Starting phenix.real_space_refine on Sat May 17 16:38:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz9_45057/05_2025/9bz9_45057_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz9_45057/05_2025/9bz9_45057.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/9bz9_45057/05_2025/9bz9_45057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz9_45057/05_2025/9bz9_45057.map" model { file = "/net/cci-nas-00/data/ceres_data/9bz9_45057/05_2025/9bz9_45057_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz9_45057/05_2025/9bz9_45057_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 68 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 8.80, per 1000 atoms: 0.55 Number of scatterers: 16038 At special positions: 0 Unit cell: (93.288, 124.722, 129.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.87 Conformation dependent library (CDL) restraints added in 1.9 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 64.1% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 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: 3.515A 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: 3.947A 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: 3.627A 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: 3.579A 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: 3.878A 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: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.026A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.634A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.068A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.881A 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 181 removed outlier: 4.936A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix removed outlier: 3.576A pdb=" N GLN C 181 " --> pdb=" O TYR C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.567A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.668A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.643A 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: 6.359A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 605 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: 7.184A 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: 4.048A 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: 6.564A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.907A 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: 8.345A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 871 hydrogen bonds defined for protein. 2568 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.74 Time building geometry restraints manager: 4.50 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: 4857 1.34 - 1.46: 3044 1.46 - 1.58: 8304 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.600 -0.060 1.25e-02 6.40e+03 2.33e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.577 -0.038 1.20e-02 6.94e+03 9.90e+00 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.032 1.08e-02 8.57e+03 8.90e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.569 -0.032 1.17e-02 7.31e+03 7.60e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.573 -0.033 1.25e-02 6.40e+03 7.09e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21564 2.09 - 4.19: 517 4.19 - 6.28: 44 6.28 - 8.38: 4 8.38 - 10.47: 5 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N SER A 609 " pdb=" CA SER A 609 " pdb=" C SER A 609 " ideal model delta sigma weight residual 110.41 119.07 -8.66 1.23e+00 6.61e-01 4.96e+01 angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.59 -6.05 1.36e+00 5.41e-01 1.98e+01 angle pdb=" C ASN A 608 " pdb=" N SER A 609 " pdb=" CA SER A 609 " ideal model delta sigma weight residual 121.06 129.21 -8.15 1.88e+00 2.83e-01 1.88e+01 angle pdb=" N ASN C 288 " pdb=" CA ASN C 288 " pdb=" CB ASN C 288 " ideal model delta sigma weight residual 110.39 103.68 6.71 1.66e+00 3.63e-01 1.63e+01 angle pdb=" N SER A 609 " pdb=" CA SER A 609 " pdb=" CB SER A 609 " ideal model delta sigma weight residual 110.38 104.92 5.46 1.37e+00 5.33e-01 1.59e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 9470 35.80 - 71.60: 337 71.60 - 107.41: 37 107.41 - 143.21: 3 143.21 - 179.01: 3 Dihedral angle restraints: 9850 sinusoidal: 4092 harmonic: 5758 Sorted by residual: dihedral pdb=" C2 TTP A 803 " pdb=" C1' TTP A 803 " pdb=" N1 TTP A 803 " pdb=" O4' TTP A 803 " ideal model delta sinusoidal sigma weight residual -58.32 120.69 -179.01 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual 301.68 151.20 150.49 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 31.88 148.09 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 9847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2150 0.094 - 0.187: 178 0.187 - 0.281: 28 0.281 - 0.374: 2 0.374 - 0.468: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.47e+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 4.58e+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 2.94e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN C 288 " -0.013 2.00e-02 2.50e+03 2.57e-02 6.58e+00 pdb=" C ASN C 288 " 0.044 2.00e-02 2.50e+03 pdb=" O ASN C 288 " -0.017 2.00e-02 2.50e+03 pdb=" N GLY C 289 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 609 " 0.011 2.00e-02 2.50e+03 2.29e-02 5.23e+00 pdb=" C SER A 609 " -0.040 2.00e-02 2.50e+03 pdb=" O SER A 609 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS A 610 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 608 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" CG ASN A 608 " -0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN A 608 " 0.011 2.00e-02 2.50e+03 pdb=" ND2 ASN A 608 " 0.010 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 130 2.51 - 3.11: 11584 3.11 - 3.70: 27097 3.70 - 4.30: 41576 4.30 - 4.90: 65504 Nonbonded interactions: 145891 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 145886 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: 1.070 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: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 33.930 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 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= 0.317 Angle : 0.754 10.473 22134 Z= 0.472 Chirality : 0.058 0.468 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.936 179.009 6154 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.40 % Allowed : 15.27 % Favored : 83.33 % 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: 0.59 (0.14), residues: 1151 sheet: 0.45 (0.41), residues: 128 loop : 0.21 (0.23), residues: 653 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 C 168 TYR 0.020 0.002 TYR D 179 ARG 0.003 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.15437 ( 869) hydrogen bonds : angle 6.52098 ( 2568) covalent geometry : bond 0.00556 (16386) covalent geometry : angle 0.75361 (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 926 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 902 time to evaluate : 1.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 33 VAL cc_start: 0.8856 (t) cc_final: 0.8425 (t) REVERT: A 51 LEU cc_start: 0.8122 (tp) cc_final: 0.7531 (tp) REVERT: A 125 VAL cc_start: 0.9045 (t) cc_final: 0.7548 (t) REVERT: A 143 LEU cc_start: 0.9043 (tp) cc_final: 0.8583 (tp) REVERT: A 166 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8023 (mm-30) REVERT: A 181 ASP cc_start: 0.8496 (m-30) cc_final: 0.8087 (m-30) REVERT: A 213 ILE cc_start: 0.8120 (mt) cc_final: 0.7564 (mp) REVERT: A 224 VAL cc_start: 0.8883 (t) cc_final: 0.7964 (p) REVERT: A 283 VAL cc_start: 0.8505 (t) cc_final: 0.7307 (t) REVERT: A 288 PHE cc_start: 0.7249 (t80) cc_final: 0.6821 (t80) REVERT: A 291 LEU cc_start: 0.9293 (mt) cc_final: 0.9073 (mp) REVERT: A 300 VAL cc_start: 0.7424 (m) cc_final: 0.7076 (m) REVERT: A 322 MET cc_start: 0.7645 (mmp) cc_final: 0.6616 (mmm) REVERT: A 342 LEU cc_start: 0.9170 (tp) cc_final: 0.8654 (tp) REVERT: A 348 MET cc_start: 0.8437 (tmm) cc_final: 0.8165 (tmm) REVERT: A 360 PHE cc_start: 0.7566 (m-80) cc_final: 0.7316 (m-10) REVERT: A 362 ASP cc_start: 0.6186 (m-30) cc_final: 0.4878 (m-30) REVERT: A 367 VAL cc_start: 0.8092 (m) cc_final: 0.7837 (m) REVERT: A 370 ASN cc_start: 0.7524 (m-40) cc_final: 0.6740 (m-40) REVERT: A 416 ILE cc_start: 0.8779 (mt) cc_final: 0.8565 (mt) REVERT: A 431 LEU cc_start: 0.8996 (mt) cc_final: 0.8643 (mm) REVERT: A 436 LEU cc_start: 0.9252 (mt) cc_final: 0.8892 (mt) REVERT: A 500 ILE cc_start: 0.9201 (mt) cc_final: 0.8609 (mt) REVERT: A 605 THR cc_start: 0.6568 (m) cc_final: 0.6306 (m) REVERT: A 634 MET cc_start: 0.8337 (mmp) cc_final: 0.7993 (mpp) REVERT: A 641 ILE cc_start: 0.9277 (mm) cc_final: 0.9048 (mm) REVERT: A 652 ILE cc_start: 0.8789 (mt) cc_final: 0.8506 (mt) REVERT: A 653 SER cc_start: 0.9052 (OUTLIER) cc_final: 0.8695 (p) REVERT: A 682 ILE cc_start: 0.8321 (mt) cc_final: 0.8039 (mt) REVERT: B 41 ILE cc_start: 0.8853 (mm) cc_final: 0.8161 (mt) REVERT: B 51 LEU cc_start: 0.8561 (tp) cc_final: 0.8189 (tp) REVERT: B 95 MET cc_start: 0.7883 (tpp) cc_final: 0.7673 (tpp) REVERT: B 98 PHE cc_start: 0.7798 (t80) cc_final: 0.7465 (t80) REVERT: B 99 LYS cc_start: 0.9167 (mmtt) cc_final: 0.8343 (mmmm) REVERT: B 100 PHE cc_start: 0.7911 (t80) cc_final: 0.7614 (t80) REVERT: B 101 TYR cc_start: 0.7554 (m-80) cc_final: 0.7048 (m-80) REVERT: B 143 LEU cc_start: 0.9038 (tp) cc_final: 0.8832 (tp) REVERT: B 149 TYR cc_start: 0.8345 (t80) cc_final: 0.7634 (t80) REVERT: B 179 LEU cc_start: 0.8607 (tp) cc_final: 0.7634 (tp) REVERT: B 191 GLN cc_start: 0.8685 (mm-40) cc_final: 0.8155 (mm-40) REVERT: B 240 MET cc_start: 0.6884 (mpt) cc_final: 0.6324 (mpt) REVERT: B 288 PHE cc_start: 0.7313 (t80) cc_final: 0.6321 (t80) REVERT: B 322 MET cc_start: 0.7357 (mmm) cc_final: 0.6021 (tpp) REVERT: B 337 ILE cc_start: 0.8308 (pt) cc_final: 0.8061 (pt) REVERT: B 361 GLN cc_start: 0.6689 (tt0) cc_final: 0.6393 (tt0) REVERT: B 362 ASP cc_start: 0.6252 (m-30) cc_final: 0.5546 (m-30) REVERT: B 373 ILE cc_start: 0.9065 (mt) cc_final: 0.8322 (mt) REVERT: B 415 ASN cc_start: 0.8552 (t0) cc_final: 0.7838 (t0) REVERT: B 418 ASN cc_start: 0.7652 (m-40) cc_final: 0.6536 (m-40) REVERT: B 425 ILE cc_start: 0.9268 (mt) cc_final: 0.8680 (mt) REVERT: B 436 LEU cc_start: 0.9378 (mt) cc_final: 0.9090 (mt) REVERT: B 493 MET cc_start: 0.7437 (tmm) cc_final: 0.7127 (tmm) REVERT: B 494 MET cc_start: 0.7842 (mtp) cc_final: 0.7589 (mtp) REVERT: B 496 ASN cc_start: 0.7072 (t0) cc_final: 0.5318 (t0) REVERT: B 575 ARG cc_start: 0.7594 (mtm110) cc_final: 0.6942 (mtm180) REVERT: B 588 GLN cc_start: 0.7455 (mm-40) cc_final: 0.6997 (mm-40) REVERT: B 601 ILE cc_start: 0.7785 (mt) cc_final: 0.7224 (mt) REVERT: B 613 TYR cc_start: 0.7838 (t80) cc_final: 0.7536 (t80) REVERT: B 641 ILE cc_start: 0.9444 (mm) cc_final: 0.9128 (mm) REVERT: B 645 GLN cc_start: 0.8410 (tp-100) cc_final: 0.8175 (tp-100) REVERT: B 656 LEU cc_start: 0.8212 (mt) cc_final: 0.7884 (mt) REVERT: C 85 GLN cc_start: 0.5803 (mt0) cc_final: 0.4899 (tt0) REVERT: C 90 LEU cc_start: 0.5509 (mt) cc_final: 0.5013 (mt) REVERT: C 106 SER cc_start: 0.6299 (m) cc_final: 0.6091 (t) REVERT: C 137 MET cc_start: 0.4147 (mtp) cc_final: 0.3271 (mtt) REVERT: C 194 ILE cc_start: 0.7431 (mt) cc_final: 0.7131 (mp) REVERT: C 205 VAL cc_start: 0.7608 (t) cc_final: 0.7386 (t) REVERT: C 275 PRO cc_start: 0.5456 (Cg_endo) cc_final: 0.4961 (Cg_exo) REVERT: D 31 LEU cc_start: 0.8392 (mt) cc_final: 0.8011 (mt) REVERT: D 100 VAL cc_start: 0.3534 (t) cc_final: 0.2981 (t) REVERT: D 205 VAL cc_start: 0.7168 (t) cc_final: 0.6729 (t) REVERT: D 317 ASP cc_start: 0.6461 (t0) cc_final: 0.5790 (t70) outliers start: 24 outliers final: 6 residues processed: 915 average time/residue: 0.3072 time to fit residues: 398.0031 Evaluate side-chains 641 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 634 time to evaluate : 1.701 ------------------------------------------------------------------------------- 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: 7.9990 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 49 optimal weight: 9.9990 chunk 98 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 150 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 174 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 43 GLN A 147 GLN A 239 GLN A 242 GLN A 320 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 304 HIS ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN C 84 HIS C 119 ASN D 71 ASN D 80 HIS ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.112936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.078670 restraints weight = 48675.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.081619 restraints weight = 29500.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.083785 restraints weight = 20711.213| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3138 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16386 Z= 0.212 Angle : 0.664 7.524 22134 Z= 0.357 Chirality : 0.043 0.304 2360 Planarity : 0.004 0.049 2818 Dihedral : 11.491 179.744 2242 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.29 % Allowed : 2.80 % 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: 1.20 (0.19), residues: 1932 helix: 1.27 (0.15), residues: 1115 sheet: -0.11 (0.40), residues: 130 loop : 0.38 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 558 HIS 0.008 0.002 HIS A 304 PHE 0.041 0.003 PHE D 178 TYR 0.023 0.002 TYR A 606 ARG 0.007 0.001 ARG A 452 Details of bonding type rmsd hydrogen bonds : bond 0.04678 ( 869) hydrogen bonds : angle 5.16633 ( 2568) covalent geometry : bond 0.00445 (16386) covalent geometry : angle 0.66355 (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 714 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 709 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 ILE cc_start: 0.9729 (mm) cc_final: 0.9245 (mt) REVERT: A 87 LYS cc_start: 0.9208 (tptm) cc_final: 0.8955 (tptm) REVERT: A 99 LYS cc_start: 0.9337 (mmtp) cc_final: 0.9005 (mmtp) REVERT: A 107 LYS cc_start: 0.9385 (mttm) cc_final: 0.9133 (mmmt) REVERT: A 143 LEU cc_start: 0.9179 (tp) cc_final: 0.8906 (tp) REVERT: A 144 MET cc_start: 0.9319 (mtm) cc_final: 0.8913 (mtm) REVERT: A 194 LYS cc_start: 0.9442 (ttpt) cc_final: 0.9113 (ttpp) REVERT: A 195 LEU cc_start: 0.9515 (mt) cc_final: 0.9237 (mt) REVERT: A 252 ASN cc_start: 0.8545 (t0) cc_final: 0.8084 (t0) REVERT: A 279 SER cc_start: 0.7623 (m) cc_final: 0.7374 (p) REVERT: A 286 ASP cc_start: 0.9188 (m-30) cc_final: 0.8447 (m-30) REVERT: A 321 GLU cc_start: 0.9335 (mp0) cc_final: 0.9074 (mp0) REVERT: A 385 VAL cc_start: 0.9575 (t) cc_final: 0.9337 (t) REVERT: A 387 GLN cc_start: 0.8603 (mt0) cc_final: 0.8202 (mt0) REVERT: A 418 ASN cc_start: 0.8998 (m110) cc_final: 0.8752 (m-40) REVERT: A 421 GLU cc_start: 0.9486 (tm-30) cc_final: 0.9260 (tm-30) REVERT: A 436 LEU cc_start: 0.9613 (mt) cc_final: 0.9376 (mt) REVERT: A 502 ARG cc_start: 0.9452 (tpt170) cc_final: 0.9198 (tpt90) REVERT: A 510 LYS cc_start: 0.9693 (mmmt) cc_final: 0.9052 (mmtm) REVERT: A 571 TYR cc_start: 0.8796 (t80) cc_final: 0.8580 (t80) REVERT: A 572 HIS cc_start: 0.9509 (m90) cc_final: 0.9148 (m90) REVERT: A 599 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8519 (mt-10) REVERT: A 615 MET cc_start: 0.8951 (mmp) cc_final: 0.8565 (mmp) REVERT: A 626 TYR cc_start: 0.8983 (m-80) cc_final: 0.8672 (m-10) REVERT: A 634 MET cc_start: 0.9305 (mmp) cc_final: 0.9046 (mpp) REVERT: A 667 LEU cc_start: 0.9438 (tt) cc_final: 0.9053 (tt) REVERT: A 683 TYR cc_start: 0.8473 (t80) cc_final: 0.7874 (t80) REVERT: B 19 GLN cc_start: 0.9369 (mt0) cc_final: 0.8896 (pp30) REVERT: B 51 LEU cc_start: 0.9413 (tp) cc_final: 0.9005 (tp) REVERT: B 77 ILE cc_start: 0.9744 (mt) cc_final: 0.9424 (mt) REVERT: B 87 LYS cc_start: 0.9293 (tptp) cc_final: 0.9005 (tptp) REVERT: B 89 PHE cc_start: 0.9197 (t80) cc_final: 0.8982 (t80) REVERT: B 95 MET cc_start: 0.9491 (tpp) cc_final: 0.8529 (tpp) REVERT: B 99 LYS cc_start: 0.9417 (mmmt) cc_final: 0.8721 (mmmt) REVERT: B 144 MET cc_start: 0.9630 (mtm) cc_final: 0.9033 (mtm) REVERT: B 149 TYR cc_start: 0.8932 (t80) cc_final: 0.8512 (t80) REVERT: B 150 GLN cc_start: 0.9037 (tp40) cc_final: 0.8746 (tp40) REVERT: B 162 LYS cc_start: 0.9247 (tppt) cc_final: 0.8986 (mttt) REVERT: B 180 ASN cc_start: 0.8966 (t160) cc_final: 0.8589 (t0) REVERT: B 191 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8840 (mm-40) REVERT: B 211 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8096 (mt-10) REVERT: B 229 LEU cc_start: 0.9200 (mt) cc_final: 0.8943 (mt) REVERT: B 236 TYR cc_start: 0.8785 (t80) cc_final: 0.8449 (t80) REVERT: B 267 ILE cc_start: 0.8756 (pt) cc_final: 0.8448 (pt) REVERT: B 286 ASP cc_start: 0.8979 (m-30) cc_final: 0.8309 (m-30) REVERT: B 317 MET cc_start: 0.8666 (pmm) cc_final: 0.8328 (pmm) REVERT: B 355 TYR cc_start: 0.9303 (m-10) cc_final: 0.8913 (m-10) REVERT: B 362 ASP cc_start: 0.8648 (m-30) cc_final: 0.7873 (m-30) REVERT: B 415 ASN cc_start: 0.9036 (t0) cc_final: 0.8121 (t0) REVERT: B 418 ASN cc_start: 0.9355 (m-40) cc_final: 0.8744 (m-40) REVERT: B 420 MET cc_start: 0.8889 (mmp) cc_final: 0.8634 (mmp) REVERT: B 458 MET cc_start: 0.9458 (mmm) cc_final: 0.9072 (mmm) REVERT: B 467 ASN cc_start: 0.9256 (m-40) cc_final: 0.8897 (m110) REVERT: B 492 PHE cc_start: 0.9737 (m-80) cc_final: 0.9470 (m-80) REVERT: B 494 MET cc_start: 0.9399 (mtp) cc_final: 0.8617 (mtp) REVERT: B 496 ASN cc_start: 0.9739 (t0) cc_final: 0.9056 (t0) REVERT: B 499 SER cc_start: 0.9922 (t) cc_final: 0.9703 (p) REVERT: B 500 ILE cc_start: 0.9749 (mt) cc_final: 0.9434 (mt) REVERT: B 501 GLN cc_start: 0.9070 (tp-100) cc_final: 0.8554 (tp-100) REVERT: B 515 ASP cc_start: 0.9070 (m-30) cc_final: 0.8739 (m-30) REVERT: B 543 ILE cc_start: 0.9393 (mp) cc_final: 0.9136 (mt) REVERT: B 570 MET cc_start: 0.9285 (tpp) cc_final: 0.8663 (tpt) REVERT: B 574 TYR cc_start: 0.8275 (m-80) cc_final: 0.7922 (m-80) REVERT: B 575 ARG cc_start: 0.8789 (mtm110) cc_final: 0.8162 (mtm110) REVERT: B 588 GLN cc_start: 0.9364 (mm-40) cc_final: 0.8741 (mm-40) REVERT: B 601 ILE cc_start: 0.9224 (mt) cc_final: 0.8983 (mp) REVERT: B 645 GLN cc_start: 0.9346 (tp-100) cc_final: 0.9056 (tp-100) REVERT: C 21 PHE cc_start: 0.8777 (m-80) cc_final: 0.8184 (m-80) REVERT: C 46 TYR cc_start: 0.7796 (m-80) cc_final: 0.7525 (m-80) REVERT: C 89 VAL cc_start: 0.7466 (t) cc_final: 0.7247 (t) REVERT: C 96 MET cc_start: 0.6559 (mmt) cc_final: 0.6012 (mmt) REVERT: C 137 MET cc_start: 0.5093 (mtp) cc_final: 0.4748 (mtt) REVERT: C 139 VAL cc_start: 0.8802 (p) cc_final: 0.8595 (t) REVERT: C 204 TYR cc_start: 0.9459 (t80) cc_final: 0.9138 (t80) REVERT: C 315 LEU cc_start: 0.8219 (mt) cc_final: 0.7783 (mt) REVERT: D 33 GLU cc_start: 0.9377 (mp0) cc_final: 0.9128 (mp0) REVERT: D 109 PHE cc_start: 0.7501 (OUTLIER) cc_final: 0.7097 (m-80) REVERT: D 185 MET cc_start: 0.6654 (mmm) cc_final: 0.6027 (mmp) REVERT: D 239 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.6350 (pp20) REVERT: D 259 PHE cc_start: 0.7697 (t80) cc_final: 0.7292 (t80) REVERT: D 317 ASP cc_start: 0.9308 (t0) cc_final: 0.8176 (t0) outliers start: 5 outliers final: 2 residues processed: 712 average time/residue: 0.2909 time to fit residues: 298.2276 Evaluate side-chains 586 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 582 time to evaluate : 1.728 ------------------------------------------------------------------------------- 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: 4.9990 chunk 168 optimal weight: 7.9990 chunk 175 optimal weight: 6.9990 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 191 optimal weight: 30.0000 chunk 57 optimal weight: 8.9990 chunk 52 optimal weight: 0.5980 chunk 171 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 141 optimal weight: 8.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 ASN B 390 GLN B 410 ASN B 676 HIS C 28 GLN C 84 HIS C 132 GLN C 238 ASN D 25 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.110720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.078095 restraints weight = 50848.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.080848 restraints weight = 30763.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.082929 restraints weight = 21213.789| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3111 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3111 r_free = 0.3111 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3111 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.5519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16386 Z= 0.207 Angle : 0.647 8.153 22134 Z= 0.344 Chirality : 0.043 0.266 2360 Planarity : 0.004 0.053 2818 Dihedral : 11.277 179.643 2242 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 16.91 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: 1.01 (0.19), residues: 1932 helix: 1.16 (0.15), residues: 1125 sheet: -0.37 (0.41), residues: 130 loop : 0.27 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 30 HIS 0.006 0.002 HIS A 438 PHE 0.036 0.002 PHE A 129 TYR 0.031 0.002 TYR C 142 ARG 0.006 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.04266 ( 869) hydrogen bonds : angle 5.02273 ( 2568) covalent geometry : bond 0.00430 (16386) covalent geometry : angle 0.64672 (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 674 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 672 time to evaluate : 1.721 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 87 LYS cc_start: 0.9271 (tptm) cc_final: 0.8800 (tptm) REVERT: A 95 MET cc_start: 0.9732 (tpt) cc_final: 0.9395 (mmm) REVERT: A 117 ARG cc_start: 0.9247 (mtp85) cc_final: 0.8837 (mmt180) REVERT: A 143 LEU cc_start: 0.9173 (tp) cc_final: 0.8947 (tp) REVERT: A 144 MET cc_start: 0.9243 (mtm) cc_final: 0.8799 (mtm) REVERT: A 145 ILE cc_start: 0.9449 (tp) cc_final: 0.9038 (tp) REVERT: A 194 LYS cc_start: 0.9445 (ttpt) cc_final: 0.9159 (ttpp) REVERT: A 202 ASN cc_start: 0.9145 (t0) cc_final: 0.8912 (t0) REVERT: A 224 VAL cc_start: 0.8864 (t) cc_final: 0.8561 (t) REVERT: A 227 MET cc_start: 0.9350 (mtp) cc_final: 0.8861 (mtp) REVERT: A 252 ASN cc_start: 0.8580 (t0) cc_final: 0.8355 (t0) REVERT: A 286 ASP cc_start: 0.8982 (m-30) cc_final: 0.8459 (m-30) REVERT: A 335 GLU cc_start: 0.9259 (tp30) cc_final: 0.8973 (tm-30) REVERT: A 362 ASP cc_start: 0.9157 (m-30) cc_final: 0.8446 (m-30) REVERT: A 370 ASN cc_start: 0.9375 (m-40) cc_final: 0.8979 (m110) REVERT: A 386 LEU cc_start: 0.9469 (mt) cc_final: 0.9238 (mt) REVERT: A 396 ASP cc_start: 0.9038 (p0) cc_final: 0.8819 (p0) REVERT: A 421 GLU cc_start: 0.9401 (tm-30) cc_final: 0.9199 (tm-30) REVERT: A 468 LEU cc_start: 0.9663 (tp) cc_final: 0.9462 (tp) REVERT: A 493 MET cc_start: 0.9367 (tmm) cc_final: 0.9145 (tmm) REVERT: A 599 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8535 (mt-10) REVERT: A 615 MET cc_start: 0.8940 (mmp) cc_final: 0.8696 (mmp) REVERT: A 626 TYR cc_start: 0.9199 (m-80) cc_final: 0.8791 (m-10) REVERT: A 645 GLN cc_start: 0.8423 (tp-100) cc_final: 0.7300 (tp-100) REVERT: A 650 GLN cc_start: 0.7644 (mm110) cc_final: 0.7279 (mm110) REVERT: A 680 LYS cc_start: 0.8422 (mttt) cc_final: 0.7906 (mttt) REVERT: B 19 GLN cc_start: 0.9298 (mt0) cc_final: 0.8944 (pp30) REVERT: B 41 ILE cc_start: 0.9732 (mm) cc_final: 0.9531 (mt) REVERT: B 51 LEU cc_start: 0.9494 (tp) cc_final: 0.9111 (tp) REVERT: B 77 ILE cc_start: 0.9693 (mt) cc_final: 0.9326 (mt) REVERT: B 81 PHE cc_start: 0.9541 (m-80) cc_final: 0.9335 (m-80) REVERT: B 87 LYS cc_start: 0.9321 (tptp) cc_final: 0.9025 (tptp) REVERT: B 89 PHE cc_start: 0.9176 (t80) cc_final: 0.8770 (t80) REVERT: B 95 MET cc_start: 0.9469 (tpp) cc_final: 0.8335 (tpp) REVERT: B 99 LYS cc_start: 0.9481 (mmmt) cc_final: 0.8715 (mmmt) REVERT: B 118 TYR cc_start: 0.9189 (t80) cc_final: 0.8981 (t80) REVERT: B 144 MET cc_start: 0.9557 (mtm) cc_final: 0.8897 (mtm) REVERT: B 149 TYR cc_start: 0.8990 (t80) cc_final: 0.8588 (t80) REVERT: B 150 GLN cc_start: 0.9088 (tp40) cc_final: 0.8846 (tp40) REVERT: B 162 LYS cc_start: 0.9353 (tppt) cc_final: 0.9075 (mttp) REVERT: B 194 LYS cc_start: 0.9237 (pttp) cc_final: 0.9017 (pttm) REVERT: B 257 ASP cc_start: 0.8404 (m-30) cc_final: 0.8134 (m-30) REVERT: B 263 ASP cc_start: 0.9436 (m-30) cc_final: 0.9235 (m-30) REVERT: B 286 ASP cc_start: 0.9002 (m-30) cc_final: 0.8359 (m-30) REVERT: B 322 MET cc_start: 0.8984 (tpt) cc_final: 0.8558 (tpt) REVERT: B 350 ARG cc_start: 0.8945 (tpp80) cc_final: 0.8289 (tpp80) REVERT: B 355 TYR cc_start: 0.9241 (m-10) cc_final: 0.8933 (m-10) REVERT: B 362 ASP cc_start: 0.8636 (m-30) cc_final: 0.7812 (m-30) REVERT: B 375 LYS cc_start: 0.9235 (mmmm) cc_final: 0.8946 (mmtp) REVERT: B 390 GLN cc_start: 0.9147 (mm110) cc_final: 0.8899 (mm-40) REVERT: B 396 ASP cc_start: 0.7906 (p0) cc_final: 0.7336 (p0) REVERT: B 399 GLU cc_start: 0.9434 (mm-30) cc_final: 0.9191 (mm-30) REVERT: B 415 ASN cc_start: 0.9014 (t0) cc_final: 0.7708 (t0) REVERT: B 416 ILE cc_start: 0.9794 (mt) cc_final: 0.9424 (mt) REVERT: B 418 ASN cc_start: 0.9152 (m-40) cc_final: 0.8612 (m-40) REVERT: B 420 MET cc_start: 0.8996 (mmp) cc_final: 0.8602 (mmp) REVERT: B 467 ASN cc_start: 0.9336 (m-40) cc_final: 0.9004 (m110) REVERT: B 472 LEU cc_start: 0.9734 (mt) cc_final: 0.9525 (mt) REVERT: B 496 ASN cc_start: 0.9696 (t0) cc_final: 0.9218 (t0) REVERT: B 499 SER cc_start: 0.9920 (t) cc_final: 0.9691 (p) REVERT: B 500 ILE cc_start: 0.9773 (mt) cc_final: 0.9562 (mt) REVERT: B 501 GLN cc_start: 0.8988 (tp-100) cc_final: 0.8415 (tp-100) REVERT: B 515 ASP cc_start: 0.9171 (m-30) cc_final: 0.8779 (m-30) REVERT: B 570 MET cc_start: 0.9106 (tpp) cc_final: 0.8597 (tpp) REVERT: B 575 ARG cc_start: 0.8874 (mtm110) cc_final: 0.8425 (mtm-85) REVERT: B 588 GLN cc_start: 0.9442 (mm-40) cc_final: 0.8791 (mm-40) REVERT: B 601 ILE cc_start: 0.9356 (mt) cc_final: 0.8741 (mp) REVERT: B 613 TYR cc_start: 0.9217 (t80) cc_final: 0.8782 (t80) REVERT: B 615 MET cc_start: 0.8887 (mmp) cc_final: 0.8229 (mmp) REVERT: B 618 LEU cc_start: 0.8918 (mt) cc_final: 0.8557 (mt) REVERT: B 650 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7872 (mm-40) REVERT: B 667 LEU cc_start: 0.9515 (tt) cc_final: 0.9177 (tt) REVERT: C 21 PHE cc_start: 0.9013 (m-80) cc_final: 0.8330 (m-80) REVERT: C 137 MET cc_start: 0.5366 (mtp) cc_final: 0.4940 (mtt) REVERT: C 139 VAL cc_start: 0.8631 (p) cc_final: 0.8431 (m) REVERT: C 157 MET cc_start: 0.5138 (ptt) cc_final: 0.4917 (ptt) REVERT: C 204 TYR cc_start: 0.9598 (t80) cc_final: 0.9210 (t80) REVERT: D 185 MET cc_start: 0.7127 (mmm) cc_final: 0.6469 (mmm) REVERT: D 239 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6838 (pp20) REVERT: D 259 PHE cc_start: 0.7730 (t80) cc_final: 0.7264 (t80) outliers start: 2 outliers final: 0 residues processed: 673 average time/residue: 0.2826 time to fit residues: 277.7539 Evaluate side-chains 575 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 574 time to evaluate : 1.730 ------------------------------------------------------------------------------- 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: 0.7980 chunk 99 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 39 optimal weight: 0.0020 chunk 50 optimal weight: 2.9990 chunk 69 optimal weight: 0.0040 chunk 71 optimal weight: 8.9990 chunk 74 optimal weight: 10.0000 chunk 148 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.8802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN D 263 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.114447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.081297 restraints weight = 49513.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.084391 restraints weight = 29410.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.086370 restraints weight = 20647.601| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 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 = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7313 moved from start: 0.5967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16386 Z= 0.130 Angle : 0.594 8.270 22134 Z= 0.314 Chirality : 0.042 0.198 2360 Planarity : 0.004 0.048 2818 Dihedral : 10.959 177.402 2242 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.19), residues: 1932 helix: 1.05 (0.15), residues: 1139 sheet: -0.74 (0.40), residues: 140 loop : 0.36 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 9 HIS 0.010 0.001 HIS C 201 PHE 0.046 0.002 PHE A 129 TYR 0.030 0.002 TYR C 142 ARG 0.007 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03914 ( 869) hydrogen bonds : angle 4.93455 ( 2568) covalent geometry : bond 0.00284 (16386) covalent geometry : angle 0.59392 (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 682 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 682 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9514 (tptp) cc_final: 0.9295 (tppt) REVERT: A 18 ILE cc_start: 0.9508 (mm) cc_final: 0.9292 (mm) REVERT: A 87 LYS cc_start: 0.9238 (tptm) cc_final: 0.8922 (tptm) REVERT: A 107 LYS cc_start: 0.9419 (mttm) cc_final: 0.9119 (mmmt) REVERT: A 129 PHE cc_start: 0.9416 (m-80) cc_final: 0.9191 (m-80) REVERT: A 136 LYS cc_start: 0.9809 (mmtt) cc_final: 0.9523 (ttpt) REVERT: A 143 LEU cc_start: 0.9152 (tp) cc_final: 0.8930 (tp) REVERT: A 144 MET cc_start: 0.9084 (mtm) cc_final: 0.8605 (mtm) REVERT: A 176 ASN cc_start: 0.8704 (t0) cc_final: 0.8413 (t0) REVERT: A 191 GLN cc_start: 0.9132 (mm110) cc_final: 0.8749 (mp10) REVERT: A 194 LYS cc_start: 0.9394 (ttpt) cc_final: 0.9177 (ttpp) REVERT: A 202 ASN cc_start: 0.8991 (t0) cc_final: 0.8597 (t0) REVERT: A 204 SER cc_start: 0.8953 (p) cc_final: 0.8747 (p) REVERT: A 227 MET cc_start: 0.9236 (mtp) cc_final: 0.8872 (mtp) REVERT: A 252 ASN cc_start: 0.8741 (t0) cc_final: 0.8412 (t0) REVERT: A 254 PHE cc_start: 0.8294 (m-10) cc_final: 0.7882 (m-10) REVERT: A 286 ASP cc_start: 0.8976 (m-30) cc_final: 0.8435 (m-30) REVERT: A 313 HIS cc_start: 0.8671 (m90) cc_final: 0.7919 (m-70) REVERT: A 315 ASP cc_start: 0.8038 (p0) cc_final: 0.7659 (p0) REVERT: A 316 GLU cc_start: 0.8897 (pt0) cc_final: 0.8388 (pt0) REVERT: A 335 GLU cc_start: 0.9193 (tp30) cc_final: 0.8872 (tm-30) REVERT: A 337 ILE cc_start: 0.9599 (pt) cc_final: 0.9333 (pt) REVERT: A 362 ASP cc_start: 0.9160 (m-30) cc_final: 0.8693 (m-30) REVERT: A 366 LYS cc_start: 0.9462 (ptpp) cc_final: 0.9043 (pttp) REVERT: A 370 ASN cc_start: 0.9396 (m-40) cc_final: 0.9040 (m110) REVERT: A 375 LYS cc_start: 0.9454 (mttt) cc_final: 0.9139 (mttt) REVERT: A 390 GLN cc_start: 0.8228 (mm-40) cc_final: 0.8016 (mm-40) REVERT: A 396 ASP cc_start: 0.9127 (p0) cc_final: 0.8861 (p0) REVERT: A 418 ASN cc_start: 0.9089 (m110) cc_final: 0.8726 (m-40) REVERT: A 421 GLU cc_start: 0.9322 (tm-30) cc_final: 0.9103 (tm-30) REVERT: A 426 GLU cc_start: 0.9477 (tm-30) cc_final: 0.9212 (tm-30) REVERT: A 468 LEU cc_start: 0.9583 (tp) cc_final: 0.9318 (tp) REVERT: A 493 MET cc_start: 0.9387 (tmm) cc_final: 0.9130 (tmm) REVERT: A 500 ILE cc_start: 0.9849 (mt) cc_final: 0.9616 (mt) REVERT: A 506 ILE cc_start: 0.9798 (mm) cc_final: 0.9534 (mm) REVERT: A 515 ASP cc_start: 0.9517 (m-30) cc_final: 0.9269 (m-30) REVERT: A 571 TYR cc_start: 0.9091 (t80) cc_final: 0.8490 (t80) REVERT: A 575 ARG cc_start: 0.8945 (ptp90) cc_final: 0.8056 (ptp90) REVERT: A 599 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8493 (mt-10) REVERT: A 602 GLU cc_start: 0.8952 (pt0) cc_final: 0.8664 (pt0) REVERT: A 626 TYR cc_start: 0.9141 (m-80) cc_final: 0.8683 (m-10) REVERT: A 632 MET cc_start: 0.8839 (mtp) cc_final: 0.8219 (mtp) REVERT: A 645 GLN cc_start: 0.8884 (tp40) cc_final: 0.7488 (tp-100) REVERT: A 667 LEU cc_start: 0.9561 (tt) cc_final: 0.9205 (tt) REVERT: A 680 LYS cc_start: 0.8530 (mttt) cc_final: 0.7972 (mttt) REVERT: B 51 LEU cc_start: 0.9432 (tp) cc_final: 0.9018 (tp) REVERT: B 77 ILE cc_start: 0.9719 (mt) cc_final: 0.9343 (mt) REVERT: B 87 LYS cc_start: 0.9337 (tptp) cc_final: 0.9056 (tptp) REVERT: B 89 PHE cc_start: 0.9183 (t80) cc_final: 0.8779 (t80) REVERT: B 95 MET cc_start: 0.9395 (tpp) cc_final: 0.8200 (tpp) REVERT: B 99 LYS cc_start: 0.9497 (mmmt) cc_final: 0.8697 (mmmt) REVERT: B 106 LEU cc_start: 0.9235 (tt) cc_final: 0.8902 (tt) REVERT: B 144 MET cc_start: 0.9480 (mtm) cc_final: 0.8887 (mtm) REVERT: B 149 TYR cc_start: 0.9153 (t80) cc_final: 0.8557 (t80) REVERT: B 190 MET cc_start: 0.9682 (mtm) cc_final: 0.9251 (tpp) REVERT: B 211 GLU cc_start: 0.8946 (mm-30) cc_final: 0.8506 (mm-30) REVERT: B 257 ASP cc_start: 0.8365 (m-30) cc_final: 0.7985 (m-30) REVERT: B 263 ASP cc_start: 0.9426 (m-30) cc_final: 0.9219 (m-30) REVERT: B 286 ASP cc_start: 0.9006 (m-30) cc_final: 0.8376 (m-30) REVERT: B 287 LYS cc_start: 0.9509 (mmtt) cc_final: 0.9299 (mmmt) REVERT: B 322 MET cc_start: 0.8978 (tpt) cc_final: 0.8640 (tpt) REVERT: B 355 TYR cc_start: 0.9252 (m-10) cc_final: 0.8934 (m-10) REVERT: B 362 ASP cc_start: 0.8764 (m-30) cc_final: 0.7904 (m-30) REVERT: B 375 LYS cc_start: 0.9193 (mmmm) cc_final: 0.8917 (mmtt) REVERT: B 390 GLN cc_start: 0.9129 (mm110) cc_final: 0.8842 (mm-40) REVERT: B 396 ASP cc_start: 0.7910 (p0) cc_final: 0.7309 (p0) REVERT: B 399 GLU cc_start: 0.9468 (mm-30) cc_final: 0.9173 (mm-30) REVERT: B 415 ASN cc_start: 0.9084 (t0) cc_final: 0.7923 (t0) REVERT: B 416 ILE cc_start: 0.9800 (mt) cc_final: 0.9411 (mt) REVERT: B 418 ASN cc_start: 0.9288 (m-40) cc_final: 0.8777 (m-40) REVERT: B 420 MET cc_start: 0.8943 (mmp) cc_final: 0.8658 (mmp) REVERT: B 426 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8655 (tm-30) REVERT: B 467 ASN cc_start: 0.9385 (m-40) cc_final: 0.9123 (m-40) REVERT: B 472 LEU cc_start: 0.9729 (mt) cc_final: 0.9489 (mt) REVERT: B 480 GLU cc_start: 0.9490 (pm20) cc_final: 0.9243 (mt-10) REVERT: B 494 MET cc_start: 0.9368 (mtp) cc_final: 0.8857 (mtp) REVERT: B 496 ASN cc_start: 0.9723 (t0) cc_final: 0.9211 (t0) REVERT: B 499 SER cc_start: 0.9907 (t) cc_final: 0.9644 (p) REVERT: B 500 ILE cc_start: 0.9777 (mt) cc_final: 0.9547 (mt) REVERT: B 501 GLN cc_start: 0.8964 (tp-100) cc_final: 0.8393 (tp-100) REVERT: B 515 ASP cc_start: 0.9184 (m-30) cc_final: 0.8798 (m-30) REVERT: B 570 MET cc_start: 0.9189 (tpp) cc_final: 0.8535 (tpt) REVERT: B 575 ARG cc_start: 0.8742 (mtm110) cc_final: 0.8046 (mtm-85) REVERT: B 588 GLN cc_start: 0.9421 (mm-40) cc_final: 0.9043 (mm-40) REVERT: B 618 LEU cc_start: 0.9017 (mt) cc_final: 0.8557 (mt) REVERT: B 667 LEU cc_start: 0.9486 (tt) cc_final: 0.9164 (tt) REVERT: C 21 PHE cc_start: 0.9097 (m-80) cc_final: 0.8512 (m-80) REVERT: C 46 TYR cc_start: 0.8536 (m-80) cc_final: 0.8059 (m-80) REVERT: C 137 MET cc_start: 0.5490 (mtp) cc_final: 0.5196 (mtt) REVERT: C 204 TYR cc_start: 0.9551 (t80) cc_final: 0.9253 (t80) REVERT: C 231 LEU cc_start: 0.9394 (mt) cc_final: 0.9101 (mt) REVERT: D 185 MET cc_start: 0.7523 (mmm) cc_final: 0.6707 (mmm) REVERT: D 189 GLU cc_start: 0.9036 (tp30) cc_final: 0.8692 (pt0) REVERT: D 259 PHE cc_start: 0.7525 (t80) cc_final: 0.6915 (t80) REVERT: D 315 LEU cc_start: 0.9134 (tt) cc_final: 0.8811 (pt) outliers start: 0 outliers final: 0 residues processed: 682 average time/residue: 0.2969 time to fit residues: 298.5878 Evaluate side-chains 582 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 582 time to evaluate : 1.743 ------------------------------------------------------------------------------- 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: 2.9990 chunk 41 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 175 optimal weight: 0.9990 chunk 182 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 192 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.113337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.080483 restraints weight = 50972.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.083262 restraints weight = 30686.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.085309 restraints weight = 21172.560| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7410 moved from start: 0.6419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16386 Z= 0.154 Angle : 0.613 14.697 22134 Z= 0.320 Chirality : 0.042 0.149 2360 Planarity : 0.004 0.071 2818 Dihedral : 10.931 176.825 2242 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.06 % Allowed : 1.34 % Favored : 98.60 % 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: 1.02 (0.15), residues: 1130 sheet: -0.67 (0.42), residues: 142 loop : 0.12 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 623 HIS 0.006 0.001 HIS C 201 PHE 0.032 0.002 PHE A 129 TYR 0.031 0.002 TYR D 142 ARG 0.005 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.03865 ( 869) hydrogen bonds : angle 4.92905 ( 2568) covalent geometry : bond 0.00333 (16386) covalent geometry : angle 0.61328 (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 643 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 642 time to evaluate : 1.823 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 8 LYS cc_start: 0.9514 (tptp) cc_final: 0.9268 (tppt) REVERT: A 87 LYS cc_start: 0.9297 (tptm) cc_final: 0.9006 (tptm) REVERT: A 103 ASP cc_start: 0.9248 (m-30) cc_final: 0.8999 (m-30) REVERT: A 107 LYS cc_start: 0.9427 (mttm) cc_final: 0.9117 (mmmt) REVERT: A 129 PHE cc_start: 0.9486 (m-80) cc_final: 0.9139 (m-80) REVERT: A 136 LYS cc_start: 0.9795 (mmtt) cc_final: 0.9585 (mmmm) REVERT: A 144 MET cc_start: 0.9067 (mtm) cc_final: 0.8585 (mtm) REVERT: A 150 GLN cc_start: 0.9184 (tp40) cc_final: 0.8974 (tp40) REVERT: A 158 ASN cc_start: 0.9484 (m110) cc_final: 0.9275 (m-40) REVERT: A 161 ARG cc_start: 0.9101 (ttm110) cc_final: 0.8823 (ttm110) REVERT: A 191 GLN cc_start: 0.9224 (mm-40) cc_final: 0.8838 (mp10) REVERT: A 202 ASN cc_start: 0.9139 (t0) cc_final: 0.8888 (t0) REVERT: A 224 VAL cc_start: 0.8974 (p) cc_final: 0.8701 (t) REVERT: A 227 MET cc_start: 0.9323 (mtp) cc_final: 0.8832 (mtp) REVERT: A 235 ARG cc_start: 0.8237 (mtm110) cc_final: 0.8017 (mtm180) REVERT: A 239 GLN cc_start: 0.8660 (tt0) cc_final: 0.8279 (tp40) REVERT: A 252 ASN cc_start: 0.8808 (t0) cc_final: 0.8553 (t0) REVERT: A 254 PHE cc_start: 0.8524 (m-10) cc_final: 0.7868 (m-10) REVERT: A 286 ASP cc_start: 0.9017 (m-30) cc_final: 0.8461 (m-30) REVERT: A 335 GLU cc_start: 0.9222 (tp30) cc_final: 0.8925 (tm-30) REVERT: A 337 ILE cc_start: 0.9621 (pt) cc_final: 0.9334 (pt) REVERT: A 362 ASP cc_start: 0.9143 (m-30) cc_final: 0.8704 (m-30) REVERT: A 366 LYS cc_start: 0.9486 (ptpp) cc_final: 0.9082 (pttp) REVERT: A 370 ASN cc_start: 0.9400 (m-40) cc_final: 0.9028 (m110) REVERT: A 375 LYS cc_start: 0.9458 (mttt) cc_final: 0.9092 (mttt) REVERT: A 396 ASP cc_start: 0.9170 (p0) cc_final: 0.8936 (p0) REVERT: A 418 ASN cc_start: 0.9003 (m110) cc_final: 0.8577 (m-40) REVERT: A 468 LEU cc_start: 0.9514 (tp) cc_final: 0.9230 (tp) REVERT: A 493 MET cc_start: 0.9473 (tmm) cc_final: 0.9147 (tmm) REVERT: A 494 MET cc_start: 0.9511 (mtt) cc_final: 0.9196 (mtp) REVERT: A 500 ILE cc_start: 0.9867 (mt) cc_final: 0.9598 (mt) REVERT: A 515 ASP cc_start: 0.9513 (m-30) cc_final: 0.9262 (m-30) REVERT: A 575 ARG cc_start: 0.9054 (ptp90) cc_final: 0.8266 (ptp-110) REVERT: A 591 THR cc_start: 0.9167 (p) cc_final: 0.8839 (p) REVERT: A 599 GLU cc_start: 0.8761 (mt-10) cc_final: 0.8510 (mt-10) REVERT: A 602 GLU cc_start: 0.8905 (pt0) cc_final: 0.8443 (pt0) REVERT: A 626 TYR cc_start: 0.9240 (m-80) cc_final: 0.8839 (m-10) REVERT: A 632 MET cc_start: 0.8881 (mtp) cc_final: 0.8388 (mtp) REVERT: A 645 GLN cc_start: 0.9004 (tp40) cc_final: 0.7630 (tp-100) REVERT: A 653 SER cc_start: 0.9204 (p) cc_final: 0.8948 (p) REVERT: A 667 LEU cc_start: 0.9611 (tt) cc_final: 0.9292 (tt) REVERT: A 680 LYS cc_start: 0.8632 (mttt) cc_final: 0.8051 (mttt) REVERT: B 51 LEU cc_start: 0.9536 (tp) cc_final: 0.9086 (tp) REVERT: B 77 ILE cc_start: 0.9656 (mt) cc_final: 0.9284 (mt) REVERT: B 81 PHE cc_start: 0.9531 (m-80) cc_final: 0.9225 (m-80) REVERT: B 87 LYS cc_start: 0.9346 (tptp) cc_final: 0.9063 (tptp) REVERT: B 95 MET cc_start: 0.9456 (tpp) cc_final: 0.8181 (tpp) REVERT: B 99 LYS cc_start: 0.9541 (mmmt) cc_final: 0.8752 (mmmt) REVERT: B 114 ILE cc_start: 0.9611 (mt) cc_final: 0.9333 (pt) REVERT: B 144 MET cc_start: 0.9455 (mtm) cc_final: 0.8895 (mtm) REVERT: B 149 TYR cc_start: 0.9166 (t80) cc_final: 0.8543 (t80) REVERT: B 191 GLN cc_start: 0.9263 (mm-40) cc_final: 0.8790 (mm-40) REVERT: B 211 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8437 (mm-30) REVERT: B 235 ARG cc_start: 0.9047 (ttp-110) cc_final: 0.8808 (mtm110) REVERT: B 257 ASP cc_start: 0.8281 (m-30) cc_final: 0.8057 (m-30) REVERT: B 263 ASP cc_start: 0.9425 (m-30) cc_final: 0.9217 (m-30) REVERT: B 286 ASP cc_start: 0.9071 (m-30) cc_final: 0.8476 (m-30) REVERT: B 287 LYS cc_start: 0.9494 (mmtt) cc_final: 0.9243 (mmtp) REVERT: B 322 MET cc_start: 0.8985 (tpt) cc_final: 0.8620 (tpt) REVERT: B 333 LYS cc_start: 0.9193 (tptp) cc_final: 0.8948 (tptp) REVERT: B 335 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8025 (mt-10) REVERT: B 355 TYR cc_start: 0.9192 (m-10) cc_final: 0.8880 (m-10) REVERT: B 362 ASP cc_start: 0.8771 (m-30) cc_final: 0.7962 (m-30) REVERT: B 373 ILE cc_start: 0.9807 (mt) cc_final: 0.9087 (mt) REVERT: B 375 LYS cc_start: 0.9163 (mmmm) cc_final: 0.8882 (mmtt) REVERT: B 390 GLN cc_start: 0.9153 (mm110) cc_final: 0.8818 (mm-40) REVERT: B 396 ASP cc_start: 0.8119 (p0) cc_final: 0.7556 (p0) REVERT: B 399 GLU cc_start: 0.9448 (mm-30) cc_final: 0.9089 (mp0) REVERT: B 415 ASN cc_start: 0.9100 (t0) cc_final: 0.8102 (t0) REVERT: B 416 ILE cc_start: 0.9812 (mt) cc_final: 0.9428 (mt) REVERT: B 418 ASN cc_start: 0.9235 (m-40) cc_final: 0.8782 (m-40) REVERT: B 420 MET cc_start: 0.8990 (mmp) cc_final: 0.8781 (mmp) REVERT: B 426 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8732 (tm-30) REVERT: B 472 LEU cc_start: 0.9732 (mt) cc_final: 0.9523 (mt) REVERT: B 480 GLU cc_start: 0.9519 (pm20) cc_final: 0.9201 (mt-10) REVERT: B 494 MET cc_start: 0.9386 (mtp) cc_final: 0.9015 (mtp) REVERT: B 496 ASN cc_start: 0.9711 (t0) cc_final: 0.8489 (t0) REVERT: B 499 SER cc_start: 0.9896 (t) cc_final: 0.9584 (p) REVERT: B 500 ILE cc_start: 0.9791 (mt) cc_final: 0.9479 (mt) REVERT: B 501 GLN cc_start: 0.8880 (tp-100) cc_final: 0.8332 (tp-100) REVERT: B 515 ASP cc_start: 0.9194 (m-30) cc_final: 0.8817 (m-30) REVERT: B 516 GLN cc_start: 0.9325 (tp-100) cc_final: 0.9075 (tt0) REVERT: B 527 TYR cc_start: 0.8764 (t80) cc_final: 0.8526 (t80) REVERT: B 570 MET cc_start: 0.9203 (tpp) cc_final: 0.8552 (tpt) REVERT: B 575 ARG cc_start: 0.8734 (mtm110) cc_final: 0.7228 (mtm180) REVERT: B 588 GLN cc_start: 0.9415 (mm-40) cc_final: 0.8905 (mm-40) REVERT: B 601 ILE cc_start: 0.9484 (mp) cc_final: 0.9136 (mp) REVERT: B 618 LEU cc_start: 0.8921 (mt) cc_final: 0.8541 (mt) REVERT: B 667 LEU cc_start: 0.9523 (tt) cc_final: 0.9245 (tt) REVERT: C 204 TYR cc_start: 0.9597 (t80) cc_final: 0.9370 (t80) REVERT: D 46 TYR cc_start: 0.8953 (m-80) cc_final: 0.8729 (m-10) REVERT: D 179 TYR cc_start: 0.9209 (t80) cc_final: 0.8966 (t80) REVERT: D 185 MET cc_start: 0.7616 (mmm) cc_final: 0.6770 (mmm) REVERT: D 189 GLU cc_start: 0.9049 (tp30) cc_final: 0.8650 (pt0) REVERT: D 201 HIS cc_start: 0.8963 (m170) cc_final: 0.8634 (m170) outliers start: 1 outliers final: 0 residues processed: 642 average time/residue: 0.2804 time to fit residues: 263.0443 Evaluate side-chains 561 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 561 time to evaluate : 1.689 ------------------------------------------------------------------------------- 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: 0.9980 chunk 62 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 156 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 115 optimal weight: 8.9990 chunk 39 optimal weight: 6.9990 chunk 169 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 177 optimal weight: 20.0000 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN A 313 HIS ** A 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 GLN D 80 HIS D 132 GLN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.103650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.072997 restraints weight = 54196.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.075406 restraints weight = 33200.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.077259 restraints weight = 23322.153| |-----------------------------------------------------------------------------| r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2990 r_free = 0.2990 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2990 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.7246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 16386 Z= 0.294 Angle : 0.739 11.300 22134 Z= 0.391 Chirality : 0.044 0.167 2360 Planarity : 0.005 0.057 2818 Dihedral : 11.452 174.579 2242 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 23.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.12 % Allowed : 2.56 % Favored : 97.32 % 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: 0.29 (0.18), residues: 1932 helix: 0.61 (0.15), residues: 1139 sheet: -0.97 (0.43), residues: 138 loop : -0.03 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 558 HIS 0.009 0.002 HIS B 372 PHE 0.029 0.003 PHE D 109 TYR 0.033 0.003 TYR B 118 ARG 0.013 0.001 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.04287 ( 869) hydrogen bonds : angle 5.21199 ( 2568) covalent geometry : bond 0.00595 (16386) covalent geometry : angle 0.73911 (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 635 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 633 time to evaluate : 1.734 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: A 8 LYS cc_start: 0.9480 (tptp) cc_final: 0.9225 (tppt) REVERT: A 65 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8572 (mm-30) REVERT: A 99 LYS cc_start: 0.9628 (mmtp) cc_final: 0.9219 (mmmm) REVERT: A 104 TYR cc_start: 0.8872 (m-80) cc_final: 0.8247 (m-80) REVERT: A 107 LYS cc_start: 0.9479 (mttm) cc_final: 0.9060 (tptt) REVERT: A 144 MET cc_start: 0.9024 (mtm) cc_final: 0.8753 (mtm) REVERT: A 168 VAL cc_start: 0.9186 (m) cc_final: 0.8981 (p) REVERT: A 227 MET cc_start: 0.9256 (mtp) cc_final: 0.8879 (mtp) REVERT: A 230 LEU cc_start: 0.9591 (mt) cc_final: 0.9379 (mt) REVERT: A 235 ARG cc_start: 0.8220 (mtm110) cc_final: 0.7940 (mtm180) REVERT: A 239 GLN cc_start: 0.8637 (tt0) cc_final: 0.8350 (tt0) REVERT: A 272 ASP cc_start: 0.9024 (p0) cc_final: 0.8710 (p0) REVERT: A 286 ASP cc_start: 0.8998 (m-30) cc_final: 0.8442 (m-30) REVERT: A 317 MET cc_start: 0.8458 (mtm) cc_final: 0.8241 (mpp) REVERT: A 322 MET cc_start: 0.9129 (mmp) cc_final: 0.8865 (mmm) REVERT: A 335 GLU cc_start: 0.9224 (tp30) cc_final: 0.9009 (tm-30) REVERT: A 337 ILE cc_start: 0.9638 (pt) cc_final: 0.9322 (pt) REVERT: A 349 LEU cc_start: 0.9503 (mt) cc_final: 0.9014 (mt) REVERT: A 350 ARG cc_start: 0.8506 (mtp85) cc_final: 0.7814 (mtp85) REVERT: A 362 ASP cc_start: 0.9163 (m-30) cc_final: 0.8530 (m-30) REVERT: A 375 LYS cc_start: 0.9412 (mttt) cc_final: 0.9019 (mttt) REVERT: A 405 LEU cc_start: 0.9194 (mt) cc_final: 0.8680 (mt) REVERT: A 414 LEU cc_start: 0.9550 (mt) cc_final: 0.9266 (mt) REVERT: A 426 GLU cc_start: 0.9461 (tm-30) cc_final: 0.9229 (tm-30) REVERT: A 468 LEU cc_start: 0.9524 (tp) cc_final: 0.9281 (tp) REVERT: A 493 MET cc_start: 0.9312 (tmm) cc_final: 0.8909 (tmm) REVERT: A 500 ILE cc_start: 0.9887 (mt) cc_final: 0.9598 (mt) REVERT: A 515 ASP cc_start: 0.9461 (m-30) cc_final: 0.9179 (m-30) REVERT: A 575 ARG cc_start: 0.9108 (ptp90) cc_final: 0.8390 (ptp-110) REVERT: A 583 SER cc_start: 0.9476 (t) cc_final: 0.9245 (t) REVERT: A 599 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8505 (mt-10) REVERT: A 602 GLU cc_start: 0.8851 (pt0) cc_final: 0.8375 (pt0) REVERT: A 632 MET cc_start: 0.9025 (mtp) cc_final: 0.8581 (mtp) REVERT: A 653 SER cc_start: 0.9219 (p) cc_final: 0.8990 (p) REVERT: A 677 ARG cc_start: 0.9312 (mmm160) cc_final: 0.9099 (mmm160) REVERT: B 51 LEU cc_start: 0.9552 (tp) cc_final: 0.9239 (tp) REVERT: B 77 ILE cc_start: 0.9644 (mt) cc_final: 0.9264 (mt) REVERT: B 81 PHE cc_start: 0.9560 (m-80) cc_final: 0.9255 (m-80) REVERT: B 87 LYS cc_start: 0.9349 (tptp) cc_final: 0.9021 (tptp) REVERT: B 95 MET cc_start: 0.9401 (tpp) cc_final: 0.8336 (tpp) REVERT: B 99 LYS cc_start: 0.9597 (mmmt) cc_final: 0.8825 (mmmt) REVERT: B 144 MET cc_start: 0.9478 (mtm) cc_final: 0.9053 (mtm) REVERT: B 161 ARG cc_start: 0.8780 (mtt-85) cc_final: 0.8512 (mtt180) REVERT: B 211 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8575 (mm-30) REVERT: B 235 ARG cc_start: 0.9119 (ttp-110) cc_final: 0.8872 (ttm110) REVERT: B 252 ASN cc_start: 0.8951 (t0) cc_final: 0.8690 (t0) REVERT: B 257 ASP cc_start: 0.8253 (m-30) cc_final: 0.7996 (m-30) REVERT: B 263 ASP cc_start: 0.9418 (m-30) cc_final: 0.9218 (m-30) REVERT: B 286 ASP cc_start: 0.9203 (m-30) cc_final: 0.8768 (m-30) REVERT: B 322 MET cc_start: 0.8779 (tpt) cc_final: 0.8571 (tpt) REVERT: B 362 ASP cc_start: 0.8919 (m-30) cc_final: 0.8093 (m-30) REVERT: B 373 ILE cc_start: 0.9816 (mt) cc_final: 0.9052 (mt) REVERT: B 390 GLN cc_start: 0.9288 (mm110) cc_final: 0.9006 (mm-40) REVERT: B 396 ASP cc_start: 0.8295 (p0) cc_final: 0.7758 (p0) REVERT: B 399 GLU cc_start: 0.9463 (mm-30) cc_final: 0.9127 (mp0) REVERT: B 415 ASN cc_start: 0.8959 (t0) cc_final: 0.8224 (t0) REVERT: B 416 ILE cc_start: 0.9833 (mt) cc_final: 0.9522 (mt) REVERT: B 418 ASN cc_start: 0.9185 (m-40) cc_final: 0.8815 (m-40) REVERT: B 426 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8671 (tm-30) REVERT: B 472 LEU cc_start: 0.9775 (mt) cc_final: 0.9560 (mt) REVERT: B 496 ASN cc_start: 0.9620 (t0) cc_final: 0.8195 (t0) REVERT: B 499 SER cc_start: 0.9845 (t) cc_final: 0.9579 (p) REVERT: B 500 ILE cc_start: 0.9771 (mt) cc_final: 0.9485 (mt) REVERT: B 501 GLN cc_start: 0.8908 (tp-100) cc_final: 0.8335 (tp-100) REVERT: B 515 ASP cc_start: 0.9169 (m-30) cc_final: 0.8771 (m-30) REVERT: B 570 MET cc_start: 0.9227 (tpp) cc_final: 0.8635 (tpt) REVERT: B 575 ARG cc_start: 0.8849 (mtm110) cc_final: 0.7275 (mtm180) REVERT: B 618 LEU cc_start: 0.8952 (mt) cc_final: 0.8609 (mt) REVERT: B 645 GLN cc_start: 0.8896 (tp-100) cc_final: 0.8656 (tp-100) REVERT: B 667 LEU cc_start: 0.9544 (tt) cc_final: 0.9314 (tt) REVERT: C 46 TYR cc_start: 0.8455 (m-80) cc_final: 0.8243 (m-80) REVERT: C 185 MET cc_start: 0.8843 (mpp) cc_final: 0.8641 (mpp) REVERT: C 204 TYR cc_start: 0.9692 (t80) cc_final: 0.9325 (t80) REVERT: D 46 TYR cc_start: 0.9062 (m-80) cc_final: 0.8825 (m-10) REVERT: D 179 TYR cc_start: 0.9135 (t80) cc_final: 0.8803 (t80) REVERT: D 185 MET cc_start: 0.7873 (mmm) cc_final: 0.6851 (mmm) REVERT: D 189 GLU cc_start: 0.9122 (tp30) cc_final: 0.8758 (pt0) REVERT: D 239 GLU cc_start: 0.7462 (OUTLIER) cc_final: 0.6673 (pt0) outliers start: 2 outliers final: 1 residues processed: 635 average time/residue: 0.2724 time to fit residues: 253.0539 Evaluate side-chains 550 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 548 time to evaluate : 1.699 ------------------------------------------------------------------------------- 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: 0.9990 chunk 85 optimal weight: 6.9990 chunk 161 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 146 optimal weight: 0.7980 chunk 184 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 GLN B 645 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 91 ASN D 270 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.109612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.078824 restraints weight = 53188.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.081540 restraints weight = 31510.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.083514 restraints weight = 21613.038| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3120 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.7431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16386 Z= 0.137 Angle : 0.627 9.055 22134 Z= 0.332 Chirality : 0.043 0.185 2360 Planarity : 0.004 0.058 2818 Dihedral : 11.121 174.318 2242 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 17.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.06 % Allowed : 1.05 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.19), residues: 1932 helix: 0.81 (0.15), residues: 1142 sheet: -0.85 (0.44), residues: 144 loop : 0.05 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 9 HIS 0.006 0.001 HIS C 201 PHE 0.027 0.002 PHE A 129 TYR 0.030 0.002 TYR C 46 ARG 0.011 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 869) hydrogen bonds : angle 5.00618 ( 2568) covalent geometry : bond 0.00301 (16386) covalent geometry : angle 0.62660 (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 646 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 645 time to evaluate : 1.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9521 (tptp) cc_final: 0.9223 (tppt) REVERT: A 18 ILE cc_start: 0.9628 (mt) cc_final: 0.9417 (mm) REVERT: A 65 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8448 (mm-30) REVERT: A 95 MET cc_start: 0.9350 (mmp) cc_final: 0.8376 (mmm) REVERT: A 99 LYS cc_start: 0.9550 (mmtp) cc_final: 0.9029 (mmtp) REVERT: A 103 ASP cc_start: 0.9387 (m-30) cc_final: 0.9160 (m-30) REVERT: A 104 TYR cc_start: 0.8749 (m-80) cc_final: 0.8366 (m-80) REVERT: A 107 LYS cc_start: 0.9477 (mttm) cc_final: 0.9171 (mmmt) REVERT: A 129 PHE cc_start: 0.9538 (m-80) cc_final: 0.9174 (m-80) REVERT: A 136 LYS cc_start: 0.9814 (mmtt) cc_final: 0.9595 (mmmm) REVERT: A 144 MET cc_start: 0.8988 (mtm) cc_final: 0.8501 (mtm) REVERT: A 161 ARG cc_start: 0.9161 (ttm110) cc_final: 0.8854 (ttm110) REVERT: A 168 VAL cc_start: 0.9233 (m) cc_final: 0.8973 (p) REVERT: A 180 ASN cc_start: 0.8880 (m110) cc_final: 0.8516 (m-40) REVERT: A 191 GLN cc_start: 0.9269 (mm-40) cc_final: 0.9047 (mp10) REVERT: A 205 LYS cc_start: 0.8785 (mmmm) cc_final: 0.8170 (mmmm) REVERT: A 227 MET cc_start: 0.9302 (mtp) cc_final: 0.8767 (mtp) REVERT: A 235 ARG cc_start: 0.8328 (mtm110) cc_final: 0.7842 (mtm180) REVERT: A 252 ASN cc_start: 0.8926 (t0) cc_final: 0.8685 (t0) REVERT: A 286 ASP cc_start: 0.9039 (m-30) cc_final: 0.8511 (m-30) REVERT: A 317 MET cc_start: 0.8677 (mtm) cc_final: 0.8381 (mpp) REVERT: A 335 GLU cc_start: 0.9216 (tp30) cc_final: 0.8992 (tm-30) REVERT: A 337 ILE cc_start: 0.9645 (pt) cc_final: 0.9347 (pt) REVERT: A 362 ASP cc_start: 0.9178 (m-30) cc_final: 0.8733 (m-30) REVERT: A 366 LYS cc_start: 0.9595 (ptpp) cc_final: 0.9149 (pttp) REVERT: A 370 ASN cc_start: 0.9377 (m110) cc_final: 0.9006 (m110) REVERT: A 375 LYS cc_start: 0.9487 (mttt) cc_final: 0.9109 (mttt) REVERT: A 385 VAL cc_start: 0.9695 (t) cc_final: 0.9418 (m) REVERT: A 402 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8761 (tm-30) REVERT: A 414 LEU cc_start: 0.9585 (mt) cc_final: 0.9318 (mt) REVERT: A 421 GLU cc_start: 0.9261 (tm-30) cc_final: 0.9032 (tm-30) REVERT: A 426 GLU cc_start: 0.9353 (tm-30) cc_final: 0.9119 (tm-30) REVERT: A 468 LEU cc_start: 0.9510 (tp) cc_final: 0.9273 (tp) REVERT: A 493 MET cc_start: 0.9237 (tmm) cc_final: 0.8912 (tmm) REVERT: A 494 MET cc_start: 0.9516 (mtt) cc_final: 0.9065 (mtp) REVERT: A 506 ILE cc_start: 0.9727 (mm) cc_final: 0.9484 (mm) REVERT: A 515 ASP cc_start: 0.9468 (m-30) cc_final: 0.9184 (m-30) REVERT: A 571 TYR cc_start: 0.8991 (t80) cc_final: 0.8479 (t80) REVERT: A 575 ARG cc_start: 0.8984 (ptp90) cc_final: 0.8090 (ptp-110) REVERT: A 598 MET cc_start: 0.8768 (ttt) cc_final: 0.8165 (mtp) REVERT: A 602 GLU cc_start: 0.8950 (pt0) cc_final: 0.8628 (pt0) REVERT: A 626 TYR cc_start: 0.9252 (m-80) cc_final: 0.9000 (m-10) REVERT: A 632 MET cc_start: 0.8764 (mtp) cc_final: 0.8490 (mtp) REVERT: A 653 SER cc_start: 0.8948 (p) cc_final: 0.8711 (p) REVERT: A 667 LEU cc_start: 0.9617 (tt) cc_final: 0.9393 (tt) REVERT: B 51 LEU cc_start: 0.9505 (tp) cc_final: 0.9133 (tp) REVERT: B 77 ILE cc_start: 0.9641 (mt) cc_final: 0.9249 (mt) REVERT: B 81 PHE cc_start: 0.9408 (m-80) cc_final: 0.9201 (m-80) REVERT: B 87 LYS cc_start: 0.9385 (tptp) cc_final: 0.9072 (tptp) REVERT: B 95 MET cc_start: 0.9314 (tpp) cc_final: 0.7994 (tpp) REVERT: B 99 LYS cc_start: 0.9617 (mmmt) cc_final: 0.8710 (mmmt) REVERT: B 114 ILE cc_start: 0.9530 (mt) cc_final: 0.9241 (pt) REVERT: B 149 TYR cc_start: 0.9408 (t80) cc_final: 0.8828 (t80) REVERT: B 161 ARG cc_start: 0.8675 (mtt-85) cc_final: 0.8270 (mtt-85) REVERT: B 191 GLN cc_start: 0.9169 (mm-40) cc_final: 0.8933 (mt0) REVERT: B 202 ASN cc_start: 0.5950 (p0) cc_final: 0.5620 (p0) REVERT: B 211 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8491 (mm-30) REVERT: B 215 ASP cc_start: 0.9429 (t0) cc_final: 0.9165 (t0) REVERT: B 218 ASN cc_start: 0.9346 (OUTLIER) cc_final: 0.9107 (t0) REVERT: B 235 ARG cc_start: 0.9139 (ttp-110) cc_final: 0.8884 (ttm110) REVERT: B 257 ASP cc_start: 0.8335 (m-30) cc_final: 0.7982 (m-30) REVERT: B 286 ASP cc_start: 0.9071 (m-30) cc_final: 0.8359 (m-30) REVERT: B 319 MET cc_start: 0.9049 (tpt) cc_final: 0.8755 (tpp) REVERT: B 322 MET cc_start: 0.8822 (tpt) cc_final: 0.8395 (ttt) REVERT: B 326 PHE cc_start: 0.9410 (m-80) cc_final: 0.8776 (m-80) REVERT: B 333 LYS cc_start: 0.9188 (tptp) cc_final: 0.8923 (tptp) REVERT: B 335 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8204 (mt-10) REVERT: B 362 ASP cc_start: 0.8881 (m-30) cc_final: 0.8172 (m-30) REVERT: B 373 ILE cc_start: 0.9666 (mt) cc_final: 0.9099 (mt) REVERT: B 375 LYS cc_start: 0.9143 (mmmm) cc_final: 0.8884 (mmtt) REVERT: B 390 GLN cc_start: 0.9186 (mm110) cc_final: 0.8844 (mm-40) REVERT: B 396 ASP cc_start: 0.8134 (p0) cc_final: 0.7621 (p0) REVERT: B 399 GLU cc_start: 0.9449 (mm-30) cc_final: 0.9092 (mp0) REVERT: B 415 ASN cc_start: 0.9265 (t0) cc_final: 0.8319 (t0) REVERT: B 416 ILE cc_start: 0.9829 (mt) cc_final: 0.9582 (mt) REVERT: B 418 ASN cc_start: 0.9366 (m-40) cc_final: 0.8958 (m-40) REVERT: B 420 MET cc_start: 0.9208 (mmp) cc_final: 0.8920 (mmm) REVERT: B 427 LYS cc_start: 0.9685 (ptpp) cc_final: 0.9307 (ptpp) REVERT: B 466 MET cc_start: 0.8821 (ptp) cc_final: 0.8329 (ptp) REVERT: B 467 ASN cc_start: 0.9146 (m-40) cc_final: 0.8254 (m-40) REVERT: B 472 LEU cc_start: 0.9732 (mt) cc_final: 0.9526 (mt) REVERT: B 480 GLU cc_start: 0.9482 (pm20) cc_final: 0.9055 (mp0) REVERT: B 496 ASN cc_start: 0.9639 (t0) cc_final: 0.8663 (t0) REVERT: B 499 SER cc_start: 0.9877 (t) cc_final: 0.9574 (p) REVERT: B 500 ILE cc_start: 0.9776 (mt) cc_final: 0.9540 (mt) REVERT: B 501 GLN cc_start: 0.8836 (tp-100) cc_final: 0.8320 (tp-100) REVERT: B 515 ASP cc_start: 0.9149 (m-30) cc_final: 0.8759 (m-30) REVERT: B 516 GLN cc_start: 0.9023 (tt0) cc_final: 0.8717 (tt0) REVERT: B 570 MET cc_start: 0.9256 (tpp) cc_final: 0.8612 (tpt) REVERT: B 575 ARG cc_start: 0.8792 (mtm110) cc_final: 0.7402 (mtm180) REVERT: B 613 TYR cc_start: 0.9079 (t80) cc_final: 0.8785 (t80) REVERT: B 618 LEU cc_start: 0.9056 (mt) cc_final: 0.8832 (mt) REVERT: B 631 ASP cc_start: 0.9550 (m-30) cc_final: 0.9300 (m-30) REVERT: B 667 LEU cc_start: 0.9577 (tt) cc_final: 0.9315 (tt) REVERT: C 179 TYR cc_start: 0.9515 (t80) cc_final: 0.9308 (t80) REVERT: C 185 MET cc_start: 0.8830 (mpp) cc_final: 0.8598 (mpp) REVERT: C 204 TYR cc_start: 0.9641 (t80) cc_final: 0.9401 (t80) REVERT: D 33 GLU cc_start: 0.9274 (mp0) cc_final: 0.8967 (mp0) REVERT: D 46 TYR cc_start: 0.9037 (m-80) cc_final: 0.8824 (m-10) REVERT: D 74 MET cc_start: 0.6688 (ttp) cc_final: 0.6025 (tmm) REVERT: D 179 TYR cc_start: 0.9098 (t80) cc_final: 0.8745 (t80) REVERT: D 185 MET cc_start: 0.7820 (mmm) cc_final: 0.6897 (mmm) REVERT: D 189 GLU cc_start: 0.9078 (tp30) cc_final: 0.8781 (pt0) REVERT: D 318 ASP cc_start: 0.9347 (m-30) cc_final: 0.9144 (m-30) outliers start: 1 outliers final: 0 residues processed: 646 average time/residue: 0.2799 time to fit residues: 261.9835 Evaluate side-chains 561 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 560 time to evaluate : 1.876 ------------------------------------------------------------------------------- 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: 0.9980 chunk 30 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 159 optimal weight: 20.0000 chunk 72 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 183 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 180 optimal weight: 0.9980 chunk 108 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN A 676 HIS ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 234 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.112124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.080839 restraints weight = 52399.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.083795 restraints weight = 31131.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.085675 restraints weight = 21548.847| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3151 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.7735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16386 Z= 0.135 Angle : 0.643 8.483 22134 Z= 0.340 Chirality : 0.043 0.169 2360 Planarity : 0.004 0.071 2818 Dihedral : 10.899 172.789 2242 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 16.18 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: 0.51 (0.19), residues: 1932 helix: 0.78 (0.15), residues: 1130 sheet: -0.92 (0.43), residues: 140 loop : 0.10 (0.24), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 558 HIS 0.006 0.001 HIS B 368 PHE 0.025 0.002 PHE A 94 TYR 0.035 0.002 TYR D 142 ARG 0.011 0.001 ARG B 665 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 869) hydrogen bonds : angle 4.91951 ( 2568) covalent geometry : bond 0.00296 (16386) covalent geometry : angle 0.64258 (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 624 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 624 time to evaluate : 1.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8513 (mm-30) REVERT: A 103 ASP cc_start: 0.9385 (m-30) cc_final: 0.9067 (m-30) REVERT: A 104 TYR cc_start: 0.8788 (m-80) cc_final: 0.8362 (m-80) REVERT: A 107 LYS cc_start: 0.9471 (mttm) cc_final: 0.9184 (mmmt) REVERT: A 120 ASP cc_start: 0.9300 (m-30) cc_final: 0.9089 (m-30) REVERT: A 129 PHE cc_start: 0.9532 (m-80) cc_final: 0.9128 (m-80) REVERT: A 136 LYS cc_start: 0.9812 (mmtt) cc_final: 0.9522 (ttpt) REVERT: A 144 MET cc_start: 0.8973 (mtm) cc_final: 0.8495 (mtm) REVERT: A 158 ASN cc_start: 0.9535 (m110) cc_final: 0.9023 (p0) REVERT: A 204 SER cc_start: 0.9237 (p) cc_final: 0.8906 (p) REVERT: A 227 MET cc_start: 0.9120 (mtp) cc_final: 0.8763 (mtp) REVERT: A 252 ASN cc_start: 0.8753 (t0) cc_final: 0.8510 (t0) REVERT: A 254 PHE cc_start: 0.8479 (m-10) cc_final: 0.8099 (m-10) REVERT: A 266 LYS cc_start: 0.9301 (ptmm) cc_final: 0.9002 (pptt) REVERT: A 286 ASP cc_start: 0.9257 (m-30) cc_final: 0.8574 (m-30) REVERT: A 314 MET cc_start: 0.8917 (ppp) cc_final: 0.8614 (ppp) REVERT: A 317 MET cc_start: 0.8599 (mtm) cc_final: 0.8351 (mpp) REVERT: A 322 MET cc_start: 0.9143 (mmp) cc_final: 0.8936 (mmm) REVERT: A 335 GLU cc_start: 0.9209 (tp30) cc_final: 0.8963 (tm-30) REVERT: A 337 ILE cc_start: 0.9656 (pt) cc_final: 0.9369 (pt) REVERT: A 362 ASP cc_start: 0.9074 (m-30) cc_final: 0.8688 (m-30) REVERT: A 366 LYS cc_start: 0.9567 (ptpp) cc_final: 0.9130 (pttp) REVERT: A 370 ASN cc_start: 0.9417 (m110) cc_final: 0.9064 (m110) REVERT: A 375 LYS cc_start: 0.9472 (mttt) cc_final: 0.9040 (mttt) REVERT: A 385 VAL cc_start: 0.9674 (t) cc_final: 0.9458 (m) REVERT: A 414 LEU cc_start: 0.9527 (mt) cc_final: 0.9271 (mt) REVERT: A 421 GLU cc_start: 0.9288 (tm-30) cc_final: 0.9008 (tm-30) REVERT: A 447 ASN cc_start: 0.9263 (m-40) cc_final: 0.8882 (m110) REVERT: A 468 LEU cc_start: 0.9511 (tp) cc_final: 0.9210 (tp) REVERT: A 493 MET cc_start: 0.9292 (tmm) cc_final: 0.8931 (tmm) REVERT: A 494 MET cc_start: 0.9482 (mtt) cc_final: 0.9193 (mmt) REVERT: A 515 ASP cc_start: 0.9472 (m-30) cc_final: 0.9196 (m-30) REVERT: A 562 LYS cc_start: 0.9795 (ttmt) cc_final: 0.9498 (tttt) REVERT: A 575 ARG cc_start: 0.9071 (ptp90) cc_final: 0.8105 (ptp-110) REVERT: A 585 SER cc_start: 0.9615 (p) cc_final: 0.9320 (t) REVERT: A 591 THR cc_start: 0.9046 (p) cc_final: 0.8744 (p) REVERT: A 598 MET cc_start: 0.8522 (ttt) cc_final: 0.8074 (tpp) REVERT: A 601 ILE cc_start: 0.9545 (tt) cc_final: 0.9337 (tt) REVERT: A 615 MET cc_start: 0.8846 (mmp) cc_final: 0.8180 (mmp) REVERT: A 626 TYR cc_start: 0.9245 (m-80) cc_final: 0.9022 (m-10) REVERT: A 632 MET cc_start: 0.9102 (mtp) cc_final: 0.8749 (mtp) REVERT: A 647 HIS cc_start: 0.8709 (m-70) cc_final: 0.8440 (m-70) REVERT: A 653 SER cc_start: 0.9059 (p) cc_final: 0.8816 (p) REVERT: B 51 LEU cc_start: 0.9478 (tp) cc_final: 0.9104 (tp) REVERT: B 77 ILE cc_start: 0.9641 (mt) cc_final: 0.9183 (mt) REVERT: B 87 LYS cc_start: 0.9378 (tptp) cc_final: 0.9124 (tptp) REVERT: B 95 MET cc_start: 0.9312 (tpp) cc_final: 0.7995 (tpp) REVERT: B 99 LYS cc_start: 0.9609 (mmmt) cc_final: 0.8711 (mmmt) REVERT: B 114 ILE cc_start: 0.9554 (mt) cc_final: 0.9224 (pt) REVERT: B 143 LEU cc_start: 0.9676 (tp) cc_final: 0.9334 (tp) REVERT: B 144 MET cc_start: 0.9388 (mtm) cc_final: 0.8928 (mtm) REVERT: B 149 TYR cc_start: 0.9437 (t80) cc_final: 0.8986 (t80) REVERT: B 161 ARG cc_start: 0.8692 (mtt-85) cc_final: 0.8324 (mtt-85) REVERT: B 191 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8752 (mt0) REVERT: B 211 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8414 (mm-30) REVERT: B 235 ARG cc_start: 0.9158 (ttp-110) cc_final: 0.8924 (ttm110) REVERT: B 252 ASN cc_start: 0.8853 (t0) cc_final: 0.8647 (t0) REVERT: B 263 ASP cc_start: 0.9315 (m-30) cc_final: 0.8997 (m-30) REVERT: B 317 MET cc_start: 0.8199 (pmm) cc_final: 0.7707 (pmm) REVERT: B 322 MET cc_start: 0.8794 (tpt) cc_final: 0.8495 (ttt) REVERT: B 333 LYS cc_start: 0.9200 (tptp) cc_final: 0.8948 (tptp) REVERT: B 335 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8173 (mt-10) REVERT: B 362 ASP cc_start: 0.8926 (m-30) cc_final: 0.8470 (m-30) REVERT: B 373 ILE cc_start: 0.9612 (mt) cc_final: 0.9106 (mt) REVERT: B 375 LYS cc_start: 0.9089 (mmmm) cc_final: 0.8882 (mmmm) REVERT: B 387 GLN cc_start: 0.8860 (mt0) cc_final: 0.8616 (mt0) REVERT: B 390 GLN cc_start: 0.9159 (mm110) cc_final: 0.8843 (mm-40) REVERT: B 396 ASP cc_start: 0.8094 (p0) cc_final: 0.7491 (p0) REVERT: B 399 GLU cc_start: 0.9458 (mm-30) cc_final: 0.9110 (mp0) REVERT: B 415 ASN cc_start: 0.9225 (t0) cc_final: 0.8525 (t0) REVERT: B 416 ILE cc_start: 0.9822 (mt) cc_final: 0.9544 (mt) REVERT: B 418 ASN cc_start: 0.9400 (m-40) cc_final: 0.8916 (m-40) REVERT: B 420 MET cc_start: 0.9229 (mmp) cc_final: 0.8903 (mmm) REVERT: B 426 GLU cc_start: 0.9314 (pm20) cc_final: 0.8885 (pm20) REVERT: B 427 LYS cc_start: 0.9718 (ptpp) cc_final: 0.9263 (ptpp) REVERT: B 466 MET cc_start: 0.8952 (ptp) cc_final: 0.8375 (ptp) REVERT: B 467 ASN cc_start: 0.9269 (m-40) cc_final: 0.8342 (m-40) REVERT: B 496 ASN cc_start: 0.9634 (t0) cc_final: 0.9081 (t0) REVERT: B 499 SER cc_start: 0.9838 (t) cc_final: 0.9599 (p) REVERT: B 500 ILE cc_start: 0.9785 (mt) cc_final: 0.9284 (mt) REVERT: B 501 GLN cc_start: 0.8886 (tp-100) cc_final: 0.8429 (tp-100) REVERT: B 515 ASP cc_start: 0.9209 (m-30) cc_final: 0.8768 (m-30) REVERT: B 516 GLN cc_start: 0.8976 (tt0) cc_final: 0.8697 (tt0) REVERT: B 570 MET cc_start: 0.9248 (tpp) cc_final: 0.8464 (tpt) REVERT: B 575 ARG cc_start: 0.8516 (mtm110) cc_final: 0.7911 (mpp80) REVERT: B 613 TYR cc_start: 0.9136 (t80) cc_final: 0.8895 (t80) REVERT: B 618 LEU cc_start: 0.9095 (mt) cc_final: 0.8854 (mt) REVERT: B 632 MET cc_start: 0.8804 (mmp) cc_final: 0.8453 (mmp) REVERT: B 650 GLN cc_start: 0.8117 (mm-40) cc_final: 0.7596 (tp-100) REVERT: B 657 PHE cc_start: 0.9160 (m-80) cc_final: 0.8918 (m-80) REVERT: B 667 LEU cc_start: 0.9593 (tt) cc_final: 0.9391 (tt) REVERT: C 155 LYS cc_start: 0.5785 (mptt) cc_final: 0.5308 (pttp) REVERT: C 176 LEU cc_start: 0.9470 (tt) cc_final: 0.9235 (pp) REVERT: C 179 TYR cc_start: 0.9505 (t80) cc_final: 0.9259 (t80) REVERT: C 185 MET cc_start: 0.8770 (mpp) cc_final: 0.8542 (mpp) REVERT: D 46 TYR cc_start: 0.9054 (m-80) cc_final: 0.8843 (m-10) REVERT: D 179 TYR cc_start: 0.9125 (t80) cc_final: 0.8786 (t80) REVERT: D 185 MET cc_start: 0.7725 (mmm) cc_final: 0.6840 (mmm) outliers start: 0 outliers final: 0 residues processed: 624 average time/residue: 0.2858 time to fit residues: 261.5203 Evaluate side-chains 532 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 532 time to evaluate : 1.848 ------------------------------------------------------------------------------- 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: 4.9990 chunk 102 optimal weight: 0.8980 chunk 182 optimal weight: 7.9990 chunk 107 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- 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 180 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.112689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.080744 restraints weight = 53267.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.083492 restraints weight = 32373.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.085359 restraints weight = 22606.401| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3117 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.7991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16386 Z= 0.169 Angle : 0.663 8.285 22134 Z= 0.352 Chirality : 0.044 0.278 2360 Planarity : 0.004 0.060 2818 Dihedral : 10.979 172.282 2242 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % 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: 0.38 (0.19), residues: 1932 helix: 0.67 (0.15), residues: 1141 sheet: -0.95 (0.42), residues: 142 loop : 0.03 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 558 HIS 0.007 0.001 HIS C 201 PHE 0.025 0.002 PHE C 154 TYR 0.086 0.002 TYR C 142 ARG 0.007 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 869) hydrogen bonds : angle 5.04178 ( 2568) covalent geometry : bond 0.00367 (16386) covalent geometry : angle 0.66253 (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 604 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 604 time to evaluate : 1.710 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: A 65 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8398 (mp0) REVERT: A 103 ASP cc_start: 0.9367 (m-30) cc_final: 0.9040 (m-30) REVERT: A 104 TYR cc_start: 0.8857 (m-80) cc_final: 0.8493 (m-80) REVERT: A 107 LYS cc_start: 0.9475 (mttm) cc_final: 0.9174 (mmmt) REVERT: A 129 PHE cc_start: 0.9528 (m-80) cc_final: 0.9114 (m-80) REVERT: A 136 LYS cc_start: 0.9808 (mmtt) cc_final: 0.9581 (mmmm) REVERT: A 144 MET cc_start: 0.8959 (mtm) cc_final: 0.8511 (mtm) REVERT: A 158 ASN cc_start: 0.9547 (m110) cc_final: 0.8913 (p0) REVERT: A 168 VAL cc_start: 0.9157 (m) cc_final: 0.8924 (p) REVERT: A 227 MET cc_start: 0.9247 (mtp) cc_final: 0.8740 (mtp) REVERT: A 235 ARG cc_start: 0.8314 (mtm180) cc_final: 0.8027 (mtm110) REVERT: A 266 LYS cc_start: 0.9358 (ptmm) cc_final: 0.9066 (pptt) REVERT: A 286 ASP cc_start: 0.9126 (m-30) cc_final: 0.8488 (m-30) REVERT: A 314 MET cc_start: 0.8930 (ppp) cc_final: 0.8336 (ppp) REVERT: A 317 MET cc_start: 0.8792 (mtm) cc_final: 0.8336 (mpp) REVERT: A 335 GLU cc_start: 0.9254 (tp30) cc_final: 0.9038 (tm-30) REVERT: A 337 ILE cc_start: 0.9644 (pt) cc_final: 0.8798 (pt) REVERT: A 359 MET cc_start: 0.9166 (ptt) cc_final: 0.8908 (ppp) REVERT: A 360 PHE cc_start: 0.9442 (m-80) cc_final: 0.9008 (m-10) REVERT: A 362 ASP cc_start: 0.9115 (m-30) cc_final: 0.8674 (m-30) REVERT: A 366 LYS cc_start: 0.9587 (ptpp) cc_final: 0.9086 (pttm) REVERT: A 370 ASN cc_start: 0.9442 (m110) cc_final: 0.9087 (m110) REVERT: A 375 LYS cc_start: 0.9439 (mttt) cc_final: 0.9038 (mttt) REVERT: A 385 VAL cc_start: 0.9666 (t) cc_final: 0.9447 (m) REVERT: A 386 LEU cc_start: 0.9601 (mt) cc_final: 0.9314 (mt) REVERT: A 414 LEU cc_start: 0.9508 (mt) cc_final: 0.9119 (mt) REVERT: A 421 GLU cc_start: 0.9179 (tm-30) cc_final: 0.8964 (tm-30) REVERT: A 493 MET cc_start: 0.9235 (tmm) cc_final: 0.8898 (tmm) REVERT: A 494 MET cc_start: 0.9484 (mtt) cc_final: 0.9021 (mtp) REVERT: A 500 ILE cc_start: 0.9891 (mt) cc_final: 0.9616 (mt) REVERT: A 515 ASP cc_start: 0.9458 (m-30) cc_final: 0.9181 (m-30) REVERT: A 550 MET cc_start: 0.8107 (mmp) cc_final: 0.7861 (mmm) REVERT: A 575 ARG cc_start: 0.9097 (ptp90) cc_final: 0.8128 (ptp-110) REVERT: A 585 SER cc_start: 0.9608 (p) cc_final: 0.9405 (t) REVERT: A 591 THR cc_start: 0.9176 (p) cc_final: 0.8871 (p) REVERT: A 598 MET cc_start: 0.8459 (ttt) cc_final: 0.8040 (tpp) REVERT: A 615 MET cc_start: 0.8940 (mmp) cc_final: 0.8562 (mmm) REVERT: A 632 MET cc_start: 0.9155 (mtp) cc_final: 0.8788 (mtp) REVERT: A 647 HIS cc_start: 0.8727 (m-70) cc_final: 0.8434 (m-70) REVERT: A 653 SER cc_start: 0.9161 (p) cc_final: 0.8948 (p) REVERT: A 667 LEU cc_start: 0.9633 (tt) cc_final: 0.9372 (tt) REVERT: B 87 LYS cc_start: 0.9338 (tptp) cc_final: 0.9117 (tptp) REVERT: B 95 MET cc_start: 0.9357 (tpp) cc_final: 0.8101 (tpp) REVERT: B 99 LYS cc_start: 0.9621 (mmmt) cc_final: 0.8770 (mmmt) REVERT: B 114 ILE cc_start: 0.9543 (mt) cc_final: 0.9212 (pt) REVERT: B 144 MET cc_start: 0.9365 (mtm) cc_final: 0.9060 (mtm) REVERT: B 149 TYR cc_start: 0.9399 (t80) cc_final: 0.8908 (t80) REVERT: B 161 ARG cc_start: 0.8653 (mtt-85) cc_final: 0.8414 (mtt180) REVERT: B 194 LYS cc_start: 0.9078 (ptmm) cc_final: 0.8726 (pttm) REVERT: B 211 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8504 (mm-30) REVERT: B 257 ASP cc_start: 0.8412 (m-30) cc_final: 0.8135 (m-30) REVERT: B 263 ASP cc_start: 0.9355 (m-30) cc_final: 0.9099 (m-30) REVERT: B 290 GLU cc_start: 0.9510 (pt0) cc_final: 0.9246 (pp20) REVERT: B 322 MET cc_start: 0.8788 (tpt) cc_final: 0.8354 (ttt) REVERT: B 333 LYS cc_start: 0.9197 (tptp) cc_final: 0.8946 (tptp) REVERT: B 335 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8160 (mt-10) REVERT: B 350 ARG cc_start: 0.9168 (tpp80) cc_final: 0.8773 (tpp80) REVERT: B 362 ASP cc_start: 0.9015 (m-30) cc_final: 0.8611 (m-30) REVERT: B 375 LYS cc_start: 0.9124 (mmmm) cc_final: 0.8920 (mmmm) REVERT: B 390 GLN cc_start: 0.9234 (mm110) cc_final: 0.8938 (mm-40) REVERT: B 396 ASP cc_start: 0.8214 (p0) cc_final: 0.7677 (p0) REVERT: B 399 GLU cc_start: 0.9463 (mm-30) cc_final: 0.9119 (mp0) REVERT: B 414 LEU cc_start: 0.9759 (mt) cc_final: 0.9548 (mt) REVERT: B 415 ASN cc_start: 0.9200 (t0) cc_final: 0.8767 (t0) REVERT: B 416 ILE cc_start: 0.9835 (mt) cc_final: 0.9549 (mt) REVERT: B 418 ASN cc_start: 0.9446 (m-40) cc_final: 0.9201 (m-40) REVERT: B 420 MET cc_start: 0.9254 (mmp) cc_final: 0.8906 (mmm) REVERT: B 426 GLU cc_start: 0.9286 (pm20) cc_final: 0.8923 (pm20) REVERT: B 427 LYS cc_start: 0.9725 (ptpp) cc_final: 0.9315 (ptpp) REVERT: B 466 MET cc_start: 0.8796 (ptp) cc_final: 0.8534 (ptp) REVERT: B 496 ASN cc_start: 0.9575 (t0) cc_final: 0.9234 (t0) REVERT: B 515 ASP cc_start: 0.9142 (m-30) cc_final: 0.8725 (m-30) REVERT: B 570 MET cc_start: 0.9303 (tpp) cc_final: 0.8622 (tpt) REVERT: B 575 ARG cc_start: 0.8629 (mtm110) cc_final: 0.8055 (mtm-85) REVERT: B 595 MET cc_start: 0.9553 (mmm) cc_final: 0.8871 (mpp) REVERT: B 613 TYR cc_start: 0.9125 (t80) cc_final: 0.8865 (t80) REVERT: B 675 HIS cc_start: 0.9281 (t70) cc_final: 0.8941 (t70) REVERT: C 17 PHE cc_start: 0.8594 (p90) cc_final: 0.7603 (p90) REVERT: C 21 PHE cc_start: 0.9435 (m-80) cc_final: 0.8826 (m-80) REVERT: C 76 ILE cc_start: 0.5083 (tt) cc_final: 0.4762 (pt) REVERT: C 176 LEU cc_start: 0.9484 (tt) cc_final: 0.9231 (pp) REVERT: C 179 TYR cc_start: 0.9515 (t80) cc_final: 0.9184 (t80) REVERT: C 185 MET cc_start: 0.8736 (mpp) cc_final: 0.8523 (mpp) REVERT: C 204 TYR cc_start: 0.9719 (t80) cc_final: 0.9239 (t80) REVERT: D 46 TYR cc_start: 0.9079 (m-80) cc_final: 0.8842 (m-10) REVERT: D 74 MET cc_start: 0.6543 (tmm) cc_final: 0.6072 (tmm) REVERT: D 178 PHE cc_start: 0.9261 (m-80) cc_final: 0.9015 (m-80) outliers start: 0 outliers final: 0 residues processed: 604 average time/residue: 0.2829 time to fit residues: 252.1830 Evaluate side-chains 531 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 531 time to evaluate : 2.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 137 optimal weight: 0.0570 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 9.9990 chunk 160 optimal weight: 5.9990 chunk 106 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 135 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 overall best weight: 4.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.106073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.075383 restraints weight = 56264.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.078056 restraints weight = 33960.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.079833 restraints weight = 24010.887| |-----------------------------------------------------------------------------| r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3000 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.8331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16386 Z= 0.256 Angle : 0.745 8.696 22134 Z= 0.397 Chirality : 0.045 0.195 2360 Planarity : 0.005 0.082 2818 Dihedral : 11.474 174.323 2242 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 23.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -0.05 (0.18), residues: 1932 helix: 0.31 (0.15), residues: 1138 sheet: -1.13 (0.42), residues: 136 loop : -0.13 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 558 HIS 0.009 0.002 HIS A 372 PHE 0.020 0.002 PHE D 227 TYR 0.027 0.002 TYR C 142 ARG 0.008 0.001 ARG C 196 Details of bonding type rmsd hydrogen bonds : bond 0.04276 ( 869) hydrogen bonds : angle 5.29826 ( 2568) covalent geometry : bond 0.00531 (16386) covalent geometry : angle 0.74459 (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 596 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 596 time to evaluate : 1.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9428 (tptp) cc_final: 0.9105 (tptp) REVERT: A 36 TYR cc_start: 0.9646 (t80) cc_final: 0.9411 (t80) REVERT: A 41 ILE cc_start: 0.9579 (mt) cc_final: 0.9366 (mt) REVERT: A 65 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8578 (mm-30) REVERT: A 94 PHE cc_start: 0.9508 (t80) cc_final: 0.9014 (t80) REVERT: A 95 MET cc_start: 0.9657 (tpt) cc_final: 0.9423 (tpp) REVERT: A 99 LYS cc_start: 0.9636 (mmtp) cc_final: 0.9102 (mmmt) REVERT: A 104 TYR cc_start: 0.8955 (m-80) cc_final: 0.8454 (m-80) REVERT: A 107 LYS cc_start: 0.9450 (mttm) cc_final: 0.9031 (tptt) REVERT: A 136 LYS cc_start: 0.9818 (mmtt) cc_final: 0.9592 (mmmm) REVERT: A 144 MET cc_start: 0.8956 (mtm) cc_final: 0.8714 (mtm) REVERT: A 158 ASN cc_start: 0.9557 (m110) cc_final: 0.8841 (p0) REVERT: A 163 ARG cc_start: 0.8985 (tpp-160) cc_final: 0.8464 (tpp-160) REVERT: A 199 VAL cc_start: 0.9411 (t) cc_final: 0.9201 (m) REVERT: A 227 MET cc_start: 0.9250 (mtp) cc_final: 0.8786 (mtp) REVERT: A 255 HIS cc_start: 0.8405 (t-90) cc_final: 0.7999 (t-90) REVERT: A 266 LYS cc_start: 0.9378 (ptmm) cc_final: 0.9085 (pptt) REVERT: A 286 ASP cc_start: 0.9072 (m-30) cc_final: 0.8555 (m-30) REVERT: A 314 MET cc_start: 0.8879 (ppp) cc_final: 0.8587 (ppp) REVERT: A 322 MET cc_start: 0.9193 (mmp) cc_final: 0.8607 (mmm) REVERT: A 337 ILE cc_start: 0.9666 (pt) cc_final: 0.8980 (pt) REVERT: A 357 TYR cc_start: 0.7937 (m-80) cc_final: 0.7440 (m-80) REVERT: A 359 MET cc_start: 0.9331 (ptt) cc_final: 0.8678 (ppp) REVERT: A 360 PHE cc_start: 0.9324 (m-80) cc_final: 0.8715 (m-10) REVERT: A 362 ASP cc_start: 0.9074 (m-30) cc_final: 0.8735 (m-30) REVERT: A 366 LYS cc_start: 0.9581 (ptpp) cc_final: 0.9148 (pttp) REVERT: A 375 LYS cc_start: 0.9398 (mttt) cc_final: 0.8961 (mttt) REVERT: A 386 LEU cc_start: 0.9584 (mt) cc_final: 0.9366 (mt) REVERT: A 414 LEU cc_start: 0.9376 (mt) cc_final: 0.9007 (mt) REVERT: A 493 MET cc_start: 0.9176 (tmm) cc_final: 0.8840 (tmm) REVERT: A 494 MET cc_start: 0.9516 (mtt) cc_final: 0.9109 (mtp) REVERT: A 500 ILE cc_start: 0.9892 (mt) cc_final: 0.9678 (mt) REVERT: A 515 ASP cc_start: 0.9448 (m-30) cc_final: 0.9212 (m-30) REVERT: A 575 ARG cc_start: 0.9008 (ptp90) cc_final: 0.8353 (ptp-110) REVERT: A 583 SER cc_start: 0.9473 (t) cc_final: 0.9236 (t) REVERT: A 591 THR cc_start: 0.9283 (p) cc_final: 0.9036 (p) REVERT: A 598 MET cc_start: 0.8492 (ttt) cc_final: 0.8075 (tpp) REVERT: A 615 MET cc_start: 0.8939 (mmp) cc_final: 0.8583 (mmm) REVERT: A 618 LEU cc_start: 0.9268 (tt) cc_final: 0.9023 (tt) REVERT: A 632 MET cc_start: 0.9180 (mtp) cc_final: 0.8789 (mtp) REVERT: A 647 HIS cc_start: 0.8706 (m-70) cc_final: 0.8431 (m-70) REVERT: A 653 SER cc_start: 0.9201 (p) cc_final: 0.8948 (p) REVERT: A 654 PHE cc_start: 0.8889 (t80) cc_final: 0.8527 (t80) REVERT: A 667 LEU cc_start: 0.9654 (tt) cc_final: 0.9407 (tt) REVERT: B 87 LYS cc_start: 0.9379 (tptp) cc_final: 0.9096 (tptp) REVERT: B 95 MET cc_start: 0.9380 (tpp) cc_final: 0.8208 (tpp) REVERT: B 99 LYS cc_start: 0.9653 (mmmt) cc_final: 0.8814 (mmmt) REVERT: B 106 LEU cc_start: 0.9139 (tt) cc_final: 0.8910 (tt) REVERT: B 114 ILE cc_start: 0.9563 (mt) cc_final: 0.9242 (pt) REVERT: B 144 MET cc_start: 0.9387 (mtm) cc_final: 0.9129 (mtm) REVERT: B 147 GLN cc_start: 0.9234 (tp-100) cc_final: 0.8635 (tp-100) REVERT: B 149 TYR cc_start: 0.9364 (t80) cc_final: 0.8911 (t80) REVERT: B 161 ARG cc_start: 0.8518 (mtt-85) cc_final: 0.8094 (mtt180) REVERT: B 190 MET cc_start: 0.9616 (mtm) cc_final: 0.9160 (mmm) REVERT: B 194 LYS cc_start: 0.9165 (ptmm) cc_final: 0.8807 (pttm) REVERT: B 211 GLU cc_start: 0.9043 (mm-30) cc_final: 0.8587 (mm-30) REVERT: B 215 ASP cc_start: 0.9471 (t0) cc_final: 0.9125 (p0) REVERT: B 252 ASN cc_start: 0.8999 (t0) cc_final: 0.8796 (t0) REVERT: B 322 MET cc_start: 0.8820 (tpt) cc_final: 0.8432 (ttt) REVERT: B 350 ARG cc_start: 0.9194 (tpp80) cc_final: 0.8849 (tpp80) REVERT: B 362 ASP cc_start: 0.8776 (m-30) cc_final: 0.8284 (m-30) REVERT: B 390 GLN cc_start: 0.9283 (mm110) cc_final: 0.8966 (mm-40) REVERT: B 396 ASP cc_start: 0.8305 (p0) cc_final: 0.7738 (p0) REVERT: B 399 GLU cc_start: 0.9464 (mm-30) cc_final: 0.9134 (mp0) REVERT: B 414 LEU cc_start: 0.9704 (mt) cc_final: 0.9441 (mt) REVERT: B 415 ASN cc_start: 0.9149 (t0) cc_final: 0.8501 (t0) REVERT: B 416 ILE cc_start: 0.9828 (mt) cc_final: 0.9517 (mt) REVERT: B 418 ASN cc_start: 0.9350 (m-40) cc_final: 0.8658 (m-40) REVERT: B 420 MET cc_start: 0.9262 (mmp) cc_final: 0.8889 (mmm) REVERT: B 426 GLU cc_start: 0.9296 (pm20) cc_final: 0.8764 (pm20) REVERT: B 427 LYS cc_start: 0.9715 (ptpp) cc_final: 0.9215 (ptpp) REVERT: B 494 MET cc_start: 0.9371 (mtp) cc_final: 0.8879 (mtp) REVERT: B 505 GLU cc_start: 0.9110 (mt-10) cc_final: 0.8825 (mt-10) REVERT: B 515 ASP cc_start: 0.9163 (m-30) cc_final: 0.8743 (m-30) REVERT: B 570 MET cc_start: 0.9350 (tpp) cc_final: 0.8689 (tpt) REVERT: B 595 MET cc_start: 0.9485 (mmm) cc_final: 0.9069 (mpp) REVERT: B 613 TYR cc_start: 0.9283 (t80) cc_final: 0.8884 (t80) REVERT: C 17 PHE cc_start: 0.8198 (p90) cc_final: 0.7310 (p90) REVERT: C 46 TYR cc_start: 0.8791 (m-80) cc_final: 0.8587 (m-80) REVERT: C 179 TYR cc_start: 0.9542 (t80) cc_final: 0.9341 (t80) REVERT: C 185 MET cc_start: 0.8781 (mpp) cc_final: 0.8570 (mpp) REVERT: C 204 TYR cc_start: 0.9732 (t80) cc_final: 0.9140 (t80) REVERT: D 46 TYR cc_start: 0.9040 (m-80) cc_final: 0.8751 (m-10) REVERT: D 74 MET cc_start: 0.7118 (tmm) cc_final: 0.6370 (tmm) REVERT: D 317 ASP cc_start: 0.9358 (t0) cc_final: 0.8812 (t70) REVERT: D 318 ASP cc_start: 0.9324 (m-30) cc_final: 0.9111 (m-30) outliers start: 0 outliers final: 0 residues processed: 596 average time/residue: 0.2797 time to fit residues: 245.0801 Evaluate side-chains 526 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 526 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 81 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 105 optimal weight: 0.0040 chunk 179 optimal weight: 9.9990 chunk 190 optimal weight: 20.0000 chunk 58 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 108 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** D 28 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 = 0.3568 r_free = 0.3568 target = 0.110167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.079489 restraints weight = 52830.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.082390 restraints weight = 30984.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.084133 restraints weight = 21471.583| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3138 r_free = 0.3138 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3138 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.8454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16386 Z= 0.146 Angle : 0.692 8.306 22134 Z= 0.367 Chirality : 0.044 0.162 2360 Planarity : 0.005 0.067 2818 Dihedral : 11.261 173.364 2242 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % 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: 0.04 (0.19), residues: 1932 helix: 0.44 (0.15), residues: 1148 sheet: -1.31 (0.42), residues: 134 loop : -0.16 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 558 HIS 0.007 0.001 HIS C 201 PHE 0.025 0.002 PHE A 129 TYR 0.036 0.002 TYR B 574 ARG 0.016 0.001 ARG C 196 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 869) hydrogen bonds : angle 5.16586 ( 2568) covalent geometry : bond 0.00324 (16386) covalent geometry : angle 0.69207 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6256.93 seconds wall clock time: 110 minutes 24.68 seconds (6624.68 seconds total)