Starting phenix.real_space_refine on Sat Jun 14 07:45:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byw_45046/06_2025/9byw_45046_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byw_45046/06_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_45046/06_2025/9byw_45046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byw_45046/06_2025/9byw_45046.map" model { file = "/net/cci-nas-00/data/ceres_data/9byw_45046/06_2025/9byw_45046_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byw_45046/06_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-5710/modules/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 10.25, per 1000 atoms: 0.64 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: 4.39 Conformation dependent library (CDL) restraints added in 2.1 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: 1.96 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: 5.35 Time building geometry restraints manager: 5.15 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: 0.000 Normalize map: mean=0, sd=1: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.670 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 39.800 Find NCS groups from input model: 1.000 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: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.720 ------------------------------------------------------------------------------- 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 : 1.861 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: 0.6569 (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: 0.7407 (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: 0.7925 (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: 0.8357 (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: 0.7829 (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: 0.6425 (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: 0.7775 (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: -0.1517 (tp) outliers start: 23 outliers final: 4 residues processed: 799 average time/residue: 0.3033 time to fit residues: 345.6210 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 : 1.689 ------------------------------------------------------------------------------- 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 = 0.3917 r_free = 0.3917 target = 0.131842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.091547 restraints weight = 43645.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.093552 restraints weight = 27819.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.096675 restraints weight = 20641.593| |-----------------------------------------------------------------------------| r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3387 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3387 r_free = 0.3387 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 = 0.3385 r_free = 0.3385 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3385 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 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 : 1.675 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: 0.9220 (t80) cc_final: 0.8738 (t80) REVERT: A 143 LEU cc_start: 0.9132 (tp) cc_final: 0.8928 (tp) REVERT: A 147 GLN cc_start: 0.9082 (mt0) cc_final: 0.8635 (mt0) REVERT: A 168 VAL cc_start: 0.8547 (t) cc_final: 0.8267 (t) REVERT: A 172 LEU cc_start: 0.8945 (mp) cc_final: 0.8497 (mp) REVERT: A 173 LEU cc_start: 0.9133 (mt) cc_final: 0.8881 (mt) REVERT: A 205 LYS cc_start: 0.7250 (mttp) cc_final: 0.6979 (mttt) REVERT: A 214 LYS cc_start: 0.9269 (mmmt) cc_final: 0.8889 (mmtt) REVERT: A 220 THR cc_start: 0.7783 (m) cc_final: 0.7537 (p) REVERT: A 239 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7330 (tt0) REVERT: A 270 ASP cc_start: 0.8742 (m-30) cc_final: 0.8118 (t70) REVERT: A 286 ASP cc_start: 0.8796 (m-30) cc_final: 0.8465 (m-30) REVERT: A 291 LEU cc_start: 0.8803 (mt) cc_final: 0.8454 (mt) REVERT: A 322 MET cc_start: 0.8765 (mmm) cc_final: 0.7897 (mmm) REVERT: A 349 LEU cc_start: 0.8483 (tp) cc_final: 0.8234 (tp) REVERT: A 359 MET cc_start: 0.7993 (ttt) cc_final: 0.7767 (ttt) REVERT: A 375 LYS cc_start: 0.9088 (mmtm) cc_final: 0.8621 (mmtm) REVERT: A 406 ASP cc_start: 0.8266 (m-30) cc_final: 0.7970 (m-30) REVERT: A 407 ILE cc_start: 0.8913 (mt) cc_final: 0.8574 (mt) REVERT: A 425 ILE cc_start: 0.9385 (mt) cc_final: 0.9173 (mt) REVERT: A 498 TYR cc_start: 0.8797 (m-80) cc_final: 0.8377 (m-80) REVERT: A 512 GLU cc_start: 0.8491 (pm20) cc_final: 0.8003 (pm20) REVERT: A 546 LEU cc_start: 0.9409 (mt) cc_final: 0.9172 (mt) REVERT: A 550 MET cc_start: 0.7316 (mtm) cc_final: 0.6387 (mtp) REVERT: A 598 MET cc_start: 0.8951 (mtm) cc_final: 0.8546 (mtt) REVERT: A 599 GLU cc_start: 0.7868 (mm-30) cc_final: 0.7218 (mm-30) REVERT: A 601 ILE cc_start: 0.8824 (tt) cc_final: 0.8561 (tt) REVERT: A 602 GLU cc_start: 0.8272 (pm20) cc_final: 0.6542 (mp0) REVERT: A 645 GLN cc_start: 0.8387 (tp40) cc_final: 0.8025 (tp-100) REVERT: A 650 GLN cc_start: 0.7740 (mt0) cc_final: 0.7128 (mt0) REVERT: A 655 THR cc_start: 0.7768 (m) cc_final: 0.7009 (m) REVERT: A 659 LYS cc_start: 0.8667 (mttt) cc_final: 0.8439 (mmmt) REVERT: B 8 LYS cc_start: 0.9446 (tttm) cc_final: 0.9194 (tppt) REVERT: B 12 LEU cc_start: 0.9583 (mt) cc_final: 0.9356 (mt) REVERT: B 95 MET cc_start: 0.9023 (tpp) cc_final: 0.7704 (tpp) REVERT: B 99 LYS cc_start: 0.9584 (mmmt) cc_final: 0.8837 (mmmt) REVERT: B 115 LEU cc_start: 0.8583 (mp) cc_final: 0.8300 (mp) REVERT: B 229 LEU cc_start: 0.7953 (mp) cc_final: 0.7706 (mt) REVERT: B 288 PHE cc_start: 0.9367 (t80) cc_final: 0.8926 (t80) REVERT: B 322 MET cc_start: 0.8530 (mmm) cc_final: 0.8216 (mmt) REVERT: B 326 PHE cc_start: 0.9322 (m-80) cc_final: 0.8608 (m-80) REVERT: B 350 ARG cc_start: 0.7884 (mtm-85) cc_final: 0.7656 (mtm110) REVERT: B 358 ILE cc_start: 0.8471 (mm) cc_final: 0.8223 (mm) REVERT: B 413 SER cc_start: 0.9230 (m) cc_final: 0.8453 (t) REVERT: B 417 LEU cc_start: 0.9368 (tt) cc_final: 0.8967 (tt) REVERT: B 425 ILE cc_start: 0.9068 (mt) cc_final: 0.8697 (mt) REVERT: B 458 MET cc_start: 0.9319 (mmm) cc_final: 0.8948 (mmm) REVERT: B 479 TYR cc_start: 0.8348 (t80) cc_final: 0.7921 (t80) REVERT: B 493 MET cc_start: 0.9216 (tmm) cc_final: 0.8977 (tmm) REVERT: B 494 MET cc_start: 0.9500 (mtp) cc_final: 0.9124 (mtp) REVERT: B 512 GLU cc_start: 0.8614 (pm20) cc_final: 0.8351 (pm20) REVERT: B 584 ILE cc_start: 0.8687 (tp) cc_final: 0.8232 (mt) REVERT: B 586 TYR cc_start: 0.9460 (m-80) cc_final: 0.9027 (m-80) REVERT: B 588 GLN cc_start: 0.9043 (mm-40) cc_final: 0.8840 (mm-40) REVERT: B 602 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8310 (pp20) REVERT: B 645 GLN cc_start: 0.8908 (tp40) cc_final: 0.8662 (tp-100) REVERT: C 38 ASN cc_start: 0.7125 (m-40) cc_final: 0.6186 (p0) REVERT: C 93 MET cc_start: 0.8825 (mtm) cc_final: 0.8557 (mmt) REVERT: C 95 MET cc_start: 0.8345 (tmm) cc_final: 0.7922 (tmm) REVERT: C 96 MET cc_start: 0.8590 (mmm) cc_final: 0.8061 (mmm) REVERT: C 141 LEU cc_start: 0.6823 (mp) cc_final: 0.6613 (pp) REVERT: C 227 PHE cc_start: 0.7916 (t80) cc_final: 0.7596 (t80) REVERT: D 55 TYR cc_start: 0.8237 (t80) cc_final: 0.8007 (t80) REVERT: D 119 ASN cc_start: 0.7723 (m110) cc_final: 0.7377 (m110) REVERT: D 154 PHE cc_start: 0.8147 (t80) cc_final: 0.7856 (t80) REVERT: D 169 TYR cc_start: 0.7641 (m-80) cc_final: 0.6807 (m-80) REVERT: D 174 TYR cc_start: 0.1991 (t80) cc_final: 0.1355 (t80) REVERT: D 178 PHE cc_start: 0.7910 (m-80) cc_final: 0.7624 (m-80) REVERT: D 201 HIS cc_start: 0.8322 (m90) cc_final: 0.7910 (m90) REVERT: D 263 ASN cc_start: 0.6964 (p0) cc_final: 0.6600 (p0) outliers start: 7 outliers final: 0 residues processed: 586 average time/residue: 0.2897 time to fit residues: 249.1851 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 : 1.867 ------------------------------------------------------------------------------- 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: 8.9990 chunk 175 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 191 optimal weight: 20.0000 chunk 57 optimal weight: 0.9990 chunk 52 optimal weight: 6.9990 chunk 171 optimal weight: 0.9980 chunk 189 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 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 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 132 GLN C 201 HIS D 71 ASN D 186 GLN D 265 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.129797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.089205 restraints weight = 48456.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.092287 restraints weight = 30478.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.094409 restraints weight = 22080.868| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3369 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3369 r_free = 0.3369 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3369 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16386 Z= 0.158 Angle : 0.573 7.134 22134 Z= 0.306 Chirality : 0.042 0.173 2360 Planarity : 0.003 0.040 2818 Dihedral : 11.340 172.513 2242 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.23 % Allowed : 2.86 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.32 (0.19), residues: 1932 helix: 1.38 (0.15), residues: 1141 sheet: -0.48 (0.39), residues: 160 loop : 0.53 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 558 HIS 0.007 0.001 HIS D 201 PHE 0.031 0.002 PHE D 166 TYR 0.022 0.002 TYR B 626 ARG 0.004 0.001 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 871) hydrogen bonds : angle 4.83284 ( 2571) covalent geometry : bond 0.00334 (16386) covalent geometry : angle 0.57311 (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 564 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 560 time to evaluate : 1.822 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: 0.8156 (mp0) cc_final: 0.7654 (mp0) REVERT: A 67 GLU cc_start: 0.9227 (tp30) cc_final: 0.8707 (tp30) REVERT: A 71 LEU cc_start: 0.9445 (mt) cc_final: 0.8937 (mt) REVERT: A 99 LYS cc_start: 0.9289 (mmtp) cc_final: 0.8794 (mttt) REVERT: A 108 THR cc_start: 0.9100 (OUTLIER) cc_final: 0.8530 (p) REVERT: A 117 ARG cc_start: 0.9047 (mmt90) cc_final: 0.8596 (mtp85) REVERT: A 119 GLU cc_start: 0.8604 (mp0) cc_final: 0.8368 (tm-30) REVERT: A 128 PHE cc_start: 0.9150 (t80) cc_final: 0.8727 (t80) REVERT: A 147 GLN cc_start: 0.9094 (mt0) cc_final: 0.8534 (mt0) REVERT: A 158 ASN cc_start: 0.8825 (m110) cc_final: 0.8593 (m110) REVERT: A 172 LEU cc_start: 0.8814 (mp) cc_final: 0.8305 (mp) REVERT: A 173 LEU cc_start: 0.9049 (mt) cc_final: 0.8804 (mt) REVERT: A 205 LYS cc_start: 0.7034 (mttp) cc_final: 0.6715 (mttt) REVERT: A 220 THR cc_start: 0.7803 (m) cc_final: 0.7285 (p) REVERT: A 260 ASP cc_start: 0.9203 (m-30) cc_final: 0.8897 (p0) REVERT: A 270 ASP cc_start: 0.8742 (m-30) cc_final: 0.8155 (t70) REVERT: A 322 MET cc_start: 0.8744 (mmm) cc_final: 0.7977 (tpp) REVERT: A 345 LYS cc_start: 0.9118 (mttp) cc_final: 0.8904 (mttm) REVERT: A 348 MET cc_start: 0.9119 (ptp) cc_final: 0.8775 (ptp) REVERT: A 349 LEU cc_start: 0.8471 (tp) cc_final: 0.8193 (tp) REVERT: A 373 ILE cc_start: 0.9537 (mt) cc_final: 0.9032 (mt) REVERT: A 375 LYS cc_start: 0.9122 (mmtm) cc_final: 0.8631 (mmtm) REVERT: A 385 VAL cc_start: 0.8733 (t) cc_final: 0.8337 (p) REVERT: A 402 GLU cc_start: 0.8795 (mp0) cc_final: 0.8555 (mp0) REVERT: A 407 ILE cc_start: 0.8898 (mt) cc_final: 0.8523 (mt) REVERT: A 427 LYS cc_start: 0.9398 (mmpt) cc_final: 0.9107 (mtmm) REVERT: A 446 ARG cc_start: 0.8579 (mmm-85) cc_final: 0.8343 (mmp80) REVERT: A 456 LYS cc_start: 0.8780 (mmtm) cc_final: 0.8301 (mmtm) REVERT: A 458 MET cc_start: 0.9146 (mmp) cc_final: 0.8857 (mmp) REVERT: A 466 MET cc_start: 0.9318 (ptt) cc_final: 0.8988 (ptp) REVERT: A 498 TYR cc_start: 0.8791 (m-80) cc_final: 0.8359 (m-80) REVERT: A 516 GLN cc_start: 0.9514 (mt0) cc_final: 0.9186 (tt0) REVERT: A 550 MET cc_start: 0.7719 (mtm) cc_final: 0.6750 (mtm) REVERT: A 598 MET cc_start: 0.8958 (mtm) cc_final: 0.8556 (mtm) REVERT: A 599 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7525 (mm-30) REVERT: A 602 GLU cc_start: 0.8987 (pm20) cc_final: 0.8189 (pm20) REVERT: A 611 THR cc_start: 0.8641 (t) cc_final: 0.8320 (t) REVERT: A 615 MET cc_start: 0.8239 (mmp) cc_final: 0.8034 (mmp) REVERT: A 645 GLN cc_start: 0.8397 (tp40) cc_final: 0.8042 (tp40) REVERT: A 650 GLN cc_start: 0.7724 (mt0) cc_final: 0.7511 (mt0) REVERT: A 659 LYS cc_start: 0.8692 (mttt) cc_final: 0.8358 (mmmt) REVERT: B 8 LYS cc_start: 0.9448 (tttm) cc_final: 0.9188 (tppt) REVERT: B 12 LEU cc_start: 0.9568 (mt) cc_final: 0.9332 (mt) REVERT: B 24 PHE cc_start: 0.8657 (m-80) cc_final: 0.8368 (m-80) REVERT: B 67 GLU cc_start: 0.8667 (mp0) cc_final: 0.8452 (mp0) REVERT: B 95 MET cc_start: 0.9030 (tpp) cc_final: 0.7524 (tpp) REVERT: B 98 PHE cc_start: 0.9592 (t80) cc_final: 0.8988 (t80) REVERT: B 99 LYS cc_start: 0.9630 (mmmt) cc_final: 0.8840 (mmmt) REVERT: B 115 LEU cc_start: 0.8638 (mp) cc_final: 0.8394 (mp) REVERT: B 162 LYS cc_start: 0.8936 (tppt) cc_final: 0.8602 (tppp) REVERT: B 228 LYS cc_start: 0.8031 (mmmm) cc_final: 0.7731 (tppt) REVERT: B 288 PHE cc_start: 0.9345 (t80) cc_final: 0.8907 (t80) REVERT: B 326 PHE cc_start: 0.9373 (m-80) cc_final: 0.8556 (m-80) REVERT: B 370 ASN cc_start: 0.9354 (m-40) cc_final: 0.8846 (t0) REVERT: B 379 SER cc_start: 0.8285 (t) cc_final: 0.8027 (t) REVERT: B 386 LEU cc_start: 0.8723 (mt) cc_final: 0.8395 (mt) REVERT: B 396 ASP cc_start: 0.8519 (m-30) cc_final: 0.8267 (m-30) REVERT: B 413 SER cc_start: 0.9236 (m) cc_final: 0.8540 (t) REVERT: B 441 GLU cc_start: 0.9415 (pt0) cc_final: 0.9097 (pt0) REVERT: B 444 ASP cc_start: 0.9112 (t0) cc_final: 0.8898 (t70) REVERT: B 458 MET cc_start: 0.9281 (mmm) cc_final: 0.9006 (mmm) REVERT: B 472 LEU cc_start: 0.9152 (mm) cc_final: 0.8819 (mm) REVERT: B 492 PHE cc_start: 0.9105 (m-80) cc_final: 0.8462 (m-80) REVERT: B 493 MET cc_start: 0.9239 (tmm) cc_final: 0.8911 (tmm) REVERT: B 494 MET cc_start: 0.9401 (mtp) cc_final: 0.8862 (mtp) REVERT: B 498 TYR cc_start: 0.8682 (m-80) cc_final: 0.8482 (m-80) REVERT: B 506 ILE cc_start: 0.9602 (mm) cc_final: 0.9247 (mm) REVERT: B 509 GLU cc_start: 0.8948 (pt0) cc_final: 0.8596 (pp20) REVERT: B 510 LYS cc_start: 0.9478 (mmtp) cc_final: 0.9084 (mmmm) REVERT: B 586 TYR cc_start: 0.9345 (m-80) cc_final: 0.9074 (m-80) REVERT: B 597 ILE cc_start: 0.9002 (pt) cc_final: 0.8715 (pt) REVERT: B 615 MET cc_start: 0.9060 (mmp) cc_final: 0.8749 (mmm) REVERT: B 645 GLN cc_start: 0.9100 (tp40) cc_final: 0.8825 (tp-100) REVERT: B 648 ILE cc_start: 0.9155 (mm) cc_final: 0.8927 (mm) REVERT: C 74 MET cc_start: 0.7487 (ttm) cc_final: 0.6920 (ptm) REVERT: C 95 MET cc_start: 0.8277 (tmm) cc_final: 0.7638 (tmm) REVERT: C 137 MET cc_start: 0.6803 (mpp) cc_final: 0.6086 (ptp) REVERT: C 141 LEU cc_start: 0.7103 (mp) cc_final: 0.6870 (pp) REVERT: C 151 ILE cc_start: 0.8322 (mm) cc_final: 0.7894 (tp) REVERT: C 227 PHE cc_start: 0.7900 (t80) cc_final: 0.7548 (t80) REVERT: C 259 PHE cc_start: 0.6382 (t80) cc_final: 0.5526 (t80) REVERT: C 276 TYR cc_start: 0.8123 (t80) cc_final: 0.7804 (t80) REVERT: D 40 ASP cc_start: 0.7216 (p0) cc_final: 0.6515 (p0) REVERT: D 169 TYR cc_start: 0.7974 (m-80) cc_final: 0.7074 (m-80) REVERT: D 178 PHE cc_start: 0.8194 (m-80) cc_final: 0.7739 (m-80) REVERT: D 249 GLN cc_start: 0.7231 (pt0) cc_final: 0.6690 (pm20) REVERT: D 263 ASN cc_start: 0.7059 (p0) cc_final: 0.6668 (p0) outliers start: 4 outliers final: 1 residues processed: 562 average time/residue: 0.2836 time to fit residues: 236.3827 Evaluate side-chains 481 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 479 time to evaluate : 1.728 ------------------------------------------------------------------------------- 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: 8.9990 chunk 99 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 39 optimal weight: 9.9990 chunk 50 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 148 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 94 optimal weight: 0.0060 overall best weight: 2.9602 ------------------------------------------------------------------------------- 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 191 GLN ** 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 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN B 44 ASN B 150 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 265 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.126810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.086225 restraints weight = 50239.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.089397 restraints weight = 31250.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.091431 restraints weight = 22461.951| |-----------------------------------------------------------------------------| 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) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.089 | | 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: 0.7131 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16386 Z= 0.199 Angle : 0.618 7.985 22134 Z= 0.329 Chirality : 0.043 0.151 2360 Planarity : 0.004 0.049 2818 Dihedral : 11.333 171.007 2242 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.12 % Allowed : 3.03 % Favored : 96.85 % 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: 1.18 (0.19), residues: 1932 helix: 1.25 (0.15), residues: 1138 sheet: -0.46 (0.41), residues: 154 loop : 0.48 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP B 558 HIS 0.017 0.002 HIS C 201 PHE 0.034 0.002 PHE B 81 TYR 0.018 0.002 TYR D 242 ARG 0.009 0.001 ARG B 485 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 871) hydrogen bonds : angle 4.96593 ( 2571) covalent geometry : bond 0.00424 (16386) covalent geometry : angle 0.61838 (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 528 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 526 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8146 (mp0) cc_final: 0.7743 (mp0) REVERT: A 67 GLU cc_start: 0.9302 (tp30) cc_final: 0.8825 (tp30) REVERT: A 71 LEU cc_start: 0.9423 (mt) cc_final: 0.9072 (mt) REVERT: A 81 PHE cc_start: 0.9268 (m-80) cc_final: 0.9042 (m-80) REVERT: A 99 LYS cc_start: 0.9368 (mmtp) cc_final: 0.8755 (mttt) REVERT: A 107 LYS cc_start: 0.8905 (mttm) cc_final: 0.8692 (mmmt) REVERT: A 117 ARG cc_start: 0.9168 (mmt90) cc_final: 0.8776 (mtp85) REVERT: A 119 GLU cc_start: 0.8714 (mp0) cc_final: 0.8411 (tm-30) REVERT: A 128 PHE cc_start: 0.9292 (t80) cc_final: 0.8815 (t80) REVERT: A 147 GLN cc_start: 0.9202 (mt0) cc_final: 0.8617 (mt0) REVERT: A 205 LYS cc_start: 0.7242 (mttp) cc_final: 0.6930 (mmtp) REVERT: A 214 LYS cc_start: 0.9308 (mmmt) cc_final: 0.8965 (mmtt) REVERT: A 220 THR cc_start: 0.8034 (m) cc_final: 0.7600 (p) REVERT: A 260 ASP cc_start: 0.9238 (m-30) cc_final: 0.8935 (p0) REVERT: A 345 LYS cc_start: 0.9176 (mttp) cc_final: 0.8883 (mttm) REVERT: A 375 LYS cc_start: 0.9106 (mmtm) cc_final: 0.8675 (mmtm) REVERT: A 385 VAL cc_start: 0.8638 (t) cc_final: 0.8376 (p) REVERT: A 386 LEU cc_start: 0.9342 (mt) cc_final: 0.9107 (mt) REVERT: A 402 GLU cc_start: 0.8872 (mp0) cc_final: 0.8615 (mp0) REVERT: A 407 ILE cc_start: 0.8979 (mt) cc_final: 0.8563 (mt) REVERT: A 425 ILE cc_start: 0.9417 (mt) cc_final: 0.9009 (mm) REVERT: A 456 LYS cc_start: 0.8800 (mmtm) cc_final: 0.8299 (mmtm) REVERT: A 466 MET cc_start: 0.9290 (ptt) cc_final: 0.9028 (ptp) REVERT: A 494 MET cc_start: 0.9527 (mmp) cc_final: 0.8888 (mmm) REVERT: A 498 TYR cc_start: 0.8935 (m-80) cc_final: 0.8569 (m-80) REVERT: A 515 ASP cc_start: 0.8697 (m-30) cc_final: 0.8492 (m-30) REVERT: A 546 LEU cc_start: 0.9420 (mt) cc_final: 0.9191 (mt) REVERT: A 550 MET cc_start: 0.7449 (mtm) cc_final: 0.6665 (mtm) REVERT: A 598 MET cc_start: 0.8901 (mtm) cc_final: 0.8495 (mtm) REVERT: A 599 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7365 (mm-30) REVERT: A 602 GLU cc_start: 0.9060 (pm20) cc_final: 0.8165 (pm20) REVERT: A 640 MET cc_start: 0.9278 (tpt) cc_final: 0.9038 (tpp) REVERT: A 650 GLN cc_start: 0.8048 (mt0) cc_final: 0.7580 (mt0) REVERT: A 659 LYS cc_start: 0.8669 (mttt) cc_final: 0.8328 (mmmt) REVERT: A 662 MET cc_start: 0.8726 (ptp) cc_final: 0.8524 (ptp) REVERT: B 8 LYS cc_start: 0.9492 (tttm) cc_final: 0.9216 (tppt) REVERT: B 12 LEU cc_start: 0.9585 (mt) cc_final: 0.9340 (mt) REVERT: B 17 MET cc_start: 0.9169 (mmm) cc_final: 0.8619 (mmp) REVERT: B 95 MET cc_start: 0.9114 (tpp) cc_final: 0.7761 (tpp) REVERT: B 98 PHE cc_start: 0.9606 (t80) cc_final: 0.8860 (t80) REVERT: B 99 LYS cc_start: 0.9649 (mmmt) cc_final: 0.8875 (mmmt) REVERT: B 184 ARG cc_start: 0.8634 (tpp-160) cc_final: 0.7528 (mmm-85) REVERT: B 288 PHE cc_start: 0.9438 (t80) cc_final: 0.9069 (t80) REVERT: B 319 MET cc_start: 0.8867 (tpp) cc_final: 0.8653 (tpp) REVERT: B 326 PHE cc_start: 0.9369 (m-80) cc_final: 0.8640 (m-80) REVERT: B 392 SER cc_start: 0.9107 (m) cc_final: 0.8893 (t) REVERT: B 413 SER cc_start: 0.9169 (m) cc_final: 0.8635 (t) REVERT: B 417 LEU cc_start: 0.9286 (tt) cc_final: 0.8844 (tt) REVERT: B 444 ASP cc_start: 0.9064 (t0) cc_final: 0.8738 (t70) REVERT: B 446 ARG cc_start: 0.8919 (mpp80) cc_final: 0.8574 (mpp80) REVERT: B 458 MET cc_start: 0.9332 (mmm) cc_final: 0.9081 (mmm) REVERT: B 459 LYS cc_start: 0.8673 (mttt) cc_final: 0.8388 (mtmt) REVERT: B 466 MET cc_start: 0.8715 (ptp) cc_final: 0.8484 (ptp) REVERT: B 472 LEU cc_start: 0.9256 (mm) cc_final: 0.9011 (mm) REVERT: B 492 PHE cc_start: 0.9223 (m-80) cc_final: 0.8624 (m-80) REVERT: B 493 MET cc_start: 0.9316 (tmm) cc_final: 0.8901 (tmm) REVERT: B 494 MET cc_start: 0.9462 (mtp) cc_final: 0.8791 (mtp) REVERT: B 506 ILE cc_start: 0.9619 (mm) cc_final: 0.9240 (mm) REVERT: B 509 GLU cc_start: 0.9029 (pt0) cc_final: 0.8759 (pp20) REVERT: B 510 LYS cc_start: 0.9528 (mmtp) cc_final: 0.9280 (mmmm) REVERT: B 570 MET cc_start: 0.8552 (mtp) cc_final: 0.8008 (mmt) REVERT: B 586 TYR cc_start: 0.9495 (m-80) cc_final: 0.9008 (m-80) REVERT: B 597 ILE cc_start: 0.8926 (pt) cc_final: 0.8631 (pt) REVERT: B 615 MET cc_start: 0.8968 (mmp) cc_final: 0.8668 (mmm) REVERT: B 645 GLN cc_start: 0.9163 (tp40) cc_final: 0.8906 (tp-100) REVERT: C 74 MET cc_start: 0.7459 (ttm) cc_final: 0.6738 (ptm) REVERT: C 95 MET cc_start: 0.8214 (tmm) cc_final: 0.7734 (tmm) REVERT: C 96 MET cc_start: 0.8434 (mmm) cc_final: 0.8000 (mmm) REVERT: C 137 MET cc_start: 0.7127 (mpp) cc_final: 0.6665 (ptp) REVERT: C 149 ASP cc_start: 0.7982 (t0) cc_final: 0.7744 (t0) REVERT: C 151 ILE cc_start: 0.8246 (mm) cc_final: 0.7914 (tp) REVERT: C 227 PHE cc_start: 0.7803 (t80) cc_final: 0.7579 (t80) REVERT: C 259 PHE cc_start: 0.6428 (t80) cc_final: 0.5576 (t80) REVERT: C 276 TYR cc_start: 0.8241 (t80) cc_final: 0.7958 (t80) REVERT: D 169 TYR cc_start: 0.8001 (m-80) cc_final: 0.7066 (m-80) REVERT: D 178 PHE cc_start: 0.8239 (m-80) cc_final: 0.8019 (m-80) REVERT: D 263 ASN cc_start: 0.7044 (p0) cc_final: 0.6649 (p0) outliers start: 2 outliers final: 0 residues processed: 526 average time/residue: 0.2792 time to fit residues: 217.2596 Evaluate side-chains 454 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 454 time to evaluate : 1.928 ------------------------------------------------------------------------------- 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: 0.5980 chunk 57 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 175 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 86 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- 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 313 HIS ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN B 218 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 608 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.129628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.088424 restraints weight = 49473.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.091681 restraints weight = 30648.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.093921 restraints weight = 21329.394| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 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 = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16386 Z= 0.138 Angle : 0.595 8.764 22134 Z= 0.312 Chirality : 0.042 0.241 2360 Planarity : 0.003 0.039 2818 Dihedral : 10.930 169.439 2242 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 12.33 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: 1.21 (0.19), residues: 1932 helix: 1.29 (0.15), residues: 1125 sheet: -0.61 (0.40), residues: 150 loop : 0.52 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 558 HIS 0.015 0.001 HIS C 201 PHE 0.020 0.002 PHE A 492 TYR 0.016 0.001 TYR B 527 ARG 0.010 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 871) hydrogen bonds : angle 4.93543 ( 2571) covalent geometry : bond 0.00303 (16386) covalent geometry : angle 0.59460 (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 541 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 540 time to evaluate : 1.770 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: 0.9231 (tp30) cc_final: 0.8683 (tp30) REVERT: A 71 LEU cc_start: 0.9448 (mt) cc_final: 0.8985 (mt) REVERT: A 81 PHE cc_start: 0.9295 (m-80) cc_final: 0.9031 (m-80) REVERT: A 99 LYS cc_start: 0.9337 (mmtp) cc_final: 0.8893 (mttt) REVERT: A 117 ARG cc_start: 0.9170 (mmt90) cc_final: 0.8771 (mtp85) REVERT: A 119 GLU cc_start: 0.8623 (mp0) cc_final: 0.8319 (tm-30) REVERT: A 147 GLN cc_start: 0.9107 (mt0) cc_final: 0.8606 (mt0) REVERT: A 181 ASP cc_start: 0.8238 (m-30) cc_final: 0.7877 (m-30) REVERT: A 214 LYS cc_start: 0.9286 (mmmt) cc_final: 0.8959 (mmtt) REVERT: A 220 THR cc_start: 0.8037 (m) cc_final: 0.7565 (p) REVERT: A 260 ASP cc_start: 0.9271 (m-30) cc_final: 0.9066 (p0) REVERT: A 312 GLN cc_start: 0.8593 (tp-100) cc_final: 0.7967 (tp-100) REVERT: A 359 MET cc_start: 0.7992 (ttt) cc_final: 0.7758 (ttt) REVERT: A 361 GLN cc_start: 0.8955 (tp40) cc_final: 0.8553 (tp40) REVERT: A 373 ILE cc_start: 0.9575 (mt) cc_final: 0.9089 (mt) REVERT: A 375 LYS cc_start: 0.9071 (mmtm) cc_final: 0.8657 (mmtm) REVERT: A 385 VAL cc_start: 0.8774 (t) cc_final: 0.8448 (p) REVERT: A 402 GLU cc_start: 0.8844 (mp0) cc_final: 0.8541 (mp0) REVERT: A 407 ILE cc_start: 0.8983 (mt) cc_final: 0.8589 (mt) REVERT: A 444 ASP cc_start: 0.7707 (t0) cc_final: 0.6349 (t0) REVERT: A 456 LYS cc_start: 0.8818 (mmtm) cc_final: 0.8308 (mmtm) REVERT: A 458 MET cc_start: 0.9040 (mmp) cc_final: 0.8735 (mmp) REVERT: A 466 MET cc_start: 0.9311 (ptt) cc_final: 0.9085 (ptp) REVERT: A 494 MET cc_start: 0.9491 (mmp) cc_final: 0.9195 (mmm) REVERT: A 498 TYR cc_start: 0.8877 (m-80) cc_final: 0.8517 (m-80) REVERT: A 501 GLN cc_start: 0.9306 (tp-100) cc_final: 0.8844 (tp-100) REVERT: A 516 GLN cc_start: 0.9545 (mt0) cc_final: 0.9225 (tt0) REVERT: A 550 MET cc_start: 0.7594 (mtm) cc_final: 0.6530 (mtm) REVERT: A 598 MET cc_start: 0.8842 (mtm) cc_final: 0.8496 (ttm) REVERT: A 611 THR cc_start: 0.8649 (t) cc_final: 0.8439 (t) REVERT: A 615 MET cc_start: 0.8242 (mmp) cc_final: 0.7480 (mmm) REVERT: A 640 MET cc_start: 0.9361 (tpt) cc_final: 0.9070 (tpp) REVERT: A 645 GLN cc_start: 0.8524 (tp40) cc_final: 0.8183 (tp-100) REVERT: A 650 GLN cc_start: 0.7840 (mt0) cc_final: 0.7304 (mt0) REVERT: A 658 LEU cc_start: 0.9325 (mt) cc_final: 0.9101 (mt) REVERT: A 659 LYS cc_start: 0.8843 (mttt) cc_final: 0.8499 (mmmt) REVERT: B 8 LYS cc_start: 0.9494 (tttm) cc_final: 0.9203 (tppt) REVERT: B 12 LEU cc_start: 0.9597 (mt) cc_final: 0.9348 (mt) REVERT: B 17 MET cc_start: 0.8944 (mmm) cc_final: 0.8386 (mmt) REVERT: B 24 PHE cc_start: 0.8732 (m-80) cc_final: 0.7885 (m-80) REVERT: B 41 ILE cc_start: 0.9565 (mm) cc_final: 0.9359 (mm) REVERT: B 95 MET cc_start: 0.9106 (tpp) cc_final: 0.7681 (tpp) REVERT: B 98 PHE cc_start: 0.9596 (t80) cc_final: 0.8989 (t80) REVERT: B 99 LYS cc_start: 0.9662 (mmmt) cc_final: 0.8897 (mmmt) REVERT: B 122 ILE cc_start: 0.9235 (mt) cc_final: 0.8980 (mt) REVERT: B 124 ILE cc_start: 0.9209 (tp) cc_final: 0.8823 (tp) REVERT: B 235 ARG cc_start: 0.7871 (mtp85) cc_final: 0.7476 (mmt90) REVERT: B 288 PHE cc_start: 0.9407 (t80) cc_final: 0.9085 (t80) REVERT: B 319 MET cc_start: 0.8872 (tpp) cc_final: 0.8640 (tpp) REVERT: B 326 PHE cc_start: 0.9214 (m-10) cc_final: 0.8655 (m-80) REVERT: B 370 ASN cc_start: 0.9377 (m-40) cc_final: 0.8751 (t0) REVERT: B 373 ILE cc_start: 0.9523 (mt) cc_final: 0.9176 (mt) REVERT: B 413 SER cc_start: 0.9160 (m) cc_final: 0.8323 (t) REVERT: B 414 LEU cc_start: 0.9162 (mt) cc_final: 0.8949 (mt) REVERT: B 444 ASP cc_start: 0.9058 (t0) cc_final: 0.8759 (t0) REVERT: B 446 ARG cc_start: 0.8890 (mpp80) cc_final: 0.8624 (mpp80) REVERT: B 459 LYS cc_start: 0.8674 (mttt) cc_final: 0.8350 (mtmt) REVERT: B 466 MET cc_start: 0.8706 (ptp) cc_final: 0.8304 (ptp) REVERT: B 472 LEU cc_start: 0.9290 (mm) cc_final: 0.8992 (mm) REVERT: B 492 PHE cc_start: 0.9262 (m-80) cc_final: 0.8564 (m-80) REVERT: B 493 MET cc_start: 0.9284 (tmm) cc_final: 0.8573 (tmm) REVERT: B 494 MET cc_start: 0.9344 (mtp) cc_final: 0.8960 (mtp) REVERT: B 506 ILE cc_start: 0.9614 (mm) cc_final: 0.9213 (mm) REVERT: B 509 GLU cc_start: 0.9104 (pt0) cc_final: 0.8805 (pp20) REVERT: B 510 LYS cc_start: 0.9550 (mmtp) cc_final: 0.9342 (mmmm) REVERT: B 558 TRP cc_start: 0.8349 (m100) cc_final: 0.7676 (m100) REVERT: B 586 TYR cc_start: 0.9480 (m-80) cc_final: 0.8993 (m-80) REVERT: B 597 ILE cc_start: 0.8873 (pt) cc_final: 0.8629 (pt) REVERT: B 645 GLN cc_start: 0.9107 (tp40) cc_final: 0.8727 (tp-100) REVERT: C 74 MET cc_start: 0.7434 (ttm) cc_final: 0.6857 (ptm) REVERT: C 95 MET cc_start: 0.8122 (tmm) cc_final: 0.7660 (tmm) REVERT: C 96 MET cc_start: 0.8483 (mmm) cc_final: 0.8045 (mmm) REVERT: C 137 MET cc_start: 0.7302 (mpp) cc_final: 0.6799 (ptp) REVERT: C 149 ASP cc_start: 0.7985 (t0) cc_final: 0.7736 (t0) REVERT: C 151 ILE cc_start: 0.8296 (mm) cc_final: 0.8035 (mm) REVERT: C 259 PHE cc_start: 0.6334 (t80) cc_final: 0.5512 (t80) REVERT: C 276 TYR cc_start: 0.8263 (t80) cc_final: 0.7998 (t80) REVERT: D 169 TYR cc_start: 0.8266 (m-80) cc_final: 0.7488 (m-80) REVERT: D 178 PHE cc_start: 0.8178 (m-80) cc_final: 0.7948 (m-80) REVERT: D 263 ASN cc_start: 0.7043 (p0) cc_final: 0.6616 (p0) outliers start: 1 outliers final: 1 residues processed: 541 average time/residue: 0.2746 time to fit residues: 220.9099 Evaluate side-chains 447 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 446 time to evaluate : 1.756 ------------------------------------------------------------------------------- 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: 3.9990 chunk 126 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 69 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 115 optimal weight: 10.0000 chunk 39 optimal weight: 3.9990 chunk 169 optimal weight: 20.0000 chunk 113 optimal weight: 8.9990 chunk 177 optimal weight: 1.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 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** B 608 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 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 = 0.3775 r_free = 0.3775 target = 0.120625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.082032 restraints weight = 52054.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.084897 restraints weight = 33007.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.086610 restraints weight = 23382.086| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3199 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3199 r_free = 0.3199 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 = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.6259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16386 Z= 0.277 Angle : 0.703 8.294 22134 Z= 0.373 Chirality : 0.045 0.180 2360 Planarity : 0.004 0.049 2818 Dihedral : 11.320 168.894 2242 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % 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: 0.78 (0.19), residues: 1932 helix: 0.95 (0.15), residues: 1124 sheet: -0.75 (0.40), residues: 148 loop : 0.30 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 623 HIS 0.012 0.002 HIS C 201 PHE 0.023 0.002 PHE B 100 TYR 0.031 0.002 TYR B 574 ARG 0.010 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04335 ( 871) hydrogen bonds : angle 5.12906 ( 2571) covalent geometry : bond 0.00583 (16386) covalent geometry : angle 0.70257 (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 504 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 502 time to evaluate : 1.939 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: 0.9335 (tp30) cc_final: 0.9049 (tp30) REVERT: A 89 PHE cc_start: 0.8982 (t80) cc_final: 0.8695 (t80) REVERT: A 99 LYS cc_start: 0.9403 (mmtp) cc_final: 0.9164 (mmtt) REVERT: A 117 ARG cc_start: 0.9133 (mmt90) cc_final: 0.8784 (mmt180) REVERT: A 147 GLN cc_start: 0.9201 (mt0) cc_final: 0.8707 (mt0) REVERT: A 164 ARG cc_start: 0.7940 (ptm-80) cc_final: 0.7509 (ptm-80) REVERT: A 214 LYS cc_start: 0.9346 (mmmt) cc_final: 0.9037 (mmtt) REVERT: A 220 THR cc_start: 0.8306 (m) cc_final: 0.7951 (p) REVERT: A 260 ASP cc_start: 0.9264 (m-30) cc_final: 0.9024 (p0) REVERT: A 270 ASP cc_start: 0.8685 (m-30) cc_final: 0.8046 (t0) REVERT: A 314 MET cc_start: 0.8517 (ppp) cc_final: 0.8203 (ppp) REVERT: A 322 MET cc_start: 0.8365 (mmm) cc_final: 0.8135 (mmm) REVERT: A 345 LYS cc_start: 0.9225 (mttp) cc_final: 0.8936 (mttt) REVERT: A 375 LYS cc_start: 0.9049 (mmtm) cc_final: 0.8602 (mmtm) REVERT: A 402 GLU cc_start: 0.8878 (mp0) cc_final: 0.8640 (mp0) REVERT: A 407 ILE cc_start: 0.9046 (mt) cc_final: 0.8687 (mt) REVERT: A 425 ILE cc_start: 0.9355 (mm) cc_final: 0.8718 (mm) REVERT: A 456 LYS cc_start: 0.8791 (mmtm) cc_final: 0.8306 (mmtm) REVERT: A 494 MET cc_start: 0.9506 (mmp) cc_final: 0.9072 (mmm) REVERT: A 498 TYR cc_start: 0.9187 (m-80) cc_final: 0.8841 (m-80) REVERT: A 501 GLN cc_start: 0.9084 (tp-100) cc_final: 0.8761 (tp-100) REVERT: A 550 MET cc_start: 0.7617 (mtm) cc_final: 0.6838 (mtm) REVERT: A 615 MET cc_start: 0.8450 (mmp) cc_final: 0.7600 (mmp) REVERT: A 640 MET cc_start: 0.9381 (tpt) cc_final: 0.8979 (tpp) REVERT: A 650 GLN cc_start: 0.7869 (mt0) cc_final: 0.7644 (mt0) REVERT: A 659 LYS cc_start: 0.8738 (mttt) cc_final: 0.8477 (mmmt) REVERT: A 662 MET cc_start: 0.8628 (ptp) cc_final: 0.8389 (ptp) REVERT: B 8 LYS cc_start: 0.9477 (tttm) cc_final: 0.9176 (tppt) REVERT: B 12 LEU cc_start: 0.9583 (mt) cc_final: 0.9340 (mt) REVERT: B 17 MET cc_start: 0.8857 (mmm) cc_final: 0.8628 (mmm) REVERT: B 95 MET cc_start: 0.9280 (tpp) cc_final: 0.7504 (tpp) REVERT: B 98 PHE cc_start: 0.9615 (t80) cc_final: 0.8027 (t80) REVERT: B 99 LYS cc_start: 0.9684 (mmmt) cc_final: 0.8805 (mmmt) REVERT: B 115 LEU cc_start: 0.8738 (mp) cc_final: 0.8333 (mp) REVERT: B 202 ASN cc_start: 0.5424 (p0) cc_final: 0.5152 (p0) REVERT: B 307 TYR cc_start: 0.9246 (t80) cc_final: 0.8826 (t80) REVERT: B 319 MET cc_start: 0.8983 (tpp) cc_final: 0.8682 (tpp) REVERT: B 326 PHE cc_start: 0.9226 (m-10) cc_final: 0.8504 (m-80) REVERT: B 379 SER cc_start: 0.8297 (t) cc_final: 0.8031 (t) REVERT: B 444 ASP cc_start: 0.9131 (t0) cc_final: 0.8901 (t70) REVERT: B 459 LYS cc_start: 0.8852 (mttt) cc_final: 0.8357 (mtpt) REVERT: B 472 LEU cc_start: 0.9259 (mm) cc_final: 0.8986 (mm) REVERT: B 493 MET cc_start: 0.9250 (tmm) cc_final: 0.8972 (tmm) REVERT: B 494 MET cc_start: 0.9415 (mtp) cc_final: 0.8812 (mtp) REVERT: B 506 ILE cc_start: 0.9637 (mm) cc_final: 0.9377 (mm) REVERT: B 586 TYR cc_start: 0.9505 (m-80) cc_final: 0.9055 (m-80) REVERT: B 613 TYR cc_start: 0.8425 (t80) cc_final: 0.8089 (t80) REVERT: B 615 MET cc_start: 0.8772 (mmp) cc_final: 0.8393 (mmm) REVERT: B 645 GLN cc_start: 0.9022 (tp40) cc_final: 0.8720 (tp-100) REVERT: C 95 MET cc_start: 0.8442 (tmm) cc_final: 0.8104 (tmm) REVERT: C 96 MET cc_start: 0.8526 (mmm) cc_final: 0.8146 (mmm) REVERT: C 98 ASN cc_start: 0.7116 (m110) cc_final: 0.6738 (m110) REVERT: C 137 MET cc_start: 0.7683 (mpp) cc_final: 0.7162 (ptp) REVERT: C 149 ASP cc_start: 0.8028 (t0) cc_final: 0.7694 (t0) REVERT: C 151 ILE cc_start: 0.8270 (mm) cc_final: 0.7864 (tp) REVERT: C 227 PHE cc_start: 0.8593 (t80) cc_final: 0.8324 (t80) REVERT: C 259 PHE cc_start: 0.6664 (t80) cc_final: 0.5840 (t80) REVERT: C 276 TYR cc_start: 0.8251 (t80) cc_final: 0.7786 (t80) REVERT: D 74 MET cc_start: 0.7863 (ttp) cc_final: 0.7340 (ppp) REVERT: D 169 TYR cc_start: 0.8041 (m-80) cc_final: 0.7165 (m-80) outliers start: 2 outliers final: 2 residues processed: 504 average time/residue: 0.2699 time to fit residues: 203.3908 Evaluate side-chains 424 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 422 time to evaluate : 1.785 ------------------------------------------------------------------------------- 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: 7.9990 chunk 85 optimal weight: 1.9990 chunk 161 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 40 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 chunk 184 optimal weight: 5.9990 chunk 119 optimal weight: 0.6980 chunk 175 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 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 180 ASN A 361 GLN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.123928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.083027 restraints weight = 51219.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.086298 restraints weight = 31814.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.088389 restraints weight = 22189.990| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 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 = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.6477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 16386 Z= 0.187 Angle : 0.643 8.301 22134 Z= 0.342 Chirality : 0.043 0.174 2360 Planarity : 0.004 0.049 2818 Dihedral : 11.013 158.964 2242 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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: 0.71 (0.19), residues: 1932 helix: 0.95 (0.15), residues: 1121 sheet: -0.97 (0.37), residues: 164 loop : 0.26 (0.25), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 9 HIS 0.010 0.001 HIS C 201 PHE 0.033 0.002 PHE D 178 TYR 0.029 0.002 TYR D 174 ARG 0.011 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04114 ( 871) hydrogen bonds : angle 5.14238 ( 2571) covalent geometry : bond 0.00404 (16386) covalent geometry : angle 0.64254 (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 506 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 505 time to evaluate : 1.849 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: 0.9313 (tp30) cc_final: 0.9006 (tp30) REVERT: A 89 PHE cc_start: 0.8812 (t80) cc_final: 0.8469 (t80) REVERT: A 117 ARG cc_start: 0.9158 (mmt90) cc_final: 0.8805 (mmt180) REVERT: A 147 GLN cc_start: 0.9130 (mt0) cc_final: 0.8627 (mt0) REVERT: A 158 ASN cc_start: 0.8936 (m110) cc_final: 0.8610 (m110) REVERT: A 214 LYS cc_start: 0.9298 (mmmt) cc_final: 0.8981 (mmtt) REVERT: A 220 THR cc_start: 0.8187 (m) cc_final: 0.7743 (p) REVERT: A 236 TYR cc_start: 0.7622 (t80) cc_final: 0.7385 (t80) REVERT: A 259 ASN cc_start: 0.8677 (p0) cc_final: 0.7992 (p0) REVERT: A 263 ASP cc_start: 0.9007 (t0) cc_final: 0.8484 (m-30) REVERT: A 270 ASP cc_start: 0.8709 (m-30) cc_final: 0.7925 (t0) REVERT: A 314 MET cc_start: 0.8443 (ppp) cc_final: 0.8210 (ppp) REVERT: A 345 LYS cc_start: 0.9144 (mttp) cc_final: 0.8839 (mttm) REVERT: A 375 LYS cc_start: 0.9061 (mmtm) cc_final: 0.8608 (mmtm) REVERT: A 385 VAL cc_start: 0.8739 (t) cc_final: 0.8512 (p) REVERT: A 402 GLU cc_start: 0.8865 (mp0) cc_final: 0.8599 (mp0) REVERT: A 407 ILE cc_start: 0.8949 (mt) cc_final: 0.8469 (mt) REVERT: A 425 ILE cc_start: 0.9353 (mm) cc_final: 0.8900 (mm) REVERT: A 456 LYS cc_start: 0.8712 (mmtm) cc_final: 0.8339 (mmtm) REVERT: A 490 THR cc_start: 0.9440 (m) cc_final: 0.8427 (p) REVERT: A 493 MET cc_start: 0.8948 (tmm) cc_final: 0.8715 (tmm) REVERT: A 494 MET cc_start: 0.9496 (mmp) cc_final: 0.8851 (mmm) REVERT: A 498 TYR cc_start: 0.9128 (m-80) cc_final: 0.8778 (m-80) REVERT: A 501 GLN cc_start: 0.9223 (tp-100) cc_final: 0.8834 (tp-100) REVERT: A 550 MET cc_start: 0.7646 (mtm) cc_final: 0.6977 (mtm) REVERT: A 615 MET cc_start: 0.8581 (mmp) cc_final: 0.7776 (mmp) REVERT: A 640 MET cc_start: 0.9363 (tpt) cc_final: 0.8987 (tpp) REVERT: A 650 GLN cc_start: 0.7846 (mt0) cc_final: 0.7432 (mt0) REVERT: B 8 LYS cc_start: 0.9477 (tttm) cc_final: 0.9145 (tppt) REVERT: B 12 LEU cc_start: 0.9567 (mt) cc_final: 0.9307 (mt) REVERT: B 24 PHE cc_start: 0.8933 (m-80) cc_final: 0.8364 (m-80) REVERT: B 95 MET cc_start: 0.9146 (tpp) cc_final: 0.7323 (tpp) REVERT: B 98 PHE cc_start: 0.9609 (t80) cc_final: 0.8312 (t80) REVERT: B 99 LYS cc_start: 0.9662 (mmmt) cc_final: 0.8779 (mmmt) REVERT: B 115 LEU cc_start: 0.8542 (mp) cc_final: 0.8279 (mp) REVERT: B 202 ASN cc_start: 0.5447 (p0) cc_final: 0.5228 (p0) REVERT: B 215 ASP cc_start: 0.8702 (m-30) cc_final: 0.8486 (m-30) REVERT: B 288 PHE cc_start: 0.9416 (t80) cc_final: 0.9185 (t80) REVERT: B 307 TYR cc_start: 0.9198 (t80) cc_final: 0.8755 (t80) REVERT: B 319 MET cc_start: 0.9007 (tpp) cc_final: 0.8711 (tpp) REVERT: B 326 PHE cc_start: 0.9236 (m-10) cc_final: 0.8675 (m-80) REVERT: B 379 SER cc_start: 0.8205 (t) cc_final: 0.7969 (t) REVERT: B 444 ASP cc_start: 0.9109 (t0) cc_final: 0.8854 (t0) REVERT: B 445 ILE cc_start: 0.8563 (mm) cc_final: 0.8348 (mm) REVERT: B 458 MET cc_start: 0.9501 (mmm) cc_final: 0.8922 (mmm) REVERT: B 459 LYS cc_start: 0.8885 (mttt) cc_final: 0.8489 (mtmt) REVERT: B 472 LEU cc_start: 0.9264 (mm) cc_final: 0.8975 (mm) REVERT: B 493 MET cc_start: 0.9229 (tmm) cc_final: 0.9018 (tmm) REVERT: B 494 MET cc_start: 0.9322 (mtp) cc_final: 0.8918 (mtp) REVERT: B 615 MET cc_start: 0.8778 (mmp) cc_final: 0.8404 (mmm) REVERT: B 645 GLN cc_start: 0.8883 (tp40) cc_final: 0.8588 (tp-100) REVERT: B 648 ILE cc_start: 0.9091 (mm) cc_final: 0.8861 (mm) REVERT: C 74 MET cc_start: 0.6702 (ttp) cc_final: 0.6455 (ptm) REVERT: C 95 MET cc_start: 0.8325 (tmm) cc_final: 0.7613 (tmm) REVERT: C 96 MET cc_start: 0.8544 (mmm) cc_final: 0.8082 (mmm) REVERT: C 149 ASP cc_start: 0.8011 (t0) cc_final: 0.7669 (t0) REVERT: C 151 ILE cc_start: 0.8290 (mm) cc_final: 0.7899 (tp) REVERT: C 227 PHE cc_start: 0.8615 (t80) cc_final: 0.8330 (t80) REVERT: C 276 TYR cc_start: 0.8354 (t80) cc_final: 0.8070 (t80) REVERT: D 74 MET cc_start: 0.8008 (ttp) cc_final: 0.7446 (tmm) REVERT: D 96 MET cc_start: 0.5769 (mmm) cc_final: 0.5544 (mmm) REVERT: D 157 MET cc_start: 0.7024 (tmm) cc_final: 0.6705 (tmm) REVERT: D 169 TYR cc_start: 0.8219 (m-80) cc_final: 0.7380 (m-80) REVERT: D 263 ASN cc_start: 0.6881 (p0) cc_final: 0.6471 (p0) outliers start: 1 outliers final: 0 residues processed: 506 average time/residue: 0.2949 time to fit residues: 223.0825 Evaluate side-chains 421 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 421 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.9990 chunk 30 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 159 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 183 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 180 optimal weight: 9.9990 chunk 108 optimal weight: 7.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 239 GLN A 365 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 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 = 0.3861 r_free = 0.3861 target = 0.126409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.087165 restraints weight = 49235.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.090357 restraints weight = 30801.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.092526 restraints weight = 21071.945| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3320 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3320 r_free = 0.3320 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 = 0.3320 r_free = 0.3320 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3320 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.6627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16386 Z= 0.128 Angle : 0.610 8.216 22134 Z= 0.322 Chirality : 0.042 0.165 2360 Planarity : 0.004 0.048 2818 Dihedral : 10.559 153.350 2242 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.81 (0.19), residues: 1932 helix: 1.02 (0.15), residues: 1135 sheet: -0.72 (0.38), residues: 160 loop : 0.24 (0.25), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 44 HIS 0.007 0.001 HIS C 201 PHE 0.028 0.002 PHE D 178 TYR 0.024 0.001 TYR D 174 ARG 0.012 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03905 ( 871) hydrogen bonds : angle 5.02773 ( 2571) covalent geometry : bond 0.00282 (16386) covalent geometry : angle 0.60965 (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 518 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 518 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8151 (mp0) cc_final: 0.7762 (mp0) REVERT: A 67 GLU cc_start: 0.9252 (tp30) cc_final: 0.8905 (tp30) REVERT: A 71 LEU cc_start: 0.9453 (mt) cc_final: 0.9154 (mt) REVERT: A 99 LYS cc_start: 0.9434 (mmtp) cc_final: 0.8771 (mttp) REVERT: A 117 ARG cc_start: 0.9167 (mmt90) cc_final: 0.8835 (mtp85) REVERT: A 147 GLN cc_start: 0.9042 (mt0) cc_final: 0.8546 (mt0) REVERT: A 163 ARG cc_start: 0.8685 (mmm-85) cc_final: 0.8358 (mmm-85) REVERT: A 202 ASN cc_start: 0.8488 (t0) cc_final: 0.8085 (t0) REVERT: A 214 LYS cc_start: 0.9271 (mmmt) cc_final: 0.8946 (mmtt) REVERT: A 220 THR cc_start: 0.8101 (m) cc_final: 0.7667 (p) REVERT: A 236 TYR cc_start: 0.7492 (t80) cc_final: 0.7267 (t80) REVERT: A 259 ASN cc_start: 0.8603 (p0) cc_final: 0.7772 (p0) REVERT: A 263 ASP cc_start: 0.8985 (t0) cc_final: 0.8496 (m-30) REVERT: A 270 ASP cc_start: 0.8645 (m-30) cc_final: 0.8012 (t0) REVERT: A 314 MET cc_start: 0.8441 (ppp) cc_final: 0.8194 (ppp) REVERT: A 345 LYS cc_start: 0.9258 (mttp) cc_final: 0.9027 (mttt) REVERT: A 375 LYS cc_start: 0.9048 (mmtm) cc_final: 0.8632 (mmtm) REVERT: A 390 GLN cc_start: 0.8151 (tm-30) cc_final: 0.7931 (tm-30) REVERT: A 402 GLU cc_start: 0.8847 (mp0) cc_final: 0.8567 (mp0) REVERT: A 407 ILE cc_start: 0.8860 (mt) cc_final: 0.8475 (mt) REVERT: A 425 ILE cc_start: 0.9294 (mm) cc_final: 0.8907 (mm) REVERT: A 427 LYS cc_start: 0.9226 (mmmt) cc_final: 0.8832 (mtmt) REVERT: A 456 LYS cc_start: 0.8857 (mmtm) cc_final: 0.8355 (mmtm) REVERT: A 458 MET cc_start: 0.8901 (mmp) cc_final: 0.8584 (mmp) REVERT: A 466 MET cc_start: 0.8187 (ptp) cc_final: 0.7481 (pmm) REVERT: A 490 THR cc_start: 0.9455 (m) cc_final: 0.8459 (p) REVERT: A 494 MET cc_start: 0.9495 (mmp) cc_final: 0.8790 (mmm) REVERT: A 498 TYR cc_start: 0.9163 (m-80) cc_final: 0.8811 (m-80) REVERT: A 501 GLN cc_start: 0.9227 (tp-100) cc_final: 0.8889 (tp-100) REVERT: A 550 MET cc_start: 0.7556 (mtm) cc_final: 0.7267 (mtm) REVERT: A 598 MET cc_start: 0.8620 (mtm) cc_final: 0.8041 (ttm) REVERT: A 602 GLU cc_start: 0.8907 (pm20) cc_final: 0.8286 (pm20) REVERT: A 611 THR cc_start: 0.8839 (t) cc_final: 0.8558 (t) REVERT: A 615 MET cc_start: 0.8671 (mmp) cc_final: 0.7995 (mmp) REVERT: A 640 MET cc_start: 0.9381 (tpt) cc_final: 0.9175 (tpp) REVERT: A 650 GLN cc_start: 0.7814 (mt0) cc_final: 0.7369 (mt0) REVERT: B 8 LYS cc_start: 0.9463 (tttm) cc_final: 0.9122 (tppt) REVERT: B 12 LEU cc_start: 0.9644 (mt) cc_final: 0.9331 (mt) REVERT: B 17 MET cc_start: 0.8777 (mmm) cc_final: 0.8312 (mmt) REVERT: B 24 PHE cc_start: 0.8736 (m-80) cc_final: 0.8261 (m-80) REVERT: B 95 MET cc_start: 0.8981 (tpp) cc_final: 0.7546 (tpp) REVERT: B 98 PHE cc_start: 0.9561 (t80) cc_final: 0.8800 (t80) REVERT: B 99 LYS cc_start: 0.9666 (mmmt) cc_final: 0.8933 (mmmt) REVERT: B 193 SER cc_start: 0.8732 (t) cc_final: 0.8473 (p) REVERT: B 256 ARG cc_start: 0.8314 (tmt-80) cc_final: 0.7791 (tmt-80) REVERT: B 259 ASN cc_start: 0.8790 (m-40) cc_final: 0.8539 (p0) REVERT: B 288 PHE cc_start: 0.9412 (t80) cc_final: 0.9133 (t80) REVERT: B 307 TYR cc_start: 0.9151 (t80) cc_final: 0.8699 (t80) REVERT: B 319 MET cc_start: 0.8905 (tpp) cc_final: 0.8521 (tpp) REVERT: B 322 MET cc_start: 0.8609 (mmm) cc_final: 0.8117 (mmm) REVERT: B 326 PHE cc_start: 0.9193 (m-10) cc_final: 0.8271 (m-80) REVERT: B 359 MET cc_start: 0.7438 (tmm) cc_final: 0.6082 (tmm) REVERT: B 361 GLN cc_start: 0.8896 (tt0) cc_final: 0.8683 (tp40) REVERT: B 376 VAL cc_start: 0.8495 (t) cc_final: 0.7601 (t) REVERT: B 379 SER cc_start: 0.8275 (t) cc_final: 0.7933 (t) REVERT: B 396 ASP cc_start: 0.8255 (m-30) cc_final: 0.7992 (m-30) REVERT: B 444 ASP cc_start: 0.9137 (t0) cc_final: 0.8629 (t0) REVERT: B 458 MET cc_start: 0.9421 (mmm) cc_final: 0.8809 (mmm) REVERT: B 459 LYS cc_start: 0.8855 (mttt) cc_final: 0.8356 (mtmm) REVERT: B 472 LEU cc_start: 0.9302 (mm) cc_final: 0.9097 (mm) REVERT: B 492 PHE cc_start: 0.9223 (m-80) cc_final: 0.8600 (m-80) REVERT: B 493 MET cc_start: 0.9219 (tmm) cc_final: 0.8994 (tmm) REVERT: B 494 MET cc_start: 0.9334 (mtp) cc_final: 0.8922 (mtp) REVERT: B 615 MET cc_start: 0.8646 (mmp) cc_final: 0.8442 (mmm) REVERT: B 645 GLN cc_start: 0.8867 (tp40) cc_final: 0.8628 (tp-100) REVERT: B 648 ILE cc_start: 0.9048 (mm) cc_final: 0.8778 (mm) REVERT: C 50 ASN cc_start: 0.8517 (t0) cc_final: 0.8298 (p0) REVERT: C 95 MET cc_start: 0.7889 (tmm) cc_final: 0.7439 (tmm) REVERT: C 96 MET cc_start: 0.8502 (mmm) cc_final: 0.8253 (mmm) REVERT: C 137 MET cc_start: 0.7476 (mpp) cc_final: 0.6502 (tpt) REVERT: C 149 ASP cc_start: 0.8070 (t0) cc_final: 0.7736 (t0) REVERT: C 151 ILE cc_start: 0.8259 (mm) cc_final: 0.7856 (tp) REVERT: C 227 PHE cc_start: 0.8492 (t80) cc_final: 0.8218 (t80) REVERT: C 276 TYR cc_start: 0.8278 (t80) cc_final: 0.7945 (t80) REVERT: D 74 MET cc_start: 0.8110 (ttp) cc_final: 0.7501 (tmm) REVERT: D 96 MET cc_start: 0.5448 (mmm) cc_final: 0.5213 (mmm) REVERT: D 157 MET cc_start: 0.6962 (tmm) cc_final: 0.6684 (tmm) REVERT: D 169 TYR cc_start: 0.8528 (m-80) cc_final: 0.7887 (m-80) outliers start: 0 outliers final: 0 residues processed: 518 average time/residue: 0.2811 time to fit residues: 216.4808 Evaluate side-chains 420 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 420 time to evaluate : 1.798 ------------------------------------------------------------------------------- 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: 0.9990 chunk 182 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 77 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 115 optimal weight: 0.9990 chunk 127 optimal weight: 0.0980 chunk 188 optimal weight: 20.0000 chunk 27 optimal weight: 8.9990 chunk 50 optimal weight: 4.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 361 GLN A 365 ASN A 370 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN D 24 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.126487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.087651 restraints weight = 49869.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.090725 restraints weight = 31712.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.091919 restraints weight = 22264.619| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 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 = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.6840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 16386 Z= 0.142 Angle : 0.630 8.308 22134 Z= 0.333 Chirality : 0.043 0.193 2360 Planarity : 0.004 0.063 2818 Dihedral : 10.422 150.829 2242 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.19), residues: 1932 helix: 0.98 (0.15), residues: 1125 sheet: -0.76 (0.39), residues: 152 loop : 0.21 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 44 HIS 0.021 0.001 HIS C 201 PHE 0.024 0.002 PHE D 178 TYR 0.029 0.002 TYR A 571 ARG 0.012 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03994 ( 871) hydrogen bonds : angle 5.07741 ( 2571) covalent geometry : bond 0.00314 (16386) covalent geometry : angle 0.63050 (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 495 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 495 time to evaluate : 2.033 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 65 GLU cc_start: 0.8159 (mp0) cc_final: 0.7630 (mp0) REVERT: A 67 GLU cc_start: 0.9230 (tp30) cc_final: 0.8947 (tp30) REVERT: A 99 LYS cc_start: 0.9452 (mmtp) cc_final: 0.9011 (mttt) REVERT: A 117 ARG cc_start: 0.9151 (mmt90) cc_final: 0.8828 (mtp85) REVERT: A 147 GLN cc_start: 0.9027 (mt0) cc_final: 0.8539 (mt0) REVERT: A 158 ASN cc_start: 0.8953 (m110) cc_final: 0.8686 (m110) REVERT: A 163 ARG cc_start: 0.8622 (mmm-85) cc_final: 0.8289 (mmm-85) REVERT: A 202 ASN cc_start: 0.8572 (t0) cc_final: 0.8167 (t0) REVERT: A 220 THR cc_start: 0.8030 (m) cc_final: 0.7617 (p) REVERT: A 236 TYR cc_start: 0.7541 (t80) cc_final: 0.7302 (t80) REVERT: A 259 ASN cc_start: 0.8572 (p0) cc_final: 0.7686 (p0) REVERT: A 263 ASP cc_start: 0.9086 (t0) cc_final: 0.8605 (m-30) REVERT: A 270 ASP cc_start: 0.8617 (m-30) cc_final: 0.7962 (t0) REVERT: A 314 MET cc_start: 0.8473 (ppp) cc_final: 0.8201 (ppp) REVERT: A 345 LYS cc_start: 0.9269 (mttp) cc_final: 0.9044 (mttm) REVERT: A 361 GLN cc_start: 0.8936 (tp40) cc_final: 0.8671 (tp-100) REVERT: A 375 LYS cc_start: 0.9035 (mmtm) cc_final: 0.8610 (mmtm) REVERT: A 386 LEU cc_start: 0.9355 (mt) cc_final: 0.9155 (mt) REVERT: A 402 GLU cc_start: 0.8887 (mp0) cc_final: 0.8619 (mp0) REVERT: A 407 ILE cc_start: 0.8909 (mt) cc_final: 0.8572 (mt) REVERT: A 425 ILE cc_start: 0.9337 (mm) cc_final: 0.8983 (mm) REVERT: A 427 LYS cc_start: 0.9300 (mmmt) cc_final: 0.8842 (mtmt) REVERT: A 456 LYS cc_start: 0.8874 (mmtm) cc_final: 0.8376 (mmtm) REVERT: A 458 MET cc_start: 0.8972 (mmp) cc_final: 0.8690 (mmp) REVERT: A 466 MET cc_start: 0.8330 (ptp) cc_final: 0.7526 (pmm) REVERT: A 490 THR cc_start: 0.9490 (m) cc_final: 0.8673 (p) REVERT: A 494 MET cc_start: 0.9473 (mmp) cc_final: 0.8997 (mmm) REVERT: A 498 TYR cc_start: 0.9187 (m-80) cc_final: 0.8856 (m-80) REVERT: A 501 GLN cc_start: 0.9231 (tp-100) cc_final: 0.8873 (tp-100) REVERT: A 550 MET cc_start: 0.7565 (mtm) cc_final: 0.7263 (mtm) REVERT: A 571 TYR cc_start: 0.8886 (t80) cc_final: 0.8661 (t80) REVERT: A 598 MET cc_start: 0.8738 (mtm) cc_final: 0.8181 (ttm) REVERT: A 602 GLU cc_start: 0.8956 (pm20) cc_final: 0.8751 (pm20) REVERT: A 611 THR cc_start: 0.8870 (t) cc_final: 0.8669 (t) REVERT: A 615 MET cc_start: 0.8628 (mmp) cc_final: 0.7956 (mmp) REVERT: A 640 MET cc_start: 0.9367 (tpt) cc_final: 0.9150 (tpp) REVERT: B 8 LYS cc_start: 0.9467 (tttm) cc_final: 0.9156 (tppt) REVERT: B 12 LEU cc_start: 0.9656 (mt) cc_final: 0.9350 (mt) REVERT: B 17 MET cc_start: 0.8839 (mmm) cc_final: 0.8462 (mmt) REVERT: B 24 PHE cc_start: 0.8985 (m-80) cc_final: 0.8324 (m-80) REVERT: B 41 ILE cc_start: 0.9363 (mm) cc_final: 0.8894 (mm) REVERT: B 95 MET cc_start: 0.8793 (tpp) cc_final: 0.7454 (tpp) REVERT: B 98 PHE cc_start: 0.9510 (t80) cc_final: 0.8863 (t80) REVERT: B 99 LYS cc_start: 0.9677 (mmmt) cc_final: 0.8890 (mmmt) REVERT: B 172 LEU cc_start: 0.8613 (mp) cc_final: 0.8410 (mp) REVERT: B 193 SER cc_start: 0.8851 (t) cc_final: 0.8631 (p) REVERT: B 235 ARG cc_start: 0.7818 (mtp85) cc_final: 0.7400 (mmt90) REVERT: B 256 ARG cc_start: 0.8397 (tmt-80) cc_final: 0.7580 (ttp80) REVERT: B 259 ASN cc_start: 0.8812 (m-40) cc_final: 0.8484 (p0) REVERT: B 288 PHE cc_start: 0.9369 (t80) cc_final: 0.9031 (t80) REVERT: B 307 TYR cc_start: 0.9142 (t80) cc_final: 0.8697 (t80) REVERT: B 322 MET cc_start: 0.8698 (mmm) cc_final: 0.8407 (mmm) REVERT: B 326 PHE cc_start: 0.9146 (m-10) cc_final: 0.8595 (m-80) REVERT: B 359 MET cc_start: 0.7519 (tmm) cc_final: 0.6841 (tmm) REVERT: B 379 SER cc_start: 0.8084 (t) cc_final: 0.7676 (t) REVERT: B 384 GLU cc_start: 0.6702 (pm20) cc_final: 0.6482 (pm20) REVERT: B 396 ASP cc_start: 0.8407 (m-30) cc_final: 0.8099 (m-30) REVERT: B 444 ASP cc_start: 0.9147 (t0) cc_final: 0.8654 (t0) REVERT: B 458 MET cc_start: 0.9429 (mmm) cc_final: 0.8917 (mmm) REVERT: B 459 LYS cc_start: 0.8857 (mttt) cc_final: 0.8349 (mtmm) REVERT: B 472 LEU cc_start: 0.9286 (mm) cc_final: 0.9061 (mm) REVERT: B 492 PHE cc_start: 0.9202 (m-80) cc_final: 0.8592 (m-80) REVERT: B 493 MET cc_start: 0.9219 (tmm) cc_final: 0.8996 (tmm) REVERT: B 494 MET cc_start: 0.9337 (mtp) cc_final: 0.8919 (mtp) REVERT: B 640 MET cc_start: 0.9095 (mmp) cc_final: 0.8857 (mmm) REVERT: B 645 GLN cc_start: 0.8897 (tp40) cc_final: 0.8655 (tp-100) REVERT: B 648 ILE cc_start: 0.9121 (mm) cc_final: 0.8855 (mm) REVERT: C 50 ASN cc_start: 0.8492 (t0) cc_final: 0.8287 (p0) REVERT: C 95 MET cc_start: 0.7980 (tmm) cc_final: 0.7500 (tmm) REVERT: C 98 ASN cc_start: 0.6983 (m110) cc_final: 0.6587 (m110) REVERT: C 137 MET cc_start: 0.7634 (mpp) cc_final: 0.6603 (tpt) REVERT: C 151 ILE cc_start: 0.8300 (mm) cc_final: 0.7983 (tp) REVERT: C 276 TYR cc_start: 0.8231 (t80) cc_final: 0.7918 (t80) REVERT: D 96 MET cc_start: 0.5481 (mmm) cc_final: 0.5248 (mmm) REVERT: D 157 MET cc_start: 0.6987 (tmm) cc_final: 0.6716 (tmm) REVERT: D 169 TYR cc_start: 0.8509 (m-80) cc_final: 0.7888 (m-80) outliers start: 0 outliers final: 0 residues processed: 495 average time/residue: 0.2839 time to fit residues: 210.2611 Evaluate side-chains 419 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 419 time to evaluate : 1.924 ------------------------------------------------------------------------------- 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: 8.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 0.9980 chunk 160 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 127 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.124428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.085438 restraints weight = 51062.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.088454 restraints weight = 31817.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.090400 restraints weight = 22260.850| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- 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: 0.7263 moved from start: 0.7005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 16386 Z= 0.174 Angle : 0.662 11.887 22134 Z= 0.350 Chirality : 0.044 0.244 2360 Planarity : 0.004 0.047 2818 Dihedral : 10.472 152.575 2242 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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: 0.65 (0.19), residues: 1932 helix: 0.90 (0.15), residues: 1140 sheet: -0.70 (0.39), residues: 152 loop : 0.10 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 623 HIS 0.019 0.001 HIS C 201 PHE 0.024 0.002 PHE D 178 TYR 0.025 0.002 TYR A 571 ARG 0.012 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 871) hydrogen bonds : angle 5.13244 ( 2571) covalent geometry : bond 0.00378 (16386) covalent geometry : angle 0.66249 (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 501 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 501 time to evaluate : 1.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8227 (mp0) cc_final: 0.7711 (mp0) REVERT: A 67 GLU cc_start: 0.9248 (tp30) cc_final: 0.8945 (tp30) REVERT: A 89 PHE cc_start: 0.8827 (t80) cc_final: 0.8412 (t80) REVERT: A 99 LYS cc_start: 0.9493 (mmtp) cc_final: 0.9010 (mttt) REVERT: A 117 ARG cc_start: 0.9121 (mmt90) cc_final: 0.8762 (mmt180) REVERT: A 139 GLU cc_start: 0.9247 (mp0) cc_final: 0.8930 (mp0) REVERT: A 147 GLN cc_start: 0.9105 (mt0) cc_final: 0.8584 (mt0) REVERT: A 158 ASN cc_start: 0.8919 (m110) cc_final: 0.8554 (m110) REVERT: A 202 ASN cc_start: 0.8672 (t0) cc_final: 0.8420 (t0) REVERT: A 220 THR cc_start: 0.8324 (m) cc_final: 0.7904 (p) REVERT: A 236 TYR cc_start: 0.7607 (t80) cc_final: 0.7337 (t80) REVERT: A 263 ASP cc_start: 0.9072 (t0) cc_final: 0.8585 (m-30) REVERT: A 270 ASP cc_start: 0.8604 (m-30) cc_final: 0.8151 (t0) REVERT: A 313 HIS cc_start: 0.8651 (m90) cc_final: 0.8197 (m90) REVERT: A 314 MET cc_start: 0.8488 (ppp) cc_final: 0.8194 (ppp) REVERT: A 316 GLU cc_start: 0.9144 (mm-30) cc_final: 0.8849 (mm-30) REVERT: A 345 LYS cc_start: 0.9243 (mttp) cc_final: 0.9025 (mttm) REVERT: A 361 GLN cc_start: 0.9025 (tp40) cc_final: 0.8743 (tp-100) REVERT: A 375 LYS cc_start: 0.9014 (mmtm) cc_final: 0.8603 (mmtm) REVERT: A 390 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7872 (tm-30) REVERT: A 402 GLU cc_start: 0.8902 (mp0) cc_final: 0.8637 (mp0) REVERT: A 425 ILE cc_start: 0.9253 (mm) cc_final: 0.8734 (mm) REVERT: A 456 LYS cc_start: 0.8941 (mmtm) cc_final: 0.8412 (mmtm) REVERT: A 466 MET cc_start: 0.8523 (ptp) cc_final: 0.7782 (pmm) REVERT: A 490 THR cc_start: 0.9506 (m) cc_final: 0.8709 (p) REVERT: A 494 MET cc_start: 0.9500 (mmp) cc_final: 0.9041 (mmm) REVERT: A 498 TYR cc_start: 0.9253 (m-80) cc_final: 0.8866 (m-80) REVERT: A 501 GLN cc_start: 0.9263 (tp-100) cc_final: 0.8887 (tp-100) REVERT: A 515 ASP cc_start: 0.8956 (m-30) cc_final: 0.8751 (m-30) REVERT: A 550 MET cc_start: 0.7360 (mtm) cc_final: 0.6954 (mtm) REVERT: A 598 MET cc_start: 0.8680 (mtm) cc_final: 0.8347 (mtt) REVERT: A 602 GLU cc_start: 0.8869 (pm20) cc_final: 0.8627 (pm20) REVERT: A 611 THR cc_start: 0.9013 (t) cc_final: 0.8611 (t) REVERT: A 615 MET cc_start: 0.8642 (mmp) cc_final: 0.7928 (mmp) REVERT: A 640 MET cc_start: 0.9400 (tpt) cc_final: 0.9182 (tpp) REVERT: A 650 GLN cc_start: 0.6594 (mm-40) cc_final: 0.6393 (mm-40) REVERT: B 8 LYS cc_start: 0.9510 (tttm) cc_final: 0.9192 (tppt) REVERT: B 12 LEU cc_start: 0.9667 (mt) cc_final: 0.9371 (mt) REVERT: B 17 MET cc_start: 0.8890 (mmm) cc_final: 0.8383 (mmt) REVERT: B 24 PHE cc_start: 0.9021 (m-80) cc_final: 0.8199 (m-80) REVERT: B 95 MET cc_start: 0.9034 (tpp) cc_final: 0.7680 (tpp) REVERT: B 98 PHE cc_start: 0.9537 (t80) cc_final: 0.8804 (t80) REVERT: B 99 LYS cc_start: 0.9696 (mmmt) cc_final: 0.8923 (mmmt) REVERT: B 115 LEU cc_start: 0.8333 (mp) cc_final: 0.8075 (mp) REVERT: B 193 SER cc_start: 0.8787 (t) cc_final: 0.8577 (p) REVERT: B 256 ARG cc_start: 0.8357 (tmt-80) cc_final: 0.8120 (tmt-80) REVERT: B 288 PHE cc_start: 0.9409 (t80) cc_final: 0.8951 (t80) REVERT: B 307 TYR cc_start: 0.9180 (t80) cc_final: 0.8744 (t80) REVERT: B 322 MET cc_start: 0.8755 (mmm) cc_final: 0.8517 (mmm) REVERT: B 326 PHE cc_start: 0.9236 (m-10) cc_final: 0.8500 (m-80) REVERT: B 333 LYS cc_start: 0.8817 (ptmt) cc_final: 0.8561 (ptmt) REVERT: B 375 LYS cc_start: 0.9320 (mptt) cc_final: 0.8740 (mmtm) REVERT: B 379 SER cc_start: 0.8056 (t) cc_final: 0.7771 (t) REVERT: B 384 GLU cc_start: 0.6658 (pm20) cc_final: 0.6385 (pm20) REVERT: B 396 ASP cc_start: 0.8439 (m-30) cc_final: 0.8133 (m-30) REVERT: B 415 ASN cc_start: 0.8329 (t0) cc_final: 0.7810 (t0) REVERT: B 444 ASP cc_start: 0.9173 (t0) cc_final: 0.8692 (t0) REVERT: B 445 ILE cc_start: 0.8467 (mm) cc_final: 0.8266 (mm) REVERT: B 458 MET cc_start: 0.9460 (mmm) cc_final: 0.8897 (mmm) REVERT: B 459 LYS cc_start: 0.8882 (mttt) cc_final: 0.8385 (mtmm) REVERT: B 493 MET cc_start: 0.9247 (tmm) cc_final: 0.9037 (tmm) REVERT: B 494 MET cc_start: 0.9381 (mtp) cc_final: 0.8966 (mtp) REVERT: B 584 ILE cc_start: 0.9052 (tp) cc_final: 0.8336 (tp) REVERT: B 640 MET cc_start: 0.9147 (mmp) cc_final: 0.8916 (mmm) REVERT: B 645 GLN cc_start: 0.8904 (tp40) cc_final: 0.8642 (tp-100) REVERT: B 648 ILE cc_start: 0.9095 (mm) cc_final: 0.8798 (mm) REVERT: B 667 LEU cc_start: 0.8177 (mp) cc_final: 0.7973 (mp) REVERT: C 95 MET cc_start: 0.8037 (tmm) cc_final: 0.7691 (tmm) REVERT: C 96 MET cc_start: 0.8381 (mmm) cc_final: 0.7954 (mmm) REVERT: C 98 ASN cc_start: 0.7212 (m110) cc_final: 0.6855 (m110) REVERT: C 137 MET cc_start: 0.7742 (mpp) cc_final: 0.6639 (tpp) REVERT: C 151 ILE cc_start: 0.8262 (mm) cc_final: 0.7943 (tp) REVERT: C 276 TYR cc_start: 0.8247 (t80) cc_final: 0.7924 (t80) REVERT: D 74 MET cc_start: 0.8286 (tmm) cc_final: 0.7296 (tmm) REVERT: D 96 MET cc_start: 0.5411 (mmm) cc_final: 0.5197 (mmm) REVERT: D 157 MET cc_start: 0.6914 (tmm) cc_final: 0.6633 (tmm) REVERT: D 169 TYR cc_start: 0.8595 (m-80) cc_final: 0.7965 (m-80) outliers start: 0 outliers final: 0 residues processed: 501 average time/residue: 0.2803 time to fit residues: 209.7328 Evaluate side-chains 422 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 422 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 81 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 179 optimal weight: 40.0000 chunk 190 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 150 GLN ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 516 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 107 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 = 0.3881 r_free = 0.3881 target = 0.127439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.088273 restraints weight = 50787.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.091352 restraints weight = 32137.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.093205 restraints weight = 23318.333| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3380 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3380 r_free = 0.3380 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3379 r_free = 0.3379 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3379 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.7125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16386 Z= 0.131 Angle : 0.639 8.835 22134 Z= 0.335 Chirality : 0.043 0.190 2360 Planarity : 0.004 0.043 2818 Dihedral : 10.222 144.130 2242 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % 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: 0.64 (0.19), residues: 1932 helix: 0.96 (0.15), residues: 1135 sheet: -0.81 (0.38), residues: 162 loop : 0.02 (0.24), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 44 HIS 0.017 0.001 HIS C 201 PHE 0.018 0.001 PHE A 378 TYR 0.024 0.001 TYR D 174 ARG 0.012 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03968 ( 871) hydrogen bonds : angle 5.07426 ( 2571) covalent geometry : bond 0.00286 (16386) covalent geometry : angle 0.63915 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6266.63 seconds wall clock time: 110 minutes 20.08 seconds (6620.08 seconds total)