Starting phenix.real_space_refine on Sat Jun 14 07:11:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz9_45057/06_2025/9bz9_45057_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz9_45057/06_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_45057/06_2025/9bz9_45057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz9_45057/06_2025/9bz9_45057.map" model { file = "/net/cci-nas-00/data/ceres_data/9bz9_45057/06_2025/9bz9_45057_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz9_45057/06_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-5710/modules/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 9.89, per 1000 atoms: 0.62 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: 4.15 Conformation dependent library (CDL) restraints added in 2.2 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: 1.73 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: 5.74 Time building geometry restraints manager: 4.89 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: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 39.220 Find NCS groups from input model: 1.010 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.000 ------------------------------------------------------------------------------- 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 : 1.891 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: 0.8427 (t) REVERT: A 51 LEU cc_start: 0.8122 (tp) cc_final: 0.7529 (tp) REVERT: A 125 VAL cc_start: 0.9045 (t) cc_final: 0.7544 (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: 0.8037 (mm-30) REVERT: A 181 ASP cc_start: 0.8496 (m-30) cc_final: 0.8086 (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: 0.7963 (p) REVERT: A 283 VAL cc_start: 0.8505 (t) cc_final: 0.7309 (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: 0.9074 (mp) REVERT: A 300 VAL cc_start: 0.7424 (m) cc_final: 0.7074 (m) REVERT: A 322 MET cc_start: 0.7645 (mmp) cc_final: 0.6614 (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: 0.4877 (m-30) REVERT: A 367 VAL cc_start: 0.8092 (m) cc_final: 0.7836 (m) REVERT: A 370 ASN cc_start: 0.7524 (m-40) cc_final: 0.6739 (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: 0.8645 (mm) REVERT: A 436 LEU cc_start: 0.9252 (mt) cc_final: 0.8889 (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: 0.6307 (m) REVERT: A 634 MET cc_start: 0.8337 (mmp) cc_final: 0.7994 (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: 0.8505 (mt) REVERT: A 653 SER cc_start: 0.9052 (OUTLIER) cc_final: 0.8694 (p) REVERT: A 682 ILE cc_start: 0.8321 (mt) cc_final: 0.8041 (mt) REVERT: B 41 ILE cc_start: 0.8853 (mm) cc_final: 0.8151 (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: 0.7670 (tpp) REVERT: B 98 PHE cc_start: 0.7798 (t80) cc_final: 0.7470 (t80) REVERT: B 99 LYS cc_start: 0.9167 (mmtt) cc_final: 0.8347 (mmmm) REVERT: B 100 PHE cc_start: 0.7911 (t80) cc_final: 0.7613 (t80) REVERT: B 101 TYR cc_start: 0.7554 (m-80) cc_final: 0.7054 (m-80) REVERT: B 143 LEU cc_start: 0.9038 (tp) cc_final: 0.8833 (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: 0.7629 (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: 0.6327 (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: 0.6015 (tpp) REVERT: B 337 ILE cc_start: 0.8308 (pt) cc_final: 0.8053 (pt) REVERT: B 361 GLN cc_start: 0.6689 (tt0) cc_final: 0.6392 (tt0) REVERT: B 362 ASP cc_start: 0.6252 (m-30) cc_final: 0.5551 (m-30) REVERT: B 373 ILE cc_start: 0.9065 (mt) cc_final: 0.8321 (mt) REVERT: B 415 ASN cc_start: 0.8552 (t0) cc_final: 0.7842 (t0) REVERT: B 418 ASN cc_start: 0.7652 (m-40) cc_final: 0.6541 (m-40) REVERT: B 425 ILE cc_start: 0.9268 (mt) cc_final: 0.8681 (mt) REVERT: B 436 LEU cc_start: 0.9378 (mt) cc_final: 0.9092 (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: 0.7227 (mt) REVERT: B 613 TYR cc_start: 0.7838 (t80) cc_final: 0.7533 (t80) REVERT: B 641 ILE cc_start: 0.9444 (mm) cc_final: 0.9127 (mm) REVERT: B 645 GLN cc_start: 0.8410 (tp-100) cc_final: 0.8176 (tp-100) REVERT: B 656 LEU cc_start: 0.8212 (mt) cc_final: 0.7879 (mt) REVERT: C 85 GLN cc_start: 0.5803 (mt0) cc_final: 0.4900 (tt0) REVERT: C 90 LEU cc_start: 0.5509 (mt) cc_final: 0.5012 (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: 0.3270 (mtt) REVERT: C 194 ILE cc_start: 0.7431 (mt) cc_final: 0.7132 (mp) REVERT: C 205 VAL cc_start: 0.7608 (t) cc_final: 0.7387 (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: 0.8012 (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: 0.6730 (t) REVERT: D 317 ASP cc_start: 0.6461 (t0) cc_final: 0.5784 (t70) outliers start: 24 outliers final: 6 residues processed: 915 average time/residue: 0.3183 time to fit residues: 412.8689 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 : 1.770 ------------------------------------------------------------------------------- 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 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 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 Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.113620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.079594 restraints weight = 48211.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.082763 restraints weight = 29277.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.084959 restraints weight = 20403.899| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3151 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3151 r_free = 0.3151 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16386 Z= 0.226 Angle : 0.664 10.516 22134 Z= 0.358 Chirality : 0.044 0.422 2360 Planarity : 0.004 0.051 2818 Dihedral : 11.429 179.732 2242 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.23 % Allowed : 2.91 % 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: 1.30 (0.19), residues: 1932 helix: 1.28 (0.15), residues: 1127 sheet: 0.06 (0.41), residues: 126 loop : 0.51 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 558 HIS 0.007 0.001 HIS B 438 PHE 0.048 0.003 PHE D 178 TYR 0.022 0.002 TYR C 55 ARG 0.007 0.001 ARG A 452 Details of bonding type rmsd hydrogen bonds : bond 0.04754 ( 869) hydrogen bonds : angle 5.16240 ( 2568) covalent geometry : bond 0.00451 (16386) covalent geometry : angle 0.66387 (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: 4 poor density : 710 time to evaluate : 1.970 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: A 18 ILE cc_start: 0.9720 (mm) cc_final: 0.9215 (mt) REVERT: A 87 LYS cc_start: 0.9241 (tptm) cc_final: 0.8987 (tptm) REVERT: A 99 LYS cc_start: 0.9332 (mmtp) cc_final: 0.9064 (mmtp) REVERT: A 107 LYS cc_start: 0.9371 (mttm) cc_final: 0.9096 (mmmt) REVERT: A 136 LYS cc_start: 0.9714 (mmpt) cc_final: 0.9511 (ttpt) REVERT: A 143 LEU cc_start: 0.9180 (tp) cc_final: 0.8901 (tp) REVERT: A 144 MET cc_start: 0.9265 (mtm) cc_final: 0.8900 (mtm) REVERT: A 149 TYR cc_start: 0.9340 (t80) cc_final: 0.8826 (t80) REVERT: A 150 GLN cc_start: 0.9160 (tp40) cc_final: 0.8781 (tp40) REVERT: A 252 ASN cc_start: 0.8535 (t0) cc_final: 0.8064 (t0) REVERT: A 279 SER cc_start: 0.7593 (m) cc_final: 0.7338 (p) REVERT: A 286 ASP cc_start: 0.9198 (m-30) cc_final: 0.8459 (m-30) REVERT: A 385 VAL cc_start: 0.9558 (t) cc_final: 0.9309 (t) REVERT: A 418 ASN cc_start: 0.8999 (m110) cc_final: 0.8656 (m110) REVERT: A 421 GLU cc_start: 0.9494 (tm-30) cc_final: 0.9262 (tm-30) REVERT: A 436 LEU cc_start: 0.9587 (mt) cc_final: 0.9381 (mt) REVERT: A 502 ARG cc_start: 0.9448 (tpt170) cc_final: 0.9185 (tpt90) REVERT: A 510 LYS cc_start: 0.9690 (mmmt) cc_final: 0.9273 (mmtm) REVERT: A 572 HIS cc_start: 0.9514 (m90) cc_final: 0.9098 (m90) REVERT: A 599 GLU cc_start: 0.8771 (mt-10) cc_final: 0.8502 (mt-10) REVERT: A 615 MET cc_start: 0.8946 (mmp) cc_final: 0.8546 (mmp) REVERT: A 626 TYR cc_start: 0.8992 (m-80) cc_final: 0.8660 (m-10) REVERT: A 634 MET cc_start: 0.9300 (mmp) cc_final: 0.9042 (mpp) REVERT: A 683 TYR cc_start: 0.8518 (t80) cc_final: 0.7993 (t80) REVERT: B 19 GLN cc_start: 0.9367 (mt0) cc_final: 0.8877 (pp30) REVERT: B 41 ILE cc_start: 0.9793 (mm) cc_final: 0.9561 (mm) REVERT: B 51 LEU cc_start: 0.9413 (tp) cc_final: 0.9027 (tp) REVERT: B 77 ILE cc_start: 0.9734 (mt) cc_final: 0.9410 (mt) REVERT: B 87 LYS cc_start: 0.9298 (tptp) cc_final: 0.9020 (tptp) REVERT: B 89 PHE cc_start: 0.9181 (t80) cc_final: 0.8971 (t80) REVERT: B 95 MET cc_start: 0.9484 (tpp) cc_final: 0.8518 (tpp) REVERT: B 99 LYS cc_start: 0.9422 (mmmt) cc_final: 0.8713 (mmmt) REVERT: B 144 MET cc_start: 0.9610 (mtm) cc_final: 0.8994 (mtm) REVERT: B 149 TYR cc_start: 0.8922 (t80) cc_final: 0.8500 (t80) REVERT: B 162 LYS cc_start: 0.9257 (tppt) cc_final: 0.8873 (mttm) REVERT: B 180 ASN cc_start: 0.9002 (t160) cc_final: 0.8582 (t0) REVERT: B 211 GLU cc_start: 0.9015 (mm-30) cc_final: 0.7995 (mt-10) REVERT: B 229 LEU cc_start: 0.9173 (mt) cc_final: 0.8972 (mt) REVERT: B 236 TYR cc_start: 0.8777 (t80) cc_final: 0.8467 (t80) REVERT: B 257 ASP cc_start: 0.8332 (m-30) cc_final: 0.8122 (m-30) REVERT: B 286 ASP cc_start: 0.8979 (m-30) cc_final: 0.8324 (m-30) REVERT: B 317 MET cc_start: 0.8693 (pmm) cc_final: 0.8406 (pmm) REVERT: B 355 TYR cc_start: 0.9272 (m-10) cc_final: 0.8873 (m-10) REVERT: B 362 ASP cc_start: 0.8668 (m-30) cc_final: 0.7919 (m-30) REVERT: B 415 ASN cc_start: 0.9010 (t0) cc_final: 0.8056 (t0) REVERT: B 418 ASN cc_start: 0.9322 (m-40) cc_final: 0.8659 (m-40) REVERT: B 458 MET cc_start: 0.9457 (mmm) cc_final: 0.9075 (mmm) REVERT: B 467 ASN cc_start: 0.9237 (m-40) cc_final: 0.8827 (m110) REVERT: B 492 PHE cc_start: 0.9750 (m-80) cc_final: 0.9465 (m-80) REVERT: B 494 MET cc_start: 0.9429 (mtp) cc_final: 0.8706 (mtp) REVERT: B 496 ASN cc_start: 0.9744 (t0) cc_final: 0.8264 (t0) REVERT: B 499 SER cc_start: 0.9932 (t) cc_final: 0.9552 (p) REVERT: B 500 ILE cc_start: 0.9753 (mt) cc_final: 0.9271 (mt) REVERT: B 501 GLN cc_start: 0.9060 (tp-100) cc_final: 0.8548 (tp-100) REVERT: B 515 ASP cc_start: 0.9050 (m-30) cc_final: 0.8732 (m-30) REVERT: B 543 ILE cc_start: 0.9399 (mp) cc_final: 0.9130 (mt) REVERT: B 570 MET cc_start: 0.9248 (tpp) cc_final: 0.8693 (tpp) REVERT: B 574 TYR cc_start: 0.8293 (m-80) cc_final: 0.8009 (m-80) REVERT: B 575 ARG cc_start: 0.8789 (mtm110) cc_final: 0.7052 (mtm180) REVERT: B 588 GLN cc_start: 0.9365 (mm-40) cc_final: 0.8911 (mm-40) REVERT: B 645 GLN cc_start: 0.9354 (tp-100) cc_final: 0.9072 (tp-100) REVERT: C 21 PHE cc_start: 0.8848 (m-80) cc_final: 0.8240 (m-80) REVERT: C 89 VAL cc_start: 0.7372 (t) cc_final: 0.7018 (t) REVERT: C 96 MET cc_start: 0.6666 (mmt) cc_final: 0.6131 (mmt) REVERT: C 137 MET cc_start: 0.5106 (mtp) cc_final: 0.4785 (mtt) REVERT: C 204 TYR cc_start: 0.9419 (t80) cc_final: 0.9150 (t80) REVERT: C 315 LEU cc_start: 0.8215 (mt) cc_final: 0.7877 (mt) REVERT: D 33 GLU cc_start: 0.9401 (mp0) cc_final: 0.9166 (mp0) REVERT: D 96 MET cc_start: 0.8454 (mmm) cc_final: 0.8207 (mmm) REVERT: D 109 PHE cc_start: 0.7489 (OUTLIER) cc_final: 0.7130 (m-80) REVERT: D 185 MET cc_start: 0.6574 (mmm) cc_final: 0.5944 (mmp) REVERT: D 239 GLU cc_start: 0.6460 (OUTLIER) cc_final: 0.6252 (pp20) REVERT: D 317 ASP cc_start: 0.9336 (t0) cc_final: 0.8191 (t0) outliers start: 4 outliers final: 0 residues processed: 713 average time/residue: 0.2997 time to fit residues: 307.7486 Evaluate side-chains 582 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 580 time to evaluate : 1.932 ------------------------------------------------------------------------------- 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: 0.9990 chunk 168 optimal weight: 5.9990 chunk 175 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 191 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 171 optimal weight: 5.9990 chunk 189 optimal weight: 10.0000 chunk 141 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 147 GLN A 191 GLN A 232 ASN A 239 GLN ** 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 390 GLN B 410 ASN B 676 HIS C 28 GLN C 84 HIS C 132 GLN D 25 ASN D 80 HIS D 91 ASN D 186 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.110498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.077023 restraints weight = 50596.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.079502 restraints weight = 31407.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.082008 restraints weight = 22286.786| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 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 = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.5416 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= 0.195 Angle : 0.643 8.136 22134 Z= 0.340 Chirality : 0.043 0.277 2360 Planarity : 0.004 0.048 2818 Dihedral : 11.257 178.500 2242 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.12 % Allowed : 2.86 % Favored : 97.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.19), residues: 1932 helix: 1.15 (0.15), residues: 1124 sheet: -0.22 (0.40), residues: 130 loop : 0.22 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 30 HIS 0.006 0.001 HIS C 201 PHE 0.035 0.002 PHE A 129 TYR 0.030 0.002 TYR C 142 ARG 0.006 0.001 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.04306 ( 869) hydrogen bonds : angle 5.06547 ( 2568) covalent geometry : bond 0.00414 (16386) covalent geometry : angle 0.64293 (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 675 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 673 time to evaluate : 1.836 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 87 LYS cc_start: 0.9271 (tptm) cc_final: 0.9041 (tptm) REVERT: A 107 LYS cc_start: 0.9415 (mttm) cc_final: 0.9097 (mmmt) REVERT: A 136 LYS cc_start: 0.9744 (mmpt) cc_final: 0.9502 (ttpt) REVERT: A 143 LEU cc_start: 0.9130 (tp) cc_final: 0.8924 (tp) REVERT: A 144 MET cc_start: 0.9223 (mtm) cc_final: 0.8803 (mtm) REVERT: A 191 GLN cc_start: 0.9341 (mm-40) cc_final: 0.8882 (mp10) REVERT: A 202 ASN cc_start: 0.8969 (t0) cc_final: 0.8768 (t0) REVERT: A 204 SER cc_start: 0.8697 (p) cc_final: 0.8480 (p) REVERT: A 227 MET cc_start: 0.9362 (mtp) cc_final: 0.8889 (mtp) REVERT: A 252 ASN cc_start: 0.8598 (t0) cc_final: 0.8145 (t0) REVERT: A 286 ASP cc_start: 0.8965 (m-30) cc_final: 0.8355 (m-30) REVERT: A 335 GLU cc_start: 0.9230 (tp30) cc_final: 0.8938 (tm-30) REVERT: A 362 ASP cc_start: 0.9163 (m-30) cc_final: 0.8739 (m-30) REVERT: A 366 LYS cc_start: 0.9247 (ptpp) cc_final: 0.8876 (pttm) REVERT: A 370 ASN cc_start: 0.9371 (m-40) cc_final: 0.8969 (m110) REVERT: A 386 LEU cc_start: 0.9473 (mt) cc_final: 0.9266 (mt) REVERT: A 396 ASP cc_start: 0.8986 (p0) cc_final: 0.8773 (p0) REVERT: A 421 GLU cc_start: 0.9428 (tm-30) cc_final: 0.9222 (tm-30) REVERT: A 493 MET cc_start: 0.9376 (tmm) cc_final: 0.9147 (tmm) REVERT: A 500 ILE cc_start: 0.9763 (mt) cc_final: 0.9384 (mt) REVERT: A 501 GLN cc_start: 0.9606 (mm-40) cc_final: 0.8898 (tp-100) REVERT: A 561 LEU cc_start: 0.9645 (tp) cc_final: 0.9339 (tp) REVERT: A 575 ARG cc_start: 0.8436 (ptp90) cc_final: 0.8081 (mtm-85) REVERT: A 599 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8517 (mt-10) REVERT: A 615 MET cc_start: 0.8942 (mmp) cc_final: 0.8709 (mmp) REVERT: A 626 TYR cc_start: 0.9150 (m-80) cc_final: 0.8738 (m-10) REVERT: A 645 GLN cc_start: 0.8381 (tp-100) cc_final: 0.7292 (tp-100) REVERT: A 650 GLN cc_start: 0.7501 (mm110) cc_final: 0.7265 (mm110) REVERT: A 653 SER cc_start: 0.9077 (p) cc_final: 0.8830 (p) REVERT: A 667 LEU cc_start: 0.9473 (tt) cc_final: 0.9267 (tt) REVERT: A 680 LYS cc_start: 0.8436 (mttt) cc_final: 0.7920 (mttt) REVERT: B 19 GLN cc_start: 0.9326 (mt0) cc_final: 0.8931 (pp30) REVERT: B 51 LEU cc_start: 0.9478 (tp) cc_final: 0.9053 (tp) REVERT: B 77 ILE cc_start: 0.9693 (mt) cc_final: 0.9331 (mt) REVERT: B 81 PHE cc_start: 0.9540 (m-80) cc_final: 0.9331 (m-80) REVERT: B 87 LYS cc_start: 0.9331 (tptp) cc_final: 0.9037 (tptp) REVERT: B 89 PHE cc_start: 0.9204 (t80) cc_final: 0.8834 (t80) REVERT: B 95 MET cc_start: 0.9498 (tpp) cc_final: 0.8459 (tpp) REVERT: B 99 LYS cc_start: 0.9470 (mmmt) cc_final: 0.8729 (mmmt) REVERT: B 144 MET cc_start: 0.9533 (mtm) cc_final: 0.8862 (mtm) REVERT: B 149 TYR cc_start: 0.8980 (t80) cc_final: 0.8666 (t80) REVERT: B 150 GLN cc_start: 0.9075 (tp40) cc_final: 0.8829 (tp40) REVERT: B 162 LYS cc_start: 0.9330 (tppt) cc_final: 0.9063 (mttp) REVERT: B 211 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8392 (mm-30) REVERT: B 259 ASN cc_start: 0.9062 (m-40) cc_final: 0.8818 (m110) REVERT: B 286 ASP cc_start: 0.8994 (m-30) cc_final: 0.8334 (m-30) REVERT: B 317 MET cc_start: 0.8716 (pmm) cc_final: 0.8331 (pmm) REVERT: B 322 MET cc_start: 0.8783 (mmm) cc_final: 0.8381 (mmm) REVERT: B 350 ARG cc_start: 0.8983 (tpp80) cc_final: 0.8430 (tpp80) REVERT: B 355 TYR cc_start: 0.9250 (m-10) cc_final: 0.8913 (m-10) REVERT: B 362 ASP cc_start: 0.8647 (m-30) cc_final: 0.7809 (m-30) REVERT: B 375 LYS cc_start: 0.9244 (mmmm) cc_final: 0.8983 (mmtt) REVERT: B 396 ASP cc_start: 0.8668 (p0) cc_final: 0.8041 (p0) REVERT: B 399 GLU cc_start: 0.9464 (mm-30) cc_final: 0.9170 (mm-30) REVERT: B 415 ASN cc_start: 0.9039 (t0) cc_final: 0.7682 (t0) REVERT: B 418 ASN cc_start: 0.9170 (m-40) cc_final: 0.8593 (m-40) REVERT: B 459 LYS cc_start: 0.8960 (mttm) cc_final: 0.8738 (mmmt) REVERT: B 467 ASN cc_start: 0.9344 (m-40) cc_final: 0.8990 (m110) REVERT: B 479 TYR cc_start: 0.8976 (t80) cc_final: 0.8756 (t80) REVERT: B 496 ASN cc_start: 0.9686 (t0) cc_final: 0.8461 (t0) REVERT: B 499 SER cc_start: 0.9915 (t) cc_final: 0.9534 (p) REVERT: B 500 ILE cc_start: 0.9769 (mt) cc_final: 0.9445 (mt) REVERT: B 501 GLN cc_start: 0.9000 (tp-100) cc_final: 0.8462 (tp-100) REVERT: B 515 ASP cc_start: 0.9195 (m-30) cc_final: 0.8805 (m-30) REVERT: B 570 MET cc_start: 0.9103 (tpp) cc_final: 0.8597 (tpp) REVERT: B 575 ARG cc_start: 0.8836 (mtm110) cc_final: 0.7260 (mtm180) REVERT: B 588 GLN cc_start: 0.9443 (mm-40) cc_final: 0.8799 (mm-40) REVERT: B 601 ILE cc_start: 0.9328 (mp) cc_final: 0.8965 (mm) REVERT: B 613 TYR cc_start: 0.9501 (t80) cc_final: 0.9068 (t80) REVERT: B 615 MET cc_start: 0.8980 (mmp) cc_final: 0.8274 (mmp) REVERT: B 618 LEU cc_start: 0.8871 (mt) cc_final: 0.8577 (mt) REVERT: B 667 LEU cc_start: 0.9515 (tt) cc_final: 0.9128 (tt) REVERT: C 21 PHE cc_start: 0.8975 (m-80) cc_final: 0.8396 (m-80) REVERT: C 46 TYR cc_start: 0.8611 (m-80) cc_final: 0.8348 (m-80) REVERT: C 76 ILE cc_start: 0.5408 (tt) cc_final: 0.5092 (pt) REVERT: C 137 MET cc_start: 0.5329 (mtp) cc_final: 0.4870 (mtt) REVERT: C 204 TYR cc_start: 0.9611 (t80) cc_final: 0.9209 (t80) REVERT: D 46 TYR cc_start: 0.8907 (m-80) cc_final: 0.8600 (m-80) REVERT: D 96 MET cc_start: 0.8508 (mmm) cc_final: 0.7947 (mmm) REVERT: D 185 MET cc_start: 0.6967 (mmm) cc_final: 0.6302 (mmm) REVERT: D 259 PHE cc_start: 0.7729 (t80) cc_final: 0.7226 (t80) outliers start: 2 outliers final: 0 residues processed: 673 average time/residue: 0.2947 time to fit residues: 288.2198 Evaluate side-chains 567 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 567 time to evaluate : 2.007 ------------------------------------------------------------------------------- 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: 1.9990 chunk 1 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 71 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 148 optimal weight: 20.0000 chunk 90 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 180 ASN ** 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** ** 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 390 GLN B 645 GLN C 238 ASN D 80 HIS D 263 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.114002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.081124 restraints weight = 49613.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.083869 restraints weight = 29998.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.086117 restraints weight = 20768.487| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- 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 = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.5935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16386 Z= 0.136 Angle : 0.597 7.197 22134 Z= 0.314 Chirality : 0.042 0.235 2360 Planarity : 0.004 0.054 2818 Dihedral : 10.989 179.808 2242 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.06 % Allowed : 2.27 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.19), residues: 1932 helix: 1.08 (0.15), residues: 1137 sheet: -0.76 (0.40), residues: 140 loop : 0.31 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 9 HIS 0.007 0.001 HIS C 201 PHE 0.045 0.002 PHE A 129 TYR 0.034 0.002 TYR C 142 ARG 0.008 0.001 ARG B 446 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 869) hydrogen bonds : angle 4.95795 ( 2568) covalent geometry : bond 0.00298 (16386) covalent geometry : angle 0.59726 (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 671 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 670 time to evaluate : 2.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.9527 (mm) cc_final: 0.9319 (mm) REVERT: A 87 LYS cc_start: 0.9278 (tptm) cc_final: 0.8863 (tptm) REVERT: A 103 ASP cc_start: 0.9271 (m-30) cc_final: 0.9061 (m-30) REVERT: A 107 LYS cc_start: 0.9420 (mttm) cc_final: 0.9116 (mmmt) REVERT: A 129 PHE cc_start: 0.9447 (m-80) cc_final: 0.9203 (m-80) REVERT: A 136 LYS cc_start: 0.9745 (mmpt) cc_final: 0.9525 (ttpt) REVERT: A 143 LEU cc_start: 0.9126 (tp) cc_final: 0.8926 (tp) REVERT: A 144 MET cc_start: 0.9081 (mtm) cc_final: 0.8587 (mtm) REVERT: A 145 ILE cc_start: 0.9464 (tp) cc_final: 0.9092 (tp) REVERT: A 168 VAL cc_start: 0.9153 (m) cc_final: 0.8894 (p) REVERT: A 176 ASN cc_start: 0.8702 (t0) cc_final: 0.8455 (t0) REVERT: A 191 GLN cc_start: 0.9212 (mm-40) cc_final: 0.8678 (mp10) REVERT: A 194 LYS cc_start: 0.9402 (ttpp) cc_final: 0.9115 (ttpp) REVERT: A 195 LEU cc_start: 0.9577 (mt) cc_final: 0.9376 (mt) REVERT: A 202 ASN cc_start: 0.8925 (t0) cc_final: 0.8682 (t0) REVERT: A 227 MET cc_start: 0.9294 (mtp) cc_final: 0.8920 (mtp) REVERT: A 252 ASN cc_start: 0.8613 (t0) cc_final: 0.7727 (t0) REVERT: A 254 PHE cc_start: 0.8174 (m-10) cc_final: 0.7568 (m-10) REVERT: A 286 ASP cc_start: 0.9016 (m-30) cc_final: 0.8454 (m-30) REVERT: A 313 HIS cc_start: 0.8578 (m90) cc_final: 0.8070 (m-70) REVERT: A 315 ASP cc_start: 0.8651 (p0) cc_final: 0.8188 (p0) REVERT: A 335 GLU cc_start: 0.9208 (tp30) cc_final: 0.8882 (tm-30) REVERT: A 337 ILE cc_start: 0.9583 (pt) cc_final: 0.9304 (pt) REVERT: A 362 ASP cc_start: 0.9200 (m-30) cc_final: 0.8713 (m-30) REVERT: A 366 LYS cc_start: 0.9281 (ptpp) cc_final: 0.9017 (pttp) REVERT: A 370 ASN cc_start: 0.9457 (m-40) cc_final: 0.9031 (m110) REVERT: A 375 LYS cc_start: 0.9469 (mttt) cc_final: 0.9155 (mttt) REVERT: A 402 GLU cc_start: 0.8951 (tm-30) cc_final: 0.8749 (tm-30) REVERT: A 418 ASN cc_start: 0.9094 (m110) cc_final: 0.8654 (m-40) REVERT: A 468 LEU cc_start: 0.9616 (tp) cc_final: 0.9354 (tp) REVERT: A 493 MET cc_start: 0.9375 (tmm) cc_final: 0.9113 (tmm) REVERT: A 500 ILE cc_start: 0.9860 (mt) cc_final: 0.9506 (mt) REVERT: A 506 ILE cc_start: 0.9784 (mm) cc_final: 0.9415 (mm) REVERT: A 515 ASP cc_start: 0.9510 (m-30) cc_final: 0.9250 (m-30) REVERT: A 575 ARG cc_start: 0.8850 (ptp90) cc_final: 0.8093 (ptp-110) REVERT: A 595 MET cc_start: 0.9167 (tpp) cc_final: 0.8950 (tpp) REVERT: A 602 GLU cc_start: 0.8697 (pt0) cc_final: 0.8495 (pt0) REVERT: A 615 MET cc_start: 0.8944 (mmp) cc_final: 0.8738 (mmp) REVERT: A 626 TYR cc_start: 0.9176 (m-80) cc_final: 0.8725 (m-10) REVERT: A 632 MET cc_start: 0.8694 (mtp) cc_final: 0.8187 (mtp) REVERT: A 645 GLN cc_start: 0.8498 (tp-100) cc_final: 0.8181 (tp-100) REVERT: A 667 LEU cc_start: 0.9524 (tt) cc_final: 0.9199 (tt) REVERT: B 51 LEU cc_start: 0.9433 (tp) cc_final: 0.9017 (tp) REVERT: B 77 ILE cc_start: 0.9721 (mt) cc_final: 0.9353 (mt) REVERT: B 87 LYS cc_start: 0.9352 (tptp) cc_final: 0.9077 (tptp) REVERT: B 95 MET cc_start: 0.9470 (tpp) cc_final: 0.8287 (tpp) REVERT: B 99 LYS cc_start: 0.9487 (mmmt) cc_final: 0.8736 (mmmt) REVERT: B 144 MET cc_start: 0.9473 (mtm) cc_final: 0.8894 (mtm) REVERT: B 149 TYR cc_start: 0.9115 (t80) cc_final: 0.8552 (t80) REVERT: B 191 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8676 (mm-40) REVERT: B 211 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8355 (mm-30) REVERT: B 286 ASP cc_start: 0.8998 (m-30) cc_final: 0.8371 (m-30) REVERT: B 312 GLN cc_start: 0.8871 (pm20) cc_final: 0.8663 (pm20) REVERT: B 317 MET cc_start: 0.8822 (pmm) cc_final: 0.8563 (pmm) REVERT: B 322 MET cc_start: 0.8796 (mmm) cc_final: 0.8209 (mmm) REVERT: B 355 TYR cc_start: 0.9236 (m-10) cc_final: 0.8905 (m-10) REVERT: B 362 ASP cc_start: 0.8770 (m-30) cc_final: 0.7980 (m-30) REVERT: B 375 LYS cc_start: 0.9199 (mmmm) cc_final: 0.8926 (mmtt) REVERT: B 396 ASP cc_start: 0.8562 (p0) cc_final: 0.8045 (p0) REVERT: B 399 GLU cc_start: 0.9445 (mm-30) cc_final: 0.9131 (mm-30) REVERT: B 415 ASN cc_start: 0.9099 (t0) cc_final: 0.8106 (t0) REVERT: B 418 ASN cc_start: 0.9256 (m-40) cc_final: 0.8681 (m-40) REVERT: B 426 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8641 (tm-30) REVERT: B 446 ARG cc_start: 0.8381 (mmt-90) cc_final: 0.7996 (mmm160) REVERT: B 459 LYS cc_start: 0.8958 (mttm) cc_final: 0.8708 (mmmt) REVERT: B 467 ASN cc_start: 0.9356 (m-40) cc_final: 0.9101 (m-40) REVERT: B 472 LEU cc_start: 0.9683 (mt) cc_final: 0.9473 (mt) REVERT: B 479 TYR cc_start: 0.8928 (t80) cc_final: 0.8468 (t80) REVERT: B 480 GLU cc_start: 0.9482 (pm20) cc_final: 0.9236 (mt-10) REVERT: B 494 MET cc_start: 0.9392 (mtp) cc_final: 0.8797 (mtp) REVERT: B 496 ASN cc_start: 0.9741 (t0) cc_final: 0.9182 (t0) REVERT: B 499 SER cc_start: 0.9906 (t) cc_final: 0.9641 (p) REVERT: B 500 ILE cc_start: 0.9777 (mt) cc_final: 0.9547 (mt) REVERT: B 501 GLN cc_start: 0.8956 (tp-100) cc_final: 0.8388 (tp-100) REVERT: B 515 ASP cc_start: 0.9187 (m-30) cc_final: 0.8812 (m-30) REVERT: B 531 TYR cc_start: 0.8256 (m-80) cc_final: 0.8023 (m-80) REVERT: B 570 MET cc_start: 0.9118 (tpp) cc_final: 0.8472 (tpt) REVERT: B 575 ARG cc_start: 0.8734 (mtm110) cc_final: 0.8115 (mtm-85) REVERT: B 588 GLN cc_start: 0.9400 (mm-40) cc_final: 0.8934 (mm-40) REVERT: B 618 LEU cc_start: 0.9061 (mt) cc_final: 0.8775 (mt) REVERT: B 667 LEU cc_start: 0.9480 (tt) cc_final: 0.9164 (tt) REVERT: C 20 MET cc_start: 0.8394 (mmm) cc_final: 0.8070 (mpp) REVERT: C 21 PHE cc_start: 0.9163 (m-80) cc_final: 0.8449 (m-80) REVERT: C 46 TYR cc_start: 0.8502 (m-80) cc_final: 0.8017 (m-80) REVERT: C 76 ILE cc_start: 0.5486 (tt) cc_final: 0.5193 (pt) REVERT: C 137 MET cc_start: 0.5476 (mtp) cc_final: 0.5186 (mtt) REVERT: C 204 TYR cc_start: 0.9565 (t80) cc_final: 0.9241 (t80) REVERT: D 185 MET cc_start: 0.7406 (mmm) cc_final: 0.6522 (mmm) REVERT: D 189 GLU cc_start: 0.9028 (tp30) cc_final: 0.8656 (pt0) REVERT: D 259 PHE cc_start: 0.7547 (t80) cc_final: 0.6940 (t80) REVERT: D 315 LEU cc_start: 0.9141 (tt) cc_final: 0.8843 (pt) outliers start: 1 outliers final: 0 residues processed: 670 average time/residue: 0.3011 time to fit residues: 294.0488 Evaluate side-chains 570 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 570 time to evaluate : 1.970 ------------------------------------------------------------------------------- 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: 9.9990 chunk 41 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 175 optimal weight: 0.9980 chunk 182 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 A 239 GLN A 242 GLN ** 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 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN D 23 ASN D 80 HIS ** D 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.109139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.077621 restraints weight = 53015.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.080054 restraints weight = 32279.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.082111 restraints weight = 22399.111| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3081 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3081 r_free = 0.3081 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.6627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 16386 Z= 0.223 Angle : 0.654 7.065 22134 Z= 0.348 Chirality : 0.043 0.195 2360 Planarity : 0.004 0.050 2818 Dihedral : 11.126 177.013 2242 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.12 % Allowed : 2.62 % Favored : 97.26 % 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: 0.61 (0.19), residues: 1932 helix: 0.86 (0.15), residues: 1131 sheet: -0.88 (0.42), residues: 142 loop : 0.13 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 623 HIS 0.009 0.002 HIS B 572 PHE 0.028 0.002 PHE A 129 TYR 0.036 0.002 TYR C 142 ARG 0.005 0.001 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 869) hydrogen bonds : angle 5.08522 ( 2568) covalent geometry : bond 0.00464 (16386) covalent geometry : angle 0.65448 (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 628 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 626 time to evaluate : 1.742 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: A 8 LYS cc_start: 0.9483 (tptp) cc_final: 0.9205 (tptp) REVERT: A 104 TYR cc_start: 0.8816 (m-80) cc_final: 0.8221 (m-80) REVERT: A 107 LYS cc_start: 0.9455 (mttm) cc_final: 0.9187 (mmmt) REVERT: A 120 ASP cc_start: 0.9351 (m-30) cc_final: 0.9117 (m-30) REVERT: A 129 PHE cc_start: 0.9546 (m-80) cc_final: 0.9186 (m-80) REVERT: A 144 MET cc_start: 0.8987 (mtm) cc_final: 0.8593 (mtm) REVERT: A 168 VAL cc_start: 0.9253 (m) cc_final: 0.8934 (p) REVERT: A 191 GLN cc_start: 0.9344 (mm-40) cc_final: 0.8976 (mp10) REVERT: A 194 LYS cc_start: 0.9432 (ttpp) cc_final: 0.9224 (ttpp) REVERT: A 227 MET cc_start: 0.9312 (mtp) cc_final: 0.8802 (mtp) REVERT: A 252 ASN cc_start: 0.8961 (t0) cc_final: 0.8624 (t0) REVERT: A 272 ASP cc_start: 0.8951 (p0) cc_final: 0.8726 (p0) REVERT: A 286 ASP cc_start: 0.8968 (m-30) cc_final: 0.8327 (m-30) REVERT: A 335 GLU cc_start: 0.9264 (tp30) cc_final: 0.9014 (tm-30) REVERT: A 337 ILE cc_start: 0.9658 (pt) cc_final: 0.9390 (pt) REVERT: A 362 ASP cc_start: 0.9157 (m-30) cc_final: 0.8871 (m-30) REVERT: A 366 LYS cc_start: 0.9306 (ptpp) cc_final: 0.8969 (pttm) REVERT: A 370 ASN cc_start: 0.9444 (m-40) cc_final: 0.9170 (m110) REVERT: A 375 LYS cc_start: 0.9469 (mttt) cc_final: 0.9105 (mttt) REVERT: A 411 LEU cc_start: 0.8736 (mp) cc_final: 0.8437 (mp) REVERT: A 414 LEU cc_start: 0.9593 (mt) cc_final: 0.9384 (mt) REVERT: A 468 LEU cc_start: 0.9588 (tp) cc_final: 0.9317 (tp) REVERT: A 493 MET cc_start: 0.9410 (tmm) cc_final: 0.9090 (tmm) REVERT: A 494 MET cc_start: 0.9502 (mtt) cc_final: 0.9109 (mtp) REVERT: A 500 ILE cc_start: 0.9877 (mt) cc_final: 0.9566 (mt) REVERT: A 515 ASP cc_start: 0.9481 (m-30) cc_final: 0.9232 (m-30) REVERT: A 575 ARG cc_start: 0.8953 (ptp90) cc_final: 0.8184 (ptp-110) REVERT: A 583 SER cc_start: 0.9492 (t) cc_final: 0.9248 (t) REVERT: A 586 TYR cc_start: 0.9084 (m-80) cc_final: 0.8879 (m-80) REVERT: A 591 THR cc_start: 0.9201 (p) cc_final: 0.8981 (p) REVERT: A 595 MET cc_start: 0.9101 (tpp) cc_final: 0.8876 (tpp) REVERT: A 598 MET cc_start: 0.8843 (ttt) cc_final: 0.8565 (tmm) REVERT: A 602 GLU cc_start: 0.8652 (pt0) cc_final: 0.7954 (pt0) REVERT: A 626 TYR cc_start: 0.9302 (m-80) cc_final: 0.8985 (m-10) REVERT: A 632 MET cc_start: 0.8895 (mtp) cc_final: 0.8634 (mtp) REVERT: A 653 SER cc_start: 0.9190 (p) cc_final: 0.8901 (p) REVERT: B 51 LEU cc_start: 0.9568 (tp) cc_final: 0.9173 (tp) REVERT: B 77 ILE cc_start: 0.9712 (mt) cc_final: 0.9382 (mt) REVERT: B 81 PHE cc_start: 0.9510 (m-80) cc_final: 0.9262 (m-80) REVERT: B 87 LYS cc_start: 0.9332 (tptp) cc_final: 0.9014 (tptp) REVERT: B 89 PHE cc_start: 0.9266 (t80) cc_final: 0.8995 (t80) REVERT: B 95 MET cc_start: 0.9451 (tpp) cc_final: 0.8239 (tpp) REVERT: B 99 LYS cc_start: 0.9575 (mmmt) cc_final: 0.8775 (mmmt) REVERT: B 114 ILE cc_start: 0.9681 (mt) cc_final: 0.9424 (pt) REVERT: B 144 MET cc_start: 0.9426 (mtm) cc_final: 0.8968 (mtm) REVERT: B 149 TYR cc_start: 0.9188 (t80) cc_final: 0.8609 (t80) REVERT: B 191 GLN cc_start: 0.9214 (mm-40) cc_final: 0.8776 (mm-40) REVERT: B 250 TYR cc_start: 0.8850 (m-80) cc_final: 0.8535 (m-80) REVERT: B 257 ASP cc_start: 0.8510 (m-30) cc_final: 0.8259 (m-30) REVERT: B 286 ASP cc_start: 0.9025 (m-30) cc_final: 0.8290 (m-30) REVERT: B 317 MET cc_start: 0.8739 (pmm) cc_final: 0.7604 (pmm) REVERT: B 355 TYR cc_start: 0.9161 (m-10) cc_final: 0.8935 (m-10) REVERT: B 359 MET cc_start: 0.8013 (ttp) cc_final: 0.7734 (ptp) REVERT: B 362 ASP cc_start: 0.8785 (m-30) cc_final: 0.7901 (m-30) REVERT: B 373 ILE cc_start: 0.9821 (mt) cc_final: 0.9119 (mt) REVERT: B 375 LYS cc_start: 0.9184 (mmmm) cc_final: 0.8945 (mmmt) REVERT: B 396 ASP cc_start: 0.8592 (p0) cc_final: 0.8086 (p0) REVERT: B 399 GLU cc_start: 0.9434 (mm-30) cc_final: 0.9154 (mm-30) REVERT: B 415 ASN cc_start: 0.9065 (t0) cc_final: 0.7702 (t0) REVERT: B 418 ASN cc_start: 0.9139 (m-40) cc_final: 0.8573 (m-40) REVERT: B 426 GLU cc_start: 0.9004 (tm-30) cc_final: 0.8692 (tm-30) REVERT: B 472 LEU cc_start: 0.9734 (mt) cc_final: 0.9496 (mt) REVERT: B 494 MET cc_start: 0.9355 (mtp) cc_final: 0.8942 (mtp) REVERT: B 496 ASN cc_start: 0.9676 (t0) cc_final: 0.8408 (t0) REVERT: B 499 SER cc_start: 0.9875 (t) cc_final: 0.9612 (p) REVERT: B 500 ILE cc_start: 0.9778 (mt) cc_final: 0.9508 (mt) REVERT: B 501 GLN cc_start: 0.8836 (tp-100) cc_final: 0.8276 (tp-100) REVERT: B 515 ASP cc_start: 0.9177 (m-30) cc_final: 0.8773 (m-30) REVERT: B 516 GLN cc_start: 0.9303 (tp-100) cc_final: 0.9075 (tt0) REVERT: B 570 MET cc_start: 0.9178 (tpp) cc_final: 0.8565 (tpt) REVERT: B 575 ARG cc_start: 0.8767 (mtm110) cc_final: 0.7354 (mtm180) REVERT: B 588 GLN cc_start: 0.9399 (mm-40) cc_final: 0.8859 (mm-40) REVERT: B 618 LEU cc_start: 0.8998 (mt) cc_final: 0.8743 (mt) REVERT: B 667 LEU cc_start: 0.9604 (tt) cc_final: 0.9357 (tt) REVERT: C 179 TYR cc_start: 0.9517 (t80) cc_final: 0.9315 (t80) REVERT: C 185 MET cc_start: 0.8958 (mpp) cc_final: 0.8753 (mpp) REVERT: C 204 TYR cc_start: 0.9664 (t80) cc_final: 0.9350 (t80) REVERT: C 231 LEU cc_start: 0.9420 (mt) cc_final: 0.9140 (mt) REVERT: D 46 TYR cc_start: 0.8994 (m-80) cc_final: 0.8766 (m-10) REVERT: D 179 TYR cc_start: 0.9185 (t80) cc_final: 0.8927 (t80) REVERT: D 185 MET cc_start: 0.7783 (mmm) cc_final: 0.6849 (mmm) REVERT: D 189 GLU cc_start: 0.9043 (tp30) cc_final: 0.8687 (pt0) outliers start: 2 outliers final: 1 residues processed: 626 average time/residue: 0.2836 time to fit residues: 260.2811 Evaluate side-chains 558 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 557 time to evaluate : 1.904 ------------------------------------------------------------------------------- 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: 2.9990 chunk 126 optimal weight: 5.9990 chunk 62 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 156 optimal weight: 5.9990 chunk 21 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 169 optimal weight: 2.9990 chunk 113 optimal weight: 9.9990 chunk 177 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- 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 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 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 192 ASN D 234 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.109684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.078071 restraints weight = 51868.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.080679 restraints weight = 31356.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.082602 restraints weight = 21759.179| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.7029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16386 Z= 0.194 Angle : 0.650 13.867 22134 Z= 0.339 Chirality : 0.043 0.275 2360 Planarity : 0.004 0.080 2818 Dihedral : 11.057 175.599 2242 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.12 % Allowed : 1.52 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.19), residues: 1932 helix: 0.88 (0.15), residues: 1135 sheet: -1.01 (0.42), residues: 138 loop : 0.12 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 558 HIS 0.007 0.001 HIS A 372 PHE 0.038 0.002 PHE D 109 TYR 0.031 0.002 TYR C 142 ARG 0.010 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 869) hydrogen bonds : angle 5.02476 ( 2568) covalent geometry : bond 0.00409 (16386) covalent geometry : angle 0.64983 (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 634 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 632 time to evaluate : 1.957 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: 0.9515 (tptp) cc_final: 0.9263 (tppt) REVERT: A 95 MET cc_start: 0.9542 (mmp) cc_final: 0.9263 (mmm) REVERT: A 104 TYR cc_start: 0.8750 (m-80) cc_final: 0.8142 (m-80) REVERT: A 107 LYS cc_start: 0.9487 (mttm) cc_final: 0.9178 (mmmt) REVERT: A 129 PHE cc_start: 0.9574 (m-80) cc_final: 0.9197 (m-80) REVERT: A 136 LYS cc_start: 0.9794 (mmtt) cc_final: 0.9574 (mmmm) REVERT: A 144 MET cc_start: 0.9019 (mtm) cc_final: 0.8647 (mtm) REVERT: A 168 VAL cc_start: 0.9203 (m) cc_final: 0.8866 (p) REVERT: A 180 ASN cc_start: 0.8804 (m110) cc_final: 0.8504 (m-40) REVERT: A 191 GLN cc_start: 0.9321 (mm-40) cc_final: 0.8988 (mp10) REVERT: A 227 MET cc_start: 0.9199 (mtp) cc_final: 0.8879 (mtp) REVERT: A 235 ARG cc_start: 0.8172 (mtm110) cc_final: 0.7910 (mtm110) REVERT: A 252 ASN cc_start: 0.8957 (t0) cc_final: 0.8655 (t0) REVERT: A 286 ASP cc_start: 0.9066 (m-30) cc_final: 0.8511 (m-30) REVERT: A 307 TYR cc_start: 0.9410 (t80) cc_final: 0.9207 (t80) REVERT: A 335 GLU cc_start: 0.9296 (tp30) cc_final: 0.9069 (tm-30) REVERT: A 337 ILE cc_start: 0.9658 (pt) cc_final: 0.9342 (pt) REVERT: A 362 ASP cc_start: 0.9201 (m-30) cc_final: 0.8662 (m-30) REVERT: A 370 ASN cc_start: 0.9418 (m-40) cc_final: 0.9091 (m110) REVERT: A 375 LYS cc_start: 0.9480 (mttt) cc_final: 0.9090 (mttt) REVERT: A 405 LEU cc_start: 0.9186 (mt) cc_final: 0.8767 (mt) REVERT: A 414 LEU cc_start: 0.9560 (mt) cc_final: 0.9283 (mt) REVERT: A 468 LEU cc_start: 0.9595 (tp) cc_final: 0.9340 (tp) REVERT: A 493 MET cc_start: 0.9401 (tmm) cc_final: 0.9049 (tmm) REVERT: A 494 MET cc_start: 0.9508 (mtt) cc_final: 0.9102 (mtp) REVERT: A 500 ILE cc_start: 0.9889 (mt) cc_final: 0.9632 (mt) REVERT: A 515 ASP cc_start: 0.9488 (m-30) cc_final: 0.9233 (m-30) REVERT: A 571 TYR cc_start: 0.8992 (t80) cc_final: 0.8427 (t80) REVERT: A 575 ARG cc_start: 0.8854 (ptp90) cc_final: 0.8283 (ptp-110) REVERT: A 583 SER cc_start: 0.9458 (t) cc_final: 0.9210 (t) REVERT: A 591 THR cc_start: 0.9163 (p) cc_final: 0.8915 (p) REVERT: A 595 MET cc_start: 0.9102 (tpp) cc_final: 0.8851 (tpp) REVERT: A 598 MET cc_start: 0.8849 (ttt) cc_final: 0.8592 (tmm) REVERT: A 602 GLU cc_start: 0.8699 (pt0) cc_final: 0.8356 (pt0) REVERT: A 615 MET cc_start: 0.8994 (mmp) cc_final: 0.8707 (mmp) REVERT: A 632 MET cc_start: 0.8954 (mtp) cc_final: 0.8496 (mtp) REVERT: A 653 SER cc_start: 0.9030 (p) cc_final: 0.8679 (p) REVERT: B 51 LEU cc_start: 0.9550 (tp) cc_final: 0.9189 (tp) REVERT: B 77 ILE cc_start: 0.9645 (mt) cc_final: 0.9277 (mt) REVERT: B 81 PHE cc_start: 0.9509 (m-80) cc_final: 0.9264 (m-80) REVERT: B 87 LYS cc_start: 0.9430 (tptp) cc_final: 0.9125 (tptp) REVERT: B 95 MET cc_start: 0.9402 (tpp) cc_final: 0.8146 (tpp) REVERT: B 99 LYS cc_start: 0.9574 (mmmt) cc_final: 0.8755 (mmmt) REVERT: B 114 ILE cc_start: 0.9618 (mt) cc_final: 0.9312 (pt) REVERT: B 144 MET cc_start: 0.9429 (mtm) cc_final: 0.8949 (mtm) REVERT: B 149 TYR cc_start: 0.9201 (t80) cc_final: 0.8648 (t80) REVERT: B 161 ARG cc_start: 0.8556 (mtp85) cc_final: 0.7975 (mtt-85) REVERT: B 191 GLN cc_start: 0.9261 (mm-40) cc_final: 0.8730 (mm-40) REVERT: B 257 ASP cc_start: 0.8487 (m-30) cc_final: 0.8264 (m-30) REVERT: B 286 ASP cc_start: 0.9152 (m-30) cc_final: 0.8481 (m-30) REVERT: B 317 MET cc_start: 0.8369 (pmm) cc_final: 0.7986 (pmm) REVERT: B 350 ARG cc_start: 0.9143 (tpp80) cc_final: 0.8796 (tpp80) REVERT: B 355 TYR cc_start: 0.9300 (m-10) cc_final: 0.9041 (m-10) REVERT: B 359 MET cc_start: 0.7955 (ttp) cc_final: 0.7716 (ptp) REVERT: B 362 ASP cc_start: 0.8845 (m-30) cc_final: 0.7975 (m-30) REVERT: B 373 ILE cc_start: 0.9823 (mt) cc_final: 0.9116 (mt) REVERT: B 375 LYS cc_start: 0.9194 (mmmm) cc_final: 0.8943 (mmmt) REVERT: B 396 ASP cc_start: 0.8605 (p0) cc_final: 0.8140 (p0) REVERT: B 399 GLU cc_start: 0.9455 (mm-30) cc_final: 0.9183 (mm-30) REVERT: B 415 ASN cc_start: 0.9079 (t0) cc_final: 0.8282 (t0) REVERT: B 418 ASN cc_start: 0.9269 (m-40) cc_final: 0.8945 (m-40) REVERT: B 427 LYS cc_start: 0.9710 (ptpp) cc_final: 0.9307 (ptpp) REVERT: B 459 LYS cc_start: 0.9118 (mmmt) cc_final: 0.8903 (mmmt) REVERT: B 467 ASN cc_start: 0.9316 (m-40) cc_final: 0.9075 (m-40) REVERT: B 472 LEU cc_start: 0.9721 (mt) cc_final: 0.9471 (mt) REVERT: B 496 ASN cc_start: 0.9680 (t0) cc_final: 0.8531 (t0) REVERT: B 499 SER cc_start: 0.9876 (t) cc_final: 0.9615 (p) REVERT: B 500 ILE cc_start: 0.9798 (mt) cc_final: 0.9553 (mt) REVERT: B 501 GLN cc_start: 0.8865 (tp-100) cc_final: 0.8305 (tp-100) REVERT: B 515 ASP cc_start: 0.9183 (m-30) cc_final: 0.8816 (m-30) REVERT: B 516 GLN cc_start: 0.9347 (tp-100) cc_final: 0.9103 (tt0) REVERT: B 570 MET cc_start: 0.9174 (tpp) cc_final: 0.8524 (tpt) REVERT: B 575 ARG cc_start: 0.8769 (mtm110) cc_final: 0.7385 (mtm180) REVERT: B 618 LEU cc_start: 0.8989 (mt) cc_final: 0.8683 (mt) REVERT: B 632 MET cc_start: 0.8866 (mmp) cc_final: 0.8611 (mmp) REVERT: B 656 LEU cc_start: 0.9488 (mt) cc_final: 0.9203 (mt) REVERT: B 667 LEU cc_start: 0.9573 (tt) cc_final: 0.9337 (tt) REVERT: C 185 MET cc_start: 0.8898 (mpp) cc_final: 0.8686 (mpp) REVERT: C 204 TYR cc_start: 0.9668 (t80) cc_final: 0.9360 (t80) REVERT: D 46 TYR cc_start: 0.8995 (m-80) cc_final: 0.8751 (m-10) REVERT: D 74 MET cc_start: 0.7245 (tmm) cc_final: 0.6970 (tmm) REVERT: D 185 MET cc_start: 0.7828 (mmm) cc_final: 0.7151 (mmm) REVERT: D 189 GLU cc_start: 0.9074 (tp30) cc_final: 0.8792 (pt0) REVERT: D 201 HIS cc_start: 0.8913 (m170) cc_final: 0.8654 (m170) REVERT: D 239 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6512 (pt0) outliers start: 2 outliers final: 1 residues processed: 634 average time/residue: 0.2968 time to fit residues: 275.3227 Evaluate side-chains 562 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 560 time to evaluate : 1.771 ------------------------------------------------------------------------------- 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: 8.9990 chunk 85 optimal weight: 0.9980 chunk 161 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 40 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 184 optimal weight: 8.9990 chunk 119 optimal weight: 3.9990 chunk 175 optimal weight: 1.9990 chunk 24 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS ** 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 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 132 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.111891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.079768 restraints weight = 51999.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.082361 restraints weight = 31362.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.084347 restraints weight = 22127.996| |-----------------------------------------------------------------------------| r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3093 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3093 r_free = 0.3093 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3093 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.7321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16386 Z= 0.167 Angle : 0.628 7.420 22134 Z= 0.331 Chirality : 0.043 0.221 2360 Planarity : 0.004 0.067 2818 Dihedral : 10.993 176.115 2242 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % 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: 0.61 (0.19), residues: 1932 helix: 0.87 (0.15), residues: 1129 sheet: -0.91 (0.43), residues: 142 loop : 0.12 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 558 HIS 0.007 0.001 HIS B 572 PHE 0.029 0.002 PHE D 109 TYR 0.056 0.002 TYR D 142 ARG 0.013 0.001 ARG B 665 Details of bonding type rmsd hydrogen bonds : bond 0.03841 ( 869) hydrogen bonds : angle 5.01240 ( 2568) covalent geometry : bond 0.00358 (16386) covalent geometry : angle 0.62777 (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 632 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 632 time to evaluate : 1.848 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: 0.9505 (tptp) cc_final: 0.9234 (tppt) REVERT: A 29 ASP cc_start: 0.9506 (t0) cc_final: 0.9133 (t70) REVERT: A 65 GLU cc_start: 0.8873 (mm-30) cc_final: 0.8439 (mm-30) REVERT: A 89 PHE cc_start: 0.9077 (t80) cc_final: 0.8844 (t80) REVERT: A 95 MET cc_start: 0.9649 (mmp) cc_final: 0.9230 (mmm) REVERT: A 99 LYS cc_start: 0.9667 (mmmm) cc_final: 0.9352 (mmmm) REVERT: A 104 TYR cc_start: 0.8803 (m-80) cc_final: 0.8257 (m-80) REVERT: A 107 LYS cc_start: 0.9486 (mttm) cc_final: 0.9023 (tptt) REVERT: A 120 ASP cc_start: 0.9348 (m-30) cc_final: 0.9058 (m-30) REVERT: A 129 PHE cc_start: 0.9573 (m-80) cc_final: 0.9221 (m-80) REVERT: A 144 MET cc_start: 0.8935 (mtm) cc_final: 0.8555 (mtm) REVERT: A 145 ILE cc_start: 0.9429 (tp) cc_final: 0.9127 (tp) REVERT: A 151 PRO cc_start: 0.9712 (Cg_exo) cc_final: 0.9393 (Cg_endo) REVERT: A 180 ASN cc_start: 0.8748 (m110) cc_final: 0.8415 (m-40) REVERT: A 205 LYS cc_start: 0.8749 (mmmm) cc_final: 0.8328 (mmmm) REVERT: A 227 MET cc_start: 0.9315 (mtp) cc_final: 0.8788 (mtp) REVERT: A 235 ARG cc_start: 0.8304 (mtm110) cc_final: 0.7907 (mtm180) REVERT: A 252 ASN cc_start: 0.8892 (t0) cc_final: 0.8593 (t0) REVERT: A 286 ASP cc_start: 0.9061 (m-30) cc_final: 0.8472 (m-30) REVERT: A 307 TYR cc_start: 0.9480 (t80) cc_final: 0.9236 (t80) REVERT: A 317 MET cc_start: 0.8617 (mpp) cc_final: 0.7933 (mpp) REVERT: A 322 MET cc_start: 0.9200 (mmp) cc_final: 0.8966 (mmm) REVERT: A 335 GLU cc_start: 0.9310 (tp30) cc_final: 0.9086 (tm-30) REVERT: A 337 ILE cc_start: 0.9660 (pt) cc_final: 0.9354 (pt) REVERT: A 362 ASP cc_start: 0.9226 (m-30) cc_final: 0.8912 (m-30) REVERT: A 366 LYS cc_start: 0.9453 (ptpp) cc_final: 0.8926 (pttm) REVERT: A 370 ASN cc_start: 0.9411 (m-40) cc_final: 0.9057 (m110) REVERT: A 375 LYS cc_start: 0.9504 (mttt) cc_final: 0.9072 (mttt) REVERT: A 414 LEU cc_start: 0.9555 (mt) cc_final: 0.9315 (mt) REVERT: A 468 LEU cc_start: 0.9582 (tp) cc_final: 0.9320 (tp) REVERT: A 493 MET cc_start: 0.9370 (tmm) cc_final: 0.9010 (tmm) REVERT: A 500 ILE cc_start: 0.9892 (mt) cc_final: 0.9647 (mt) REVERT: A 515 ASP cc_start: 0.9482 (m-30) cc_final: 0.9221 (m-30) REVERT: A 571 TYR cc_start: 0.8969 (t80) cc_final: 0.8424 (t80) REVERT: A 575 ARG cc_start: 0.8876 (ptp90) cc_final: 0.8330 (ptp-110) REVERT: A 583 SER cc_start: 0.9413 (t) cc_final: 0.9136 (t) REVERT: A 595 MET cc_start: 0.9076 (tpp) cc_final: 0.8817 (tpp) REVERT: A 598 MET cc_start: 0.8837 (ttt) cc_final: 0.8601 (tmm) REVERT: A 602 GLU cc_start: 0.8753 (pt0) cc_final: 0.8336 (pt0) REVERT: A 615 MET cc_start: 0.9047 (mmp) cc_final: 0.8742 (mmp) REVERT: A 632 MET cc_start: 0.8964 (mtp) cc_final: 0.8536 (mtp) REVERT: A 653 SER cc_start: 0.9049 (p) cc_final: 0.8722 (p) REVERT: A 667 LEU cc_start: 0.9575 (tt) cc_final: 0.9362 (tt) REVERT: B 51 LEU cc_start: 0.9514 (tp) cc_final: 0.9188 (tp) REVERT: B 77 ILE cc_start: 0.9659 (mt) cc_final: 0.9274 (mt) REVERT: B 81 PHE cc_start: 0.9461 (m-80) cc_final: 0.9226 (m-80) REVERT: B 87 LYS cc_start: 0.9415 (tptp) cc_final: 0.9108 (tptp) REVERT: B 95 MET cc_start: 0.9362 (tpp) cc_final: 0.8154 (tpp) REVERT: B 99 LYS cc_start: 0.9594 (mmmt) cc_final: 0.8725 (mmmt) REVERT: B 114 ILE cc_start: 0.9580 (mt) cc_final: 0.9325 (pt) REVERT: B 144 MET cc_start: 0.9333 (mtm) cc_final: 0.8938 (mtm) REVERT: B 149 TYR cc_start: 0.9253 (t80) cc_final: 0.8543 (t80) REVERT: B 191 GLN cc_start: 0.9239 (mm-40) cc_final: 0.8757 (mm-40) REVERT: B 235 ARG cc_start: 0.8791 (mtm110) cc_final: 0.8167 (mtm110) REVERT: B 257 ASP cc_start: 0.8437 (m-30) cc_final: 0.8084 (m-30) REVERT: B 286 ASP cc_start: 0.9182 (m-30) cc_final: 0.8594 (m-30) REVERT: B 322 MET cc_start: 0.8391 (ttt) cc_final: 0.7904 (ttt) REVERT: B 350 ARG cc_start: 0.9157 (tpp80) cc_final: 0.8896 (tpp80) REVERT: B 355 TYR cc_start: 0.9265 (m-10) cc_final: 0.9063 (m-80) REVERT: B 362 ASP cc_start: 0.8869 (m-30) cc_final: 0.8059 (m-30) REVERT: B 373 ILE cc_start: 0.9783 (mt) cc_final: 0.9063 (mt) REVERT: B 375 LYS cc_start: 0.9177 (mmmm) cc_final: 0.8921 (mmmt) REVERT: B 396 ASP cc_start: 0.8576 (p0) cc_final: 0.8119 (p0) REVERT: B 399 GLU cc_start: 0.9437 (mm-30) cc_final: 0.9157 (mm-30) REVERT: B 415 ASN cc_start: 0.9288 (t0) cc_final: 0.8401 (t0) REVERT: B 416 ILE cc_start: 0.9825 (mt) cc_final: 0.9557 (mt) REVERT: B 418 ASN cc_start: 0.9294 (m-40) cc_final: 0.8954 (m-40) REVERT: B 420 MET cc_start: 0.9196 (mmm) cc_final: 0.8783 (mmm) REVERT: B 426 GLU cc_start: 0.9284 (pm20) cc_final: 0.8919 (pm20) REVERT: B 427 LYS cc_start: 0.9700 (ptpp) cc_final: 0.9323 (ptpp) REVERT: B 446 ARG cc_start: 0.8588 (mpt180) cc_final: 0.8202 (mmt-90) REVERT: B 467 ASN cc_start: 0.9368 (m-40) cc_final: 0.9130 (m110) REVERT: B 472 LEU cc_start: 0.9755 (mt) cc_final: 0.9534 (mt) REVERT: B 496 ASN cc_start: 0.9660 (t0) cc_final: 0.8628 (t0) REVERT: B 499 SER cc_start: 0.9875 (t) cc_final: 0.9610 (p) REVERT: B 500 ILE cc_start: 0.9805 (mt) cc_final: 0.9575 (mt) REVERT: B 501 GLN cc_start: 0.8862 (tp-100) cc_final: 0.8346 (tp-100) REVERT: B 515 ASP cc_start: 0.9146 (m-30) cc_final: 0.8754 (m-30) REVERT: B 516 GLN cc_start: 0.9319 (tp-100) cc_final: 0.9062 (tt0) REVERT: B 570 MET cc_start: 0.9183 (tpp) cc_final: 0.8534 (tpt) REVERT: B 575 ARG cc_start: 0.8753 (mtm110) cc_final: 0.7362 (mtm180) REVERT: B 588 GLN cc_start: 0.9410 (mm110) cc_final: 0.9141 (mm110) REVERT: B 595 MET cc_start: 0.9644 (mmt) cc_final: 0.9101 (mpp) REVERT: B 618 LEU cc_start: 0.8923 (mt) cc_final: 0.8681 (mt) REVERT: B 631 ASP cc_start: 0.9498 (m-30) cc_final: 0.9238 (m-30) REVERT: B 650 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7859 (mm-40) REVERT: B 667 LEU cc_start: 0.9603 (tt) cc_final: 0.9343 (tt) REVERT: C 46 TYR cc_start: 0.8748 (m-80) cc_final: 0.8513 (m-80) REVERT: C 179 TYR cc_start: 0.9240 (t80) cc_final: 0.8869 (t80) REVERT: C 204 TYR cc_start: 0.9656 (t80) cc_final: 0.9352 (t80) REVERT: D 46 TYR cc_start: 0.9022 (m-80) cc_final: 0.8767 (m-10) REVERT: D 179 TYR cc_start: 0.9089 (t80) cc_final: 0.8735 (t80) REVERT: D 185 MET cc_start: 0.7768 (mmm) cc_final: 0.6831 (mmm) REVERT: D 189 GLU cc_start: 0.9035 (tp30) cc_final: 0.8712 (pt0) REVERT: D 201 HIS cc_start: 0.9050 (m170) cc_final: 0.8819 (m170) outliers start: 0 outliers final: 0 residues processed: 632 average time/residue: 0.2881 time to fit residues: 266.1908 Evaluate side-chains 551 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 551 time to evaluate : 1.935 ------------------------------------------------------------------------------- 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: 7.9990 chunk 51 optimal weight: 6.9990 chunk 159 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 183 optimal weight: 8.9990 chunk 52 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 365 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 320 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** 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 = 0.3563 r_free = 0.3563 target = 0.114214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.081684 restraints weight = 53211.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.084367 restraints weight = 32145.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.086286 restraints weight = 22601.319| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.7616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16386 Z= 0.159 Angle : 0.625 8.370 22134 Z= 0.330 Chirality : 0.042 0.193 2360 Planarity : 0.004 0.064 2818 Dihedral : 10.969 176.143 2242 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.19), residues: 1932 helix: 0.81 (0.15), residues: 1127 sheet: -0.99 (0.43), residues: 144 loop : 0.16 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 558 HIS 0.006 0.001 HIS A 372 PHE 0.028 0.002 PHE C 92 TYR 0.033 0.002 TYR A 684 ARG 0.011 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 869) hydrogen bonds : angle 4.97339 ( 2568) covalent geometry : bond 0.00342 (16386) covalent geometry : angle 0.62501 (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 621 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 621 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: A 8 LYS cc_start: 0.9471 (tptp) cc_final: 0.9213 (tppt) REVERT: A 65 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8531 (mm-30) REVERT: A 95 MET cc_start: 0.9566 (mmp) cc_final: 0.9108 (mmm) REVERT: A 99 LYS cc_start: 0.9680 (mmmm) cc_final: 0.9259 (mmmm) REVERT: A 104 TYR cc_start: 0.8823 (m-80) cc_final: 0.8286 (m-80) REVERT: A 107 LYS cc_start: 0.9466 (mttm) cc_final: 0.9022 (tptt) REVERT: A 120 ASP cc_start: 0.9345 (m-30) cc_final: 0.9141 (m-30) REVERT: A 129 PHE cc_start: 0.9591 (m-80) cc_final: 0.9229 (m-80) REVERT: A 144 MET cc_start: 0.8872 (mtm) cc_final: 0.8495 (mtm) REVERT: A 161 ARG cc_start: 0.9272 (ttm110) cc_final: 0.8884 (ttm110) REVERT: A 205 LYS cc_start: 0.8737 (mmmm) cc_final: 0.8347 (mmmm) REVERT: A 227 MET cc_start: 0.9182 (mtp) cc_final: 0.8836 (mtp) REVERT: A 235 ARG cc_start: 0.8359 (mtm110) cc_final: 0.8148 (mtm110) REVERT: A 252 ASN cc_start: 0.8863 (t0) cc_final: 0.8587 (t0) REVERT: A 266 LYS cc_start: 0.9335 (ptmm) cc_final: 0.9035 (pptt) REVERT: A 286 ASP cc_start: 0.9062 (m-30) cc_final: 0.8478 (m-30) REVERT: A 307 TYR cc_start: 0.9490 (t80) cc_final: 0.9222 (t80) REVERT: A 317 MET cc_start: 0.8377 (mpp) cc_final: 0.7794 (mpp) REVERT: A 322 MET cc_start: 0.9253 (mmp) cc_final: 0.9016 (mmm) REVERT: A 335 GLU cc_start: 0.9288 (tp30) cc_final: 0.9070 (tm-30) REVERT: A 337 ILE cc_start: 0.9668 (pt) cc_final: 0.9341 (pt) REVERT: A 362 ASP cc_start: 0.9201 (m-30) cc_final: 0.8678 (m-30) REVERT: A 366 LYS cc_start: 0.9428 (ptpp) cc_final: 0.9076 (pttp) REVERT: A 370 ASN cc_start: 0.9419 (m-40) cc_final: 0.9115 (m110) REVERT: A 375 LYS cc_start: 0.9474 (mttt) cc_final: 0.9123 (mttt) REVERT: A 385 VAL cc_start: 0.9680 (t) cc_final: 0.9401 (m) REVERT: A 414 LEU cc_start: 0.9554 (mt) cc_final: 0.9259 (mt) REVERT: A 421 GLU cc_start: 0.9289 (tm-30) cc_final: 0.9076 (tm-30) REVERT: A 468 LEU cc_start: 0.9582 (tp) cc_final: 0.9340 (tp) REVERT: A 493 MET cc_start: 0.9246 (tmm) cc_final: 0.8890 (tmm) REVERT: A 494 MET cc_start: 0.9537 (mtt) cc_final: 0.9045 (mtp) REVERT: A 500 ILE cc_start: 0.9887 (mt) cc_final: 0.9636 (mt) REVERT: A 515 ASP cc_start: 0.9474 (m-30) cc_final: 0.9220 (m-30) REVERT: A 571 TYR cc_start: 0.8892 (t80) cc_final: 0.8319 (t80) REVERT: A 575 ARG cc_start: 0.8946 (ptp90) cc_final: 0.8319 (ptp-110) REVERT: A 583 SER cc_start: 0.9383 (t) cc_final: 0.9113 (t) REVERT: A 595 MET cc_start: 0.9030 (tpp) cc_final: 0.8727 (tpp) REVERT: A 598 MET cc_start: 0.8818 (ttt) cc_final: 0.8609 (tmm) REVERT: A 601 ILE cc_start: 0.9208 (tt) cc_final: 0.8990 (tt) REVERT: A 602 GLU cc_start: 0.8737 (pt0) cc_final: 0.8411 (mp0) REVERT: A 615 MET cc_start: 0.9071 (mmp) cc_final: 0.7943 (mmp) REVERT: A 632 MET cc_start: 0.8886 (mtp) cc_final: 0.8626 (mtp) REVERT: A 653 SER cc_start: 0.9111 (p) cc_final: 0.8836 (p) REVERT: A 667 LEU cc_start: 0.9571 (tt) cc_final: 0.9340 (tt) REVERT: B 51 LEU cc_start: 0.9484 (tp) cc_final: 0.9174 (tp) REVERT: B 77 ILE cc_start: 0.9661 (mt) cc_final: 0.9281 (mt) REVERT: B 87 LYS cc_start: 0.9392 (tptp) cc_final: 0.9110 (tptp) REVERT: B 95 MET cc_start: 0.9318 (tpp) cc_final: 0.8128 (tpp) REVERT: B 99 LYS cc_start: 0.9609 (mmmt) cc_final: 0.8743 (mmmt) REVERT: B 114 ILE cc_start: 0.9547 (mt) cc_final: 0.9269 (pt) REVERT: B 149 TYR cc_start: 0.9284 (t80) cc_final: 0.8466 (t80) REVERT: B 191 GLN cc_start: 0.9238 (mm-40) cc_final: 0.8788 (mm-40) REVERT: B 235 ARG cc_start: 0.8794 (mtm110) cc_final: 0.8126 (mtm110) REVERT: B 252 ASN cc_start: 0.8955 (t0) cc_final: 0.8683 (t0) REVERT: B 257 ASP cc_start: 0.8430 (m-30) cc_final: 0.8111 (m-30) REVERT: B 286 ASP cc_start: 0.9174 (m-30) cc_final: 0.8528 (m-30) REVERT: B 312 GLN cc_start: 0.8962 (pm20) cc_final: 0.8761 (pm20) REVERT: B 317 MET cc_start: 0.7991 (pmm) cc_final: 0.7777 (pmm) REVERT: B 350 ARG cc_start: 0.9155 (tpp80) cc_final: 0.8359 (tpp80) REVERT: B 362 ASP cc_start: 0.8873 (m-30) cc_final: 0.8157 (m-30) REVERT: B 373 ILE cc_start: 0.9790 (mt) cc_final: 0.9094 (mt) REVERT: B 375 LYS cc_start: 0.9169 (mmmm) cc_final: 0.8938 (mmmt) REVERT: B 396 ASP cc_start: 0.8509 (p0) cc_final: 0.8023 (p0) REVERT: B 399 GLU cc_start: 0.9415 (mm-30) cc_final: 0.9100 (mm-30) REVERT: B 415 ASN cc_start: 0.9313 (t0) cc_final: 0.8361 (t0) REVERT: B 416 ILE cc_start: 0.9826 (mt) cc_final: 0.9518 (mt) REVERT: B 418 ASN cc_start: 0.9302 (m-40) cc_final: 0.8938 (m-40) REVERT: B 420 MET cc_start: 0.9231 (mmm) cc_final: 0.8797 (mmm) REVERT: B 426 GLU cc_start: 0.9239 (pm20) cc_final: 0.8874 (pm20) REVERT: B 427 LYS cc_start: 0.9705 (ptpp) cc_final: 0.9311 (ptpp) REVERT: B 446 ARG cc_start: 0.8568 (mpt180) cc_final: 0.8181 (mmt-90) REVERT: B 496 ASN cc_start: 0.9634 (t0) cc_final: 0.8521 (t0) REVERT: B 499 SER cc_start: 0.9862 (t) cc_final: 0.9551 (p) REVERT: B 500 ILE cc_start: 0.9800 (mt) cc_final: 0.9513 (mt) REVERT: B 501 GLN cc_start: 0.8845 (tp-100) cc_final: 0.8352 (tp-100) REVERT: B 515 ASP cc_start: 0.9147 (m-30) cc_final: 0.8746 (m-30) REVERT: B 516 GLN cc_start: 0.9310 (tp-100) cc_final: 0.9071 (tt0) REVERT: B 570 MET cc_start: 0.9216 (tpp) cc_final: 0.8546 (tpt) REVERT: B 575 ARG cc_start: 0.8733 (mtm110) cc_final: 0.7222 (mtm180) REVERT: B 588 GLN cc_start: 0.9464 (mm110) cc_final: 0.9109 (mm110) REVERT: B 618 LEU cc_start: 0.8967 (mt) cc_final: 0.8734 (mt) REVERT: B 631 ASP cc_start: 0.9413 (m-30) cc_final: 0.9211 (m-30) REVERT: B 655 THR cc_start: 0.9238 (m) cc_final: 0.9037 (m) REVERT: B 667 LEU cc_start: 0.9596 (tt) cc_final: 0.9283 (tt) REVERT: B 675 HIS cc_start: 0.9403 (t70) cc_final: 0.9182 (t70) REVERT: C 20 MET cc_start: 0.8466 (mmm) cc_final: 0.7963 (tpt) REVERT: C 46 TYR cc_start: 0.8767 (m-80) cc_final: 0.8518 (m-80) REVERT: C 74 MET cc_start: 0.4930 (ppp) cc_final: 0.4710 (ppp) REVERT: C 179 TYR cc_start: 0.9246 (t80) cc_final: 0.8963 (t80) REVERT: C 204 TYR cc_start: 0.9671 (t80) cc_final: 0.9432 (t80) REVERT: D 46 TYR cc_start: 0.9045 (m-80) cc_final: 0.8793 (m-10) REVERT: D 74 MET cc_start: 0.7296 (tmm) cc_final: 0.6914 (tmm) REVERT: D 96 MET cc_start: 0.8881 (mmm) cc_final: 0.8509 (mmt) outliers start: 0 outliers final: 0 residues processed: 621 average time/residue: 0.2815 time to fit residues: 255.7831 Evaluate side-chains 541 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 541 time to evaluate : 1.918 ------------------------------------------------------------------------------- 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: 2.9990 chunk 102 optimal weight: 0.7980 chunk 182 optimal weight: 5.9990 chunk 107 optimal weight: 0.0470 chunk 77 optimal weight: 7.9990 chunk 96 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 127 optimal weight: 0.8980 chunk 188 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 overall best weight: 1.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 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** ** 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 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** 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 = 0.3584 r_free = 0.3584 target = 0.114610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.082471 restraints weight = 51040.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.085237 restraints weight = 31698.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.087042 restraints weight = 22197.992| |-----------------------------------------------------------------------------| r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 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 = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.7796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16386 Z= 0.135 Angle : 0.630 7.399 22134 Z= 0.331 Chirality : 0.043 0.232 2360 Planarity : 0.004 0.048 2818 Dihedral : 10.785 175.844 2242 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.06 % Allowed : 0.52 % Favored : 99.42 % 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: 0.59 (0.19), residues: 1932 helix: 0.81 (0.15), residues: 1123 sheet: -1.01 (0.42), residues: 146 loop : 0.23 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 558 HIS 0.008 0.001 HIS C 201 PHE 0.026 0.002 PHE A 129 TYR 0.034 0.002 TYR C 142 ARG 0.011 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03809 ( 869) hydrogen bonds : angle 4.97183 ( 2568) covalent geometry : bond 0.00296 (16386) covalent geometry : angle 0.63004 (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 617 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 616 time to evaluate : 1.900 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: A 95 MET cc_start: 0.9545 (mmp) cc_final: 0.8800 (mmm) REVERT: A 99 LYS cc_start: 0.9679 (mmmm) cc_final: 0.8947 (mttp) REVERT: A 104 TYR cc_start: 0.8828 (m-80) cc_final: 0.8509 (m-80) REVERT: A 107 LYS cc_start: 0.9479 (mttm) cc_final: 0.9189 (mmmt) REVERT: A 119 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8646 (mt-10) REVERT: A 120 ASP cc_start: 0.9288 (m-30) cc_final: 0.9076 (m-30) REVERT: A 129 PHE cc_start: 0.9599 (m-80) cc_final: 0.9295 (m-80) REVERT: A 136 LYS cc_start: 0.9813 (mmtt) cc_final: 0.9523 (ttpt) REVERT: A 144 MET cc_start: 0.8860 (mtm) cc_final: 0.8426 (mtm) REVERT: A 205 LYS cc_start: 0.8704 (mmmm) cc_final: 0.8325 (mmmm) REVERT: A 226 VAL cc_start: 0.9260 (t) cc_final: 0.9045 (t) REVERT: A 227 MET cc_start: 0.9274 (mtp) cc_final: 0.8810 (mtp) REVERT: A 252 ASN cc_start: 0.8857 (t0) cc_final: 0.8596 (t0) REVERT: A 266 LYS cc_start: 0.9316 (ptmm) cc_final: 0.9017 (pptt) REVERT: A 286 ASP cc_start: 0.9020 (m-30) cc_final: 0.8441 (m-30) REVERT: A 307 TYR cc_start: 0.9552 (t80) cc_final: 0.9343 (t80) REVERT: A 314 MET cc_start: 0.8677 (ppp) cc_final: 0.8031 (ppp) REVERT: A 317 MET cc_start: 0.8534 (mpp) cc_final: 0.8076 (mpp) REVERT: A 322 MET cc_start: 0.9286 (mmp) cc_final: 0.8963 (mmm) REVERT: A 335 GLU cc_start: 0.9230 (tp30) cc_final: 0.8979 (tm-30) REVERT: A 337 ILE cc_start: 0.9653 (pt) cc_final: 0.9313 (pt) REVERT: A 350 ARG cc_start: 0.8490 (mtp85) cc_final: 0.8064 (mtp85) REVERT: A 362 ASP cc_start: 0.9085 (m-30) cc_final: 0.8673 (m-30) REVERT: A 366 LYS cc_start: 0.9399 (ptpp) cc_final: 0.9048 (pttp) REVERT: A 370 ASN cc_start: 0.9442 (m-40) cc_final: 0.9116 (m110) REVERT: A 375 LYS cc_start: 0.9475 (mttt) cc_final: 0.9104 (mttt) REVERT: A 385 VAL cc_start: 0.9650 (t) cc_final: 0.9356 (m) REVERT: A 414 LEU cc_start: 0.9539 (mt) cc_final: 0.9268 (mt) REVERT: A 421 GLU cc_start: 0.9287 (tm-30) cc_final: 0.9066 (tm-30) REVERT: A 426 GLU cc_start: 0.9416 (tm-30) cc_final: 0.8910 (tm-30) REVERT: A 468 LEU cc_start: 0.9577 (tp) cc_final: 0.9292 (tp) REVERT: A 479 TYR cc_start: 0.8870 (t80) cc_final: 0.8200 (t80) REVERT: A 493 MET cc_start: 0.9246 (tmm) cc_final: 0.8906 (tmm) REVERT: A 494 MET cc_start: 0.9492 (mtt) cc_final: 0.9117 (mmt) REVERT: A 500 ILE cc_start: 0.9881 (mt) cc_final: 0.9647 (mt) REVERT: A 515 ASP cc_start: 0.9516 (m-30) cc_final: 0.9277 (m-30) REVERT: A 562 LYS cc_start: 0.9796 (ttmt) cc_final: 0.9425 (tttt) REVERT: A 571 TYR cc_start: 0.8842 (t80) cc_final: 0.8337 (t80) REVERT: A 575 ARG cc_start: 0.8935 (ptp90) cc_final: 0.8320 (ptp-110) REVERT: A 595 MET cc_start: 0.8965 (tpp) cc_final: 0.8709 (tpp) REVERT: A 598 MET cc_start: 0.8893 (ttt) cc_final: 0.8643 (tmm) REVERT: A 602 GLU cc_start: 0.8958 (pt0) cc_final: 0.8221 (mp0) REVERT: A 615 MET cc_start: 0.9057 (mmp) cc_final: 0.7696 (mmp) REVERT: A 632 MET cc_start: 0.9064 (mtp) cc_final: 0.8695 (mtp) REVERT: A 653 SER cc_start: 0.9139 (p) cc_final: 0.8751 (p) REVERT: A 667 LEU cc_start: 0.9563 (tt) cc_final: 0.9360 (tt) REVERT: A 677 ARG cc_start: 0.9413 (mmm-85) cc_final: 0.8776 (mmm-85) REVERT: B 51 LEU cc_start: 0.9515 (tp) cc_final: 0.9218 (tp) REVERT: B 87 LYS cc_start: 0.9360 (tptp) cc_final: 0.9113 (tptp) REVERT: B 95 MET cc_start: 0.9276 (tpp) cc_final: 0.7980 (tpp) REVERT: B 99 LYS cc_start: 0.9613 (mmmt) cc_final: 0.8741 (mmmt) REVERT: B 143 LEU cc_start: 0.9669 (tp) cc_final: 0.9451 (tp) REVERT: B 144 MET cc_start: 0.9421 (mtm) cc_final: 0.8969 (mtm) REVERT: B 149 TYR cc_start: 0.9314 (t80) cc_final: 0.8512 (t80) REVERT: B 191 GLN cc_start: 0.9132 (mm-40) cc_final: 0.8699 (mm-40) REVERT: B 235 ARG cc_start: 0.8795 (mtm110) cc_final: 0.8239 (mtm110) REVERT: B 252 ASN cc_start: 0.8954 (t0) cc_final: 0.8655 (t0) REVERT: B 257 ASP cc_start: 0.8468 (m-30) cc_final: 0.8140 (m-30) REVERT: B 286 ASP cc_start: 0.9203 (m-30) cc_final: 0.8556 (m-30) REVERT: B 333 LYS cc_start: 0.9056 (tptp) cc_final: 0.8790 (tptp) REVERT: B 335 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8237 (mt-10) REVERT: B 362 ASP cc_start: 0.8918 (m-30) cc_final: 0.8138 (m-30) REVERT: B 373 ILE cc_start: 0.9765 (mt) cc_final: 0.9081 (mt) REVERT: B 375 LYS cc_start: 0.9124 (mmmm) cc_final: 0.8897 (mmmt) REVERT: B 381 LEU cc_start: 0.8917 (pt) cc_final: 0.8676 (pt) REVERT: B 396 ASP cc_start: 0.8439 (p0) cc_final: 0.8225 (p0) REVERT: B 399 GLU cc_start: 0.9383 (mm-30) cc_final: 0.9082 (mm-30) REVERT: B 407 ILE cc_start: 0.8704 (mt) cc_final: 0.8223 (mt) REVERT: B 415 ASN cc_start: 0.9142 (t0) cc_final: 0.8389 (t0) REVERT: B 416 ILE cc_start: 0.9813 (mt) cc_final: 0.9555 (mt) REVERT: B 418 ASN cc_start: 0.9378 (m-40) cc_final: 0.8982 (m-40) REVERT: B 420 MET cc_start: 0.9241 (mmm) cc_final: 0.8778 (mmm) REVERT: B 426 GLU cc_start: 0.9250 (pm20) cc_final: 0.8843 (pm20) REVERT: B 427 LYS cc_start: 0.9719 (ptpp) cc_final: 0.9298 (ptpp) REVERT: B 446 ARG cc_start: 0.8570 (mpt180) cc_final: 0.8176 (mmt-90) REVERT: B 459 LYS cc_start: 0.9193 (mmtt) cc_final: 0.8899 (mmmt) REVERT: B 496 ASN cc_start: 0.9636 (t0) cc_final: 0.8610 (t0) REVERT: B 499 SER cc_start: 0.9866 (t) cc_final: 0.9513 (p) REVERT: B 500 ILE cc_start: 0.9784 (mt) cc_final: 0.9520 (mt) REVERT: B 501 GLN cc_start: 0.8838 (tp-100) cc_final: 0.8360 (tp-100) REVERT: B 515 ASP cc_start: 0.9137 (m-30) cc_final: 0.8741 (m-30) REVERT: B 516 GLN cc_start: 0.9284 (tp-100) cc_final: 0.9018 (tt0) REVERT: B 570 MET cc_start: 0.9260 (tpp) cc_final: 0.8707 (tpt) REVERT: B 575 ARG cc_start: 0.8631 (mtm110) cc_final: 0.7274 (mtm180) REVERT: B 588 GLN cc_start: 0.9542 (mm110) cc_final: 0.9267 (mm110) REVERT: B 595 MET cc_start: 0.9412 (mmm) cc_final: 0.8977 (mpp) REVERT: B 598 MET cc_start: 0.9099 (mtp) cc_final: 0.8801 (mtp) REVERT: B 618 LEU cc_start: 0.8934 (mt) cc_final: 0.8635 (mt) REVERT: B 631 ASP cc_start: 0.9377 (m-30) cc_final: 0.9127 (m-30) REVERT: B 656 LEU cc_start: 0.9452 (mt) cc_final: 0.9214 (mt) REVERT: B 657 PHE cc_start: 0.9355 (m-80) cc_final: 0.8723 (m-80) REVERT: B 667 LEU cc_start: 0.9583 (tt) cc_final: 0.9381 (tt) REVERT: B 675 HIS cc_start: 0.9420 (t70) cc_final: 0.9204 (t70) REVERT: C 20 MET cc_start: 0.8465 (mmm) cc_final: 0.8073 (tpt) REVERT: C 21 PHE cc_start: 0.9443 (m-80) cc_final: 0.8845 (m-80) REVERT: C 46 TYR cc_start: 0.8767 (m-80) cc_final: 0.8545 (m-80) REVERT: C 179 TYR cc_start: 0.9222 (t80) cc_final: 0.8825 (t80) REVERT: C 204 TYR cc_start: 0.9660 (t80) cc_final: 0.9410 (t80) REVERT: D 46 TYR cc_start: 0.9055 (m-80) cc_final: 0.8849 (m-10) REVERT: D 178 PHE cc_start: 0.9232 (m-80) cc_final: 0.8970 (m-80) REVERT: D 311 THR cc_start: 0.9599 (m) cc_final: 0.9368 (p) outliers start: 1 outliers final: 1 residues processed: 616 average time/residue: 0.2923 time to fit residues: 262.7635 Evaluate side-chains 545 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 544 time to evaluate : 1.907 ------------------------------------------------------------------------------- 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: 4.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 8.9990 chunk 160 optimal weight: 20.0000 chunk 106 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 135 optimal weight: 0.6980 chunk 148 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 overall best weight: 2.3384 ------------------------------------------------------------------------------- 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 365 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** ** 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 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** 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 = 0.3586 r_free = 0.3586 target = 0.113582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.080690 restraints weight = 53163.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.083394 restraints weight = 32085.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.085344 restraints weight = 22445.925| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.8031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16386 Z= 0.177 Angle : 0.673 8.663 22134 Z= 0.355 Chirality : 0.043 0.201 2360 Planarity : 0.004 0.050 2818 Dihedral : 10.883 175.952 2242 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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: 0.47 (0.19), residues: 1932 helix: 0.74 (0.15), residues: 1124 sheet: -1.16 (0.43), residues: 144 loop : 0.16 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 558 HIS 0.007 0.001 HIS A 372 PHE 0.022 0.002 PHE A 129 TYR 0.025 0.002 TYR A 684 ARG 0.008 0.001 ARG B 243 Details of bonding type rmsd hydrogen bonds : bond 0.03926 ( 869) hydrogen bonds : angle 5.07104 ( 2568) covalent geometry : bond 0.00379 (16386) covalent geometry : angle 0.67252 (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 601 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 601 time to evaluate : 1.772 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 36 TYR cc_start: 0.9582 (t80) cc_final: 0.9330 (t80) REVERT: A 41 ILE cc_start: 0.9521 (mt) cc_final: 0.9298 (mt) REVERT: A 65 GLU cc_start: 0.8886 (mm-30) cc_final: 0.8540 (mm-30) REVERT: A 89 PHE cc_start: 0.9120 (t80) cc_final: 0.8877 (t80) REVERT: A 95 MET cc_start: 0.9575 (mmp) cc_final: 0.9174 (mmm) REVERT: A 99 LYS cc_start: 0.9693 (mmmm) cc_final: 0.9344 (mmmm) REVERT: A 104 TYR cc_start: 0.8880 (m-80) cc_final: 0.8582 (m-80) REVERT: A 107 LYS cc_start: 0.9499 (mttm) cc_final: 0.9031 (tptt) REVERT: A 119 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8650 (mt-10) REVERT: A 129 PHE cc_start: 0.9614 (m-80) cc_final: 0.9285 (m-80) REVERT: A 136 LYS cc_start: 0.9813 (mmtt) cc_final: 0.9600 (mmmm) REVERT: A 144 MET cc_start: 0.8867 (mtm) cc_final: 0.8438 (mtm) REVERT: A 161 ARG cc_start: 0.9123 (ttm110) cc_final: 0.8911 (ttm110) REVERT: A 205 LYS cc_start: 0.8682 (mmmm) cc_final: 0.8407 (mmmm) REVERT: A 227 MET cc_start: 0.9181 (mtp) cc_final: 0.8828 (mtp) REVERT: A 230 LEU cc_start: 0.9545 (mt) cc_final: 0.9318 (mt) REVERT: A 235 ARG cc_start: 0.8304 (mtm110) cc_final: 0.8091 (mtm110) REVERT: A 252 ASN cc_start: 0.8937 (t0) cc_final: 0.8608 (t0) REVERT: A 266 LYS cc_start: 0.9324 (ptmm) cc_final: 0.9011 (pptt) REVERT: A 286 ASP cc_start: 0.9012 (m-30) cc_final: 0.8443 (m-30) REVERT: A 307 TYR cc_start: 0.9565 (t80) cc_final: 0.9350 (t80) REVERT: A 314 MET cc_start: 0.8855 (ppp) cc_final: 0.8566 (ppp) REVERT: A 317 MET cc_start: 0.8587 (mpp) cc_final: 0.8041 (mpp) REVERT: A 322 MET cc_start: 0.9285 (mmp) cc_final: 0.8675 (mmm) REVERT: A 335 GLU cc_start: 0.9302 (tp30) cc_final: 0.9044 (tm-30) REVERT: A 337 ILE cc_start: 0.9679 (pt) cc_final: 0.9382 (pt) REVERT: A 362 ASP cc_start: 0.9125 (m-30) cc_final: 0.8767 (m-30) REVERT: A 366 LYS cc_start: 0.9433 (ptpp) cc_final: 0.9002 (pttp) REVERT: A 370 ASN cc_start: 0.9485 (m-40) cc_final: 0.9213 (m110) REVERT: A 375 LYS cc_start: 0.9446 (mttt) cc_final: 0.9076 (mttt) REVERT: A 385 VAL cc_start: 0.9688 (t) cc_final: 0.9429 (m) REVERT: A 414 LEU cc_start: 0.9569 (mt) cc_final: 0.9206 (mt) REVERT: A 421 GLU cc_start: 0.9315 (tm-30) cc_final: 0.9110 (tm-30) REVERT: A 426 GLU cc_start: 0.9433 (tm-30) cc_final: 0.8904 (tm-30) REVERT: A 444 ASP cc_start: 0.8756 (t70) cc_final: 0.7745 (t0) REVERT: A 468 LEU cc_start: 0.9600 (tp) cc_final: 0.9333 (tp) REVERT: A 493 MET cc_start: 0.9170 (tmm) cc_final: 0.8838 (tmm) REVERT: A 494 MET cc_start: 0.9513 (mtt) cc_final: 0.9072 (mmt) REVERT: A 500 ILE cc_start: 0.9880 (mt) cc_final: 0.9667 (mt) REVERT: A 501 GLN cc_start: 0.9586 (mm-40) cc_final: 0.8848 (tp-100) REVERT: A 515 ASP cc_start: 0.9507 (m-30) cc_final: 0.9271 (m-30) REVERT: A 562 LYS cc_start: 0.9766 (ttmt) cc_final: 0.9463 (tttt) REVERT: A 575 ARG cc_start: 0.8949 (ptp90) cc_final: 0.8305 (ptp-110) REVERT: A 595 MET cc_start: 0.8945 (tpp) cc_final: 0.8671 (tpp) REVERT: A 598 MET cc_start: 0.8894 (ttt) cc_final: 0.8646 (tmm) REVERT: A 602 GLU cc_start: 0.8805 (pt0) cc_final: 0.8550 (mp0) REVERT: A 615 MET cc_start: 0.9039 (mmp) cc_final: 0.7927 (mmp) REVERT: A 632 MET cc_start: 0.9114 (mtp) cc_final: 0.8802 (mtp) REVERT: A 667 LEU cc_start: 0.9587 (tt) cc_final: 0.9383 (tt) REVERT: A 683 TYR cc_start: 0.8200 (t80) cc_final: 0.7917 (t80) REVERT: B 51 LEU cc_start: 0.9524 (tp) cc_final: 0.8962 (tp) REVERT: B 75 GLU cc_start: 0.9582 (mp0) cc_final: 0.9360 (pm20) REVERT: B 77 ILE cc_start: 0.9607 (mt) cc_final: 0.9206 (mt) REVERT: B 81 PHE cc_start: 0.9608 (m-10) cc_final: 0.9286 (m-80) REVERT: B 87 LYS cc_start: 0.9397 (tptp) cc_final: 0.9162 (tptp) REVERT: B 95 MET cc_start: 0.9297 (tpp) cc_final: 0.8140 (tpp) REVERT: B 99 LYS cc_start: 0.9613 (mmmt) cc_final: 0.8779 (mmmt) REVERT: B 114 ILE cc_start: 0.9535 (mt) cc_final: 0.9278 (pt) REVERT: B 144 MET cc_start: 0.9452 (mtm) cc_final: 0.8919 (mtm) REVERT: B 149 TYR cc_start: 0.9324 (t80) cc_final: 0.8565 (t80) REVERT: B 190 MET cc_start: 0.9638 (mtm) cc_final: 0.9196 (mmp) REVERT: B 191 GLN cc_start: 0.9185 (mm-40) cc_final: 0.8742 (mm-40) REVERT: B 211 GLU cc_start: 0.8458 (mm-30) cc_final: 0.6970 (mt-10) REVERT: B 235 ARG cc_start: 0.8803 (mtm110) cc_final: 0.8230 (mtm110) REVERT: B 257 ASP cc_start: 0.8503 (m-30) cc_final: 0.8176 (m-30) REVERT: B 286 ASP cc_start: 0.9241 (m-30) cc_final: 0.8621 (m-30) REVERT: B 307 TYR cc_start: 0.9403 (t80) cc_final: 0.9173 (t80) REVERT: B 319 MET cc_start: 0.9095 (tpt) cc_final: 0.8861 (tpp) REVERT: B 322 MET cc_start: 0.8738 (tpt) cc_final: 0.8050 (tpp) REVERT: B 326 PHE cc_start: 0.9442 (m-80) cc_final: 0.8444 (m-80) REVERT: B 333 LYS cc_start: 0.9060 (tptp) cc_final: 0.8797 (tptp) REVERT: B 335 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8262 (mt-10) REVERT: B 357 TYR cc_start: 0.9070 (m-10) cc_final: 0.8189 (m-10) REVERT: B 362 ASP cc_start: 0.8878 (m-30) cc_final: 0.8128 (m-30) REVERT: B 373 ILE cc_start: 0.9773 (mt) cc_final: 0.9197 (mt) REVERT: B 396 ASP cc_start: 0.8547 (p0) cc_final: 0.8293 (p0) REVERT: B 399 GLU cc_start: 0.9430 (mm-30) cc_final: 0.9163 (mm-30) REVERT: B 415 ASN cc_start: 0.9029 (t0) cc_final: 0.8206 (t0) REVERT: B 416 ILE cc_start: 0.9822 (mt) cc_final: 0.9532 (mt) REVERT: B 418 ASN cc_start: 0.9345 (m-40) cc_final: 0.8971 (m-40) REVERT: B 420 MET cc_start: 0.9226 (mmm) cc_final: 0.8722 (mmm) REVERT: B 426 GLU cc_start: 0.9273 (pm20) cc_final: 0.8879 (pm20) REVERT: B 427 LYS cc_start: 0.9714 (ptpp) cc_final: 0.9268 (ptpp) REVERT: B 459 LYS cc_start: 0.9229 (mmtt) cc_final: 0.8969 (mmtm) REVERT: B 496 ASN cc_start: 0.9681 (t0) cc_final: 0.8612 (t0) REVERT: B 499 SER cc_start: 0.9862 (t) cc_final: 0.9623 (p) REVERT: B 500 ILE cc_start: 0.9796 (mt) cc_final: 0.9559 (mt) REVERT: B 501 GLN cc_start: 0.8901 (tp-100) cc_final: 0.8423 (tp-100) REVERT: B 515 ASP cc_start: 0.9135 (m-30) cc_final: 0.8687 (m-30) REVERT: B 516 GLN cc_start: 0.9320 (tp-100) cc_final: 0.9107 (tt0) REVERT: B 570 MET cc_start: 0.9250 (tpp) cc_final: 0.8670 (tpt) REVERT: B 575 ARG cc_start: 0.8751 (mtm110) cc_final: 0.7357 (mtm180) REVERT: B 588 GLN cc_start: 0.9515 (mm110) cc_final: 0.9289 (mm110) REVERT: B 595 MET cc_start: 0.9442 (mmm) cc_final: 0.8970 (mpp) REVERT: B 613 TYR cc_start: 0.9223 (t80) cc_final: 0.8937 (t80) REVERT: B 618 LEU cc_start: 0.8972 (mt) cc_final: 0.8758 (mt) REVERT: B 631 ASP cc_start: 0.9399 (m-30) cc_final: 0.9185 (m-30) REVERT: B 654 PHE cc_start: 0.8975 (t80) cc_final: 0.8378 (t80) REVERT: B 655 THR cc_start: 0.9268 (m) cc_final: 0.8961 (m) REVERT: B 656 LEU cc_start: 0.9482 (mt) cc_final: 0.9227 (mt) REVERT: B 675 HIS cc_start: 0.9379 (t70) cc_final: 0.9166 (t70) REVERT: C 17 PHE cc_start: 0.8636 (p90) cc_final: 0.7691 (p90) REVERT: C 21 PHE cc_start: 0.9419 (m-80) cc_final: 0.8818 (m-80) REVERT: C 74 MET cc_start: 0.5371 (ppp) cc_final: 0.5068 (ppp) REVERT: C 179 TYR cc_start: 0.9276 (t80) cc_final: 0.8887 (t80) REVERT: C 204 TYR cc_start: 0.9735 (t80) cc_final: 0.9145 (t80) REVERT: D 33 GLU cc_start: 0.9222 (mp0) cc_final: 0.9011 (mp0) REVERT: D 46 TYR cc_start: 0.9042 (m-80) cc_final: 0.8757 (m-10) REVERT: D 74 MET cc_start: 0.7438 (tmm) cc_final: 0.6977 (tmm) REVERT: D 178 PHE cc_start: 0.9295 (m-80) cc_final: 0.9080 (m-80) REVERT: D 185 MET cc_start: 0.7458 (mmm) cc_final: 0.7073 (mmp) REVERT: D 311 THR cc_start: 0.9596 (m) cc_final: 0.9390 (p) outliers start: 0 outliers final: 0 residues processed: 601 average time/residue: 0.3207 time to fit residues: 285.2896 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 : 1.917 ------------------------------------------------------------------------------- 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: 4.9990 chunk 16 optimal weight: 0.2980 chunk 2 optimal weight: 0.7980 chunk 97 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 179 optimal weight: 6.9990 chunk 190 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 180 optimal weight: 7.9990 chunk 108 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 365 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 646 GLN ** 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 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** 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 = 0.3632 r_free = 0.3632 target = 0.114164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.083765 restraints weight = 52777.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.086596 restraints weight = 30855.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.088640 restraints weight = 21231.668| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.8164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16386 Z= 0.137 Angle : 0.648 8.377 22134 Z= 0.343 Chirality : 0.043 0.200 2360 Planarity : 0.004 0.047 2818 Dihedral : 10.728 175.678 2242 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.19), residues: 1932 helix: 0.80 (0.15), residues: 1110 sheet: -1.23 (0.43), residues: 142 loop : 0.19 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 558 HIS 0.008 0.001 HIS C 201 PHE 0.026 0.002 PHE A 129 TYR 0.030 0.002 TYR C 46 ARG 0.007 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 869) hydrogen bonds : angle 5.03482 ( 2568) covalent geometry : bond 0.00304 (16386) covalent geometry : angle 0.64850 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6554.39 seconds wall clock time: 115 minutes 3.30 seconds (6903.30 seconds total)