight: 7.9990 chunk 106 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 148 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 70 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 ASN B 387 GLN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.124675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.085252 restraints weight = 51600.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.088488 restraints weight = 31668.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.090458 restraints weight = 21898.163| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3288 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3288 r_free = 0.3288 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3288 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.7056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 16386 Z= 0.142 Angle : 0.661 9.591 22134 Z= 0.346 Chirality : 0.043 0.167 2360 Planarity : 0.004 0.049 2818 Dihedral : 10.350 148.429 2242 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.67 (0.19), residues: 1932 helix: 0.92 (0.15), residues: 1118 sheet: -0.46 (0.46), residues: 112 loop : 0.01 (0.23), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 44 HIS 0.012 0.001 HIS C 201 PHE 0.017 0.002 PHE B 100 TYR 0.027 0.002 TYR D 174 ARG 0.016 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04066 ( 871) hydrogen bonds : angle 5.15902 ( 2571) covalent geometry : bond 0.00315 (16386) covalent geometry : angle 0.66123 (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 511 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 511 time to evaluate : 1.993 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 65 GLU cc_start: 0.8254 (mp0) cc_final: 0.7876 (mp0) REVERT: A 67 GLU cc_start: 0.9264 (tp30) cc_final: 0.8985 (tp30) REVERT: A 99 LYS cc_start: 0.9515 (mmtp) cc_final: 0.8996 (mttt) REVERT: A 117 ARG cc_start: 0.9173 (mmt90) cc_final: 0.8817 (mmt180) REVERT: A 139 GLU cc_start: 0.9243 (mp0) cc_final: 0.9030 (pm20) REVERT: A 147 GLN cc_start: 0.9133 (mt0) cc_final: 0.8703 (mt0) REVERT: A 158 ASN cc_start: 0.8961 (m110) cc_final: 0.8673 (m110) REVERT: A 202 ASN cc_start: 0.8828 (t0) cc_final: 0.8552 (t0) REVERT: A 214 LYS cc_start: 0.9328 (mmmt) cc_final: 0.8983 (mmtt) REVERT: A 220 THR cc_start: 0.8165 (m) cc_final: 0.7823 (p) REVERT: A 259 ASN cc_start: 0.8432 (p0) cc_final: 0.7893 (p0) REVERT: A 263 ASP cc_start: 0.9148 (t0) cc_final: 0.8702 (m-30) REVERT: A 270 ASP cc_start: 0.8773 (m-30) cc_final: 0.8164 (p0) REVERT: A 314 MET cc_start: 0.8452 (ppp) cc_final: 0.8243 (ppp) REVERT: A 345 LYS cc_start: 0.9211 (mttp) cc_final: 0.8914 (mttt) REVERT: A 370 ASN cc_start: 0.9495 (m-40) cc_final: 0.9262 (m110) REVERT: A 400 GLU cc_start: 0.9452 (mm-30) cc_final: 0.9115 (tp30) REVERT: A 402 GLU cc_start: 0.8854 (mp0) cc_final: 0.8583 (mp0) REVERT: A 407 ILE cc_start: 0.8833 (mt) cc_final: 0.8583 (mt) REVERT: A 425 ILE cc_start: 0.9176 (mp) cc_final: 0.8875 (mp) REVERT: A 441 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8634 (mt-10) REVERT: A 455 ASN cc_start: 0.8956 (t0) cc_final: 0.8748 (t0) REVERT: A 456 LYS cc_start: 0.8913 (mmtm) cc_final: 0.8319 (mmtm) REVERT: A 490 THR cc_start: 0.9371 (m) cc_final: 0.8323 (p) REVERT: A 493 MET cc_start: 0.8985 (tmm) cc_final: 0.8331 (tmm) REVERT: A 494 MET cc_start: 0.9495 (mmm) cc_final: 0.8946 (mmt) REVERT: A 498 TYR cc_start: 0.9220 (m-80) cc_final: 0.8833 (m-80) REVERT: A 501 GLN cc_start: 0.9342 (tp40) cc_final: 0.8871 (tp-100) REVERT: A 571 TYR cc_start: 0.8730 (t80) cc_final: 0.8339 (t80) REVERT: A 604 ARG cc_start: 0.8592 (mmm-85) cc_final: 0.8380 (tpp80) REVERT: A 615 MET cc_start: 0.8089 (mmp) cc_final: 0.7786 (mmp) REVERT: A 640 MET cc_start: 0.9464 (tpt) cc_final: 0.9203 (tpp) REVERT: A 650 GLN cc_start: 0.6957 (mm-40) cc_final: 0.6377 (mm110) REVERT: B 8 LYS cc_start: 0.9485 (tttm) cc_final: 0.9158 (tppt) REVERT: B 12 LEU cc_start: 0.9582 (mt) cc_final: 0.9297 (mt) REVERT: B 17 MET cc_start: 0.9395 (mtp) cc_final: 0.8994 (mmt) REVERT: B 24 PHE cc_start: 0.9038 (m-80) cc_final: 0.8178 (m-80) REVERT: B 95 MET cc_start: 0.8990 (tpp) cc_final: 0.7713 (tpp) REVERT: B 98 PHE cc_start: 0.9546 (t80) cc_final: 0.8933 (t80) REVERT: B 99 LYS cc_start: 0.9703 (mmmt) cc_final: 0.8945 (mmmt) REVERT: B 119 GLU cc_start: 0.8230 (mp0) cc_final: 0.7028 (mt-10) REVERT: B 235 ARG cc_start: 0.7672 (mmm-85) cc_final: 0.6962 (mmt90) REVERT: B 256 ARG cc_start: 0.8125 (tmt-80) cc_final: 0.7533 (tmt-80) REVERT: B 259 ASN cc_start: 0.8812 (m-40) cc_final: 0.8503 (p0) REVERT: B 288 PHE cc_start: 0.9373 (t80) cc_final: 0.9143 (t80) REVERT: B 307 TYR cc_start: 0.9225 (t80) cc_final: 0.8752 (t80) REVERT: B 319 MET cc_start: 0.9029 (tpp) cc_final: 0.8588 (tpp) REVERT: B 326 PHE cc_start: 0.9259 (m-10) cc_final: 0.8334 (m-80) REVERT: B 375 LYS cc_start: 0.9264 (mptt) cc_final: 0.8803 (mptt) REVERT: B 396 ASP cc_start: 0.8808 (m-30) cc_final: 0.8514 (m-30) REVERT: B 444 ASP cc_start: 0.9035 (t0) cc_final: 0.8535 (t0) REVERT: B 458 MET cc_start: 0.9365 (mmm) cc_final: 0.8895 (mmm) REVERT: B 472 LEU cc_start: 0.9276 (mm) cc_final: 0.9014 (mm) REVERT: B 492 PHE cc_start: 0.9255 (m-80) cc_final: 0.8624 (m-80) REVERT: B 493 MET cc_start: 0.9234 (tmm) cc_final: 0.8388 (tmm) REVERT: B 494 MET cc_start: 0.9294 (mtp) cc_final: 0.8794 (mtp) REVERT: B 550 MET cc_start: 0.6938 (mmt) cc_final: 0.6705 (mpp) REVERT: B 558 TRP cc_start: 0.8274 (m100) cc_final: 0.7727 (m100) REVERT: B 584 ILE cc_start: 0.9063 (tp) cc_final: 0.8840 (tp) REVERT: B 613 TYR cc_start: 0.8429 (t80) cc_final: 0.8091 (t80) REVERT: B 645 GLN cc_start: 0.9011 (tp40) cc_final: 0.8811 (tp-100) REVERT: B 662 MET cc_start: 0.9306 (ttp) cc_final: 0.8837 (tmm) REVERT: B 675 HIS cc_start: 0.8779 (t-90) cc_final: 0.8455 (t-90) REVERT: C 93 MET cc_start: 0.8601 (ppp) cc_final: 0.8233 (ppp) REVERT: C 95 MET cc_start: 0.8239 (tmm) cc_final: 0.7689 (tmm) REVERT: C 96 MET cc_start: 0.8608 (mmt) cc_final: 0.8140 (mmm) REVERT: C 129 LYS cc_start: 0.9004 (tptp) cc_final: 0.8789 (tmtt) REVERT: C 138 ILE cc_start: 0.9045 (mm) cc_final: 0.8623 (pt) REVERT: C 149 ASP cc_start: 0.8099 (t0) cc_final: 0.7873 (t0) REVERT: C 151 ILE cc_start: 0.8344 (mm) cc_final: 0.8077 (mm) REVERT: C 276 TYR cc_start: 0.8335 (t80) cc_final: 0.8032 (t80) REVERT: D 74 MET cc_start: 0.7447 (tmm) cc_final: 0.6419 (tmm) REVERT: D 96 MET cc_start: 0.5592 (tpt) cc_final: 0.5271 (tpp) REVERT: D 169 TYR cc_start: 0.8581 (m-80) cc_final: 0.7942 (m-80) outliers start: 0 outliers final: 0 residues processed: 511 average time/residue: 0.2782 time to fit residues: 209.8753 Evaluate side-chains 425 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 425 time to evaluate : 1.783 ------------------------------------------------------------------------------- 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: 6.9990 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 179 optimal weight: 40.0000 chunk 190 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 180 optimal weight: 10.0000 chunk 108 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 HIS ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.123631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.084598 restraints weight = 51356.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.087695 restraints weight = 31542.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.089793 restraints weight = 21936.726| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 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 = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.7207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 16386 Z= 0.154 Angle : 0.654 8.702 22134 Z= 0.344 Chirality : 0.043 0.168 2360 Planarity : 0.004 0.050 2818 Dihedral : 10.126 141.285 2242 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 16.12 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: 0.65 (0.19), residues: 1932 helix: 0.88 (0.15), residues: 1134 sheet: -0.63 (0.44), residues: 122 loop : 0.08 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 44 HIS 0.012 0.001 HIS C 201 PHE 0.025 0.002 PHE D 122 TYR 0.028 0.002 TYR D 174 ARG 0.013 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04053 ( 871) hydrogen bonds : angle 5.16595 ( 2571) covalent geometry : bond 0.00339 (16386) covalent geometry : angle 0.65377 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6003.68 seconds wall clock time: 105 minutes 57.85 seconds (6357.85 seconds total)