Starting phenix.real_space_refine on Sat May 17 16:55:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzd_45064/05_2025/9bzd_45064_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzd_45064/05_2025/9bzd_45064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bzd_45064/05_2025/9bzd_45064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzd_45064/05_2025/9bzd_45064.map" model { file = "/net/cci-nas-00/data/ceres_data/9bzd_45064/05_2025/9bzd_45064_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzd_45064/05_2025/9bzd_45064_neut.cif" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 9.27, per 1000 atoms: 0.58 Number of scatterers: 16038 At special positions: 0 Unit cell: (93.288, 128.778, 129.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.69 Conformation dependent library (CDL) restraints added in 2.0 seconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.73 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: 4.094A 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: 3.984A 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: 3.953A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.664A 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: 4.128A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.694A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.850A 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: 3.580A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.677A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.878A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A 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: 6.027A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.068A 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: 3.544A 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 180 removed outlier: 4.934A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.668A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A 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: 7.426A 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: 6.605A 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: 6.453A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.478A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.185A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.049A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.549A 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: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.89 Time building geometry restraints manager: 4.32 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: 4892 1.34 - 1.46: 3091 1.46 - 1.58: 8222 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.060 1.25e-02 6.40e+03 2.34e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.579 -0.039 1.20e-02 6.94e+03 1.07e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.033 1.08e-02 8.57e+03 9.08e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.568 -0.031 1.17e-02 7.31e+03 7.11e+00 bond pdb=" CA ILE C 35 " pdb=" CB ILE C 35 " ideal model delta sigma weight residual 1.537 1.568 -0.031 1.21e-02 6.83e+03 6.69e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 21579 2.10 - 4.19: 513 4.19 - 6.29: 37 6.29 - 8.38: 1 8.38 - 10.48: 4 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.60 -6.06 1.36e+00 5.41e-01 1.99e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.14 -4.43 1.15e+00 7.56e-01 1.48e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.22 -3.94 1.09e+00 8.42e-01 1.31e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.82 -4.32 1.23e+00 6.61e-01 1.23e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.73 -4.02 1.15e+00 7.56e-01 1.22e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 9470 35.80 - 71.60: 337 71.60 - 107.40: 37 107.40 - 143.20: 3 143.20 - 178.99: 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 -58.32 120.68 -178.99 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 301.68 151.21 150.47 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 31.93 148.04 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 9847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2147 0.093 - 0.187: 180 0.187 - 0.280: 28 0.280 - 0.373: 3 0.373 - 0.467: 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 5.44e+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 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.017 2.00e-02 2.50e+03 1.10e-02 2.13e+00 pdb=" CG PHE D 92 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 169 " 0.017 2.00e-02 2.50e+03 1.01e-02 2.04e+00 pdb=" CG TYR C 169 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 169 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 169 " 0.008 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 131 2.51 - 3.11: 11547 3.11 - 3.70: 27037 3.70 - 4.30: 41565 4.30 - 4.90: 65447 Nonbonded interactions: 145727 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.911 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.962 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.012 3.040 ... (remaining 145722 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: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 35.460 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 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= 0.316 Angle : 0.740 10.479 22134 Z= 0.463 Chirality : 0.058 0.467 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.948 178.994 6154 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.34 % Allowed : 15.33 % 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: 0.57 (0.18), residues: 1932 helix: 0.59 (0.14), residues: 1149 sheet: 0.46 (0.42), residues: 124 loop : 0.24 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE C 168 TYR 0.021 0.002 TYR D 179 ARG 0.003 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.15424 ( 871) hydrogen bonds : angle 6.51733 ( 2571) covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74031 (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 1098 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 1075 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLN cc_start: 0.8048 (mt0) cc_final: 0.7537 (mt0) REVERT: A 12 LEU cc_start: 0.7978 (mt) cc_final: 0.7763 (mp) REVERT: A 28 LYS cc_start: 0.8502 (mmtm) cc_final: 0.8297 (tppp) REVERT: A 76 ASP cc_start: 0.7984 (m-30) cc_final: 0.7332 (m-30) REVERT: A 127 LEU cc_start: 0.8536 (mt) cc_final: 0.8214 (mt) REVERT: A 179 LEU cc_start: 0.8732 (tp) cc_final: 0.8488 (tp) REVERT: A 181 ASP cc_start: 0.7596 (m-30) cc_final: 0.7209 (m-30) REVERT: A 204 SER cc_start: 0.8470 (m) cc_final: 0.8033 (t) REVERT: A 265 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8596 (mmmt) REVERT: A 280 ILE cc_start: 0.8960 (pt) cc_final: 0.8676 (pt) REVERT: A 348 MET cc_start: 0.7366 (tmm) cc_final: 0.6796 (tmm) REVERT: A 352 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6377 (mt-10) REVERT: A 362 ASP cc_start: 0.5957 (m-30) cc_final: 0.5567 (m-30) REVERT: A 598 MET cc_start: 0.7520 (mtm) cc_final: 0.6921 (mtp) REVERT: A 604 ARG cc_start: 0.7657 (mmp80) cc_final: 0.6301 (mmt90) REVERT: A 606 TYR cc_start: 0.6419 (m-80) cc_final: 0.5933 (m-80) REVERT: A 645 GLN cc_start: 0.8195 (tp40) cc_final: 0.7656 (tp40) REVERT: B 11 GLN cc_start: 0.7881 (mt0) cc_final: 0.7486 (mt0) REVERT: B 12 LEU cc_start: 0.8243 (mt) cc_final: 0.7947 (mt) REVERT: B 109 ASN cc_start: 0.8024 (m-40) cc_final: 0.7571 (p0) REVERT: B 121 ARG cc_start: 0.8401 (tpm170) cc_final: 0.7995 (tpp-160) REVERT: B 187 ASP cc_start: 0.6443 (t70) cc_final: 0.6214 (t0) REVERT: B 286 ASP cc_start: 0.6756 (OUTLIER) cc_final: 0.6118 (m-30) REVERT: B 295 ASP cc_start: 0.8038 (t0) cc_final: 0.7827 (t0) REVERT: B 350 ARG cc_start: 0.7566 (mtp85) cc_final: 0.7293 (mtp85) REVERT: B 362 ASP cc_start: 0.6613 (m-30) cc_final: 0.6365 (m-30) REVERT: B 366 LYS cc_start: 0.8398 (ptpp) cc_final: 0.8182 (ttmt) REVERT: B 381 LEU cc_start: 0.8713 (tp) cc_final: 0.8396 (tp) REVERT: B 387 GLN cc_start: 0.7785 (mt0) cc_final: 0.7580 (mt0) REVERT: B 458 MET cc_start: 0.8485 (mmm) cc_final: 0.8245 (mmm) REVERT: B 460 SER cc_start: 0.8996 (t) cc_final: 0.8747 (p) REVERT: B 471 TYR cc_start: 0.8414 (t80) cc_final: 0.7952 (t80) REVERT: B 485 ARG cc_start: 0.7856 (mtm-85) cc_final: 0.7324 (mtm-85) REVERT: B 493 MET cc_start: 0.8356 (tmm) cc_final: 0.8142 (tmm) REVERT: B 496 ASN cc_start: 0.8372 (t0) cc_final: 0.8095 (t0) REVERT: B 500 ILE cc_start: 0.8730 (mt) cc_final: 0.8376 (mt) REVERT: B 546 LEU cc_start: 0.9032 (mt) cc_final: 0.8740 (mt) REVERT: B 550 MET cc_start: 0.7893 (mtm) cc_final: 0.7341 (mtm) REVERT: B 601 ILE cc_start: 0.8458 (mt) cc_final: 0.8133 (mt) REVERT: B 604 ARG cc_start: 0.7109 (mmp80) cc_final: 0.6761 (tpp80) REVERT: B 612 TYR cc_start: 0.7795 (m-80) cc_final: 0.7494 (m-80) REVERT: B 664 THR cc_start: 0.8952 (p) cc_final: 0.8738 (p) REVERT: C 106 SER cc_start: 0.7759 (m) cc_final: 0.6427 (m) REVERT: C 212 ILE cc_start: 0.6000 (mt) cc_final: 0.5755 (mt) REVERT: D 178 PHE cc_start: 0.5471 (m-80) cc_final: 0.5101 (m-80) REVERT: D 193 LEU cc_start: 0.7895 (mt) cc_final: 0.7621 (mt) REVERT: D 256 VAL cc_start: 0.6964 (t) cc_final: 0.6762 (p) REVERT: D 260 ILE cc_start: 0.7126 (mt) cc_final: 0.6805 (mt) REVERT: D 315 LEU cc_start: 0.7098 (mt) cc_final: 0.6830 (mt) outliers start: 23 outliers final: 7 residues processed: 1082 average time/residue: 0.2990 time to fit residues: 460.0151 Evaluate side-chains 722 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 714 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 174 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN B 329 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 501 GLN B 646 GLN B 676 HIS C 24 GLN C 28 GLN C 80 HIS C 85 GLN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN C 270 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 80 HIS D 91 ASN D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.124964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.088771 restraints weight = 34871.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.092369 restraints weight = 16243.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.094729 restraints weight = 9637.285| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16386 Z= 0.190 Angle : 0.729 15.294 22134 Z= 0.378 Chirality : 0.046 0.215 2360 Planarity : 0.004 0.043 2818 Dihedral : 11.595 179.876 2256 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.02 % Allowed : 22.55 % Favored : 73.43 % 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: 1.37 (0.19), residues: 1932 helix: 1.39 (0.15), residues: 1129 sheet: 0.21 (0.44), residues: 130 loop : 0.42 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP D 30 HIS 0.010 0.001 HIS C 201 PHE 0.031 0.002 PHE C 168 TYR 0.020 0.002 TYR B 72 ARG 0.007 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04914 ( 871) hydrogen bonds : angle 5.14877 ( 2571) covalent geometry : bond 0.00413 (16386) covalent geometry : angle 0.72933 (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 840 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 771 time to evaluate : 1.761 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: A 65 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8375 (mm-30) REVERT: A 66 GLU cc_start: 0.8660 (tp30) cc_final: 0.8455 (tp30) REVERT: A 144 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8779 (mtm) REVERT: A 181 ASP cc_start: 0.8742 (m-30) cc_final: 0.8360 (m-30) REVERT: A 220 THR cc_start: 0.8893 (m) cc_final: 0.8640 (p) REVERT: A 221 LYS cc_start: 0.8901 (mmtp) cc_final: 0.8646 (mttp) REVERT: A 243 ARG cc_start: 0.7659 (ttp80) cc_final: 0.7381 (tmm-80) REVERT: A 257 ASP cc_start: 0.9317 (m-30) cc_final: 0.8752 (m-30) REVERT: A 335 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8690 (mm-30) REVERT: A 348 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.7292 (tmm) REVERT: A 352 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7110 (mt-10) REVERT: A 359 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8193 (ttp) REVERT: A 384 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8114 (pm20) REVERT: A 415 ASN cc_start: 0.9362 (t0) cc_final: 0.9119 (t0) REVERT: A 420 MET cc_start: 0.9323 (mmm) cc_final: 0.8921 (mmm) REVERT: A 492 PHE cc_start: 0.9252 (m-80) cc_final: 0.8968 (m-10) REVERT: A 493 MET cc_start: 0.9068 (tmm) cc_final: 0.8620 (tmm) REVERT: A 494 MET cc_start: 0.9380 (OUTLIER) cc_final: 0.8999 (mtt) REVERT: A 505 GLU cc_start: 0.9085 (mt-10) cc_final: 0.8607 (mt-10) REVERT: A 527 TYR cc_start: 0.8868 (t80) cc_final: 0.8568 (t80) REVERT: A 586 TYR cc_start: 0.8731 (m-80) cc_final: 0.8441 (m-10) REVERT: A 598 MET cc_start: 0.8710 (mtm) cc_final: 0.8243 (mtp) REVERT: A 602 GLU cc_start: 0.7879 (pt0) cc_final: 0.6864 (pt0) REVERT: A 604 ARG cc_start: 0.8877 (mmp80) cc_final: 0.8240 (mmt90) REVERT: A 615 MET cc_start: 0.9399 (mmm) cc_final: 0.9185 (mmm) REVERT: A 630 TYR cc_start: 0.8615 (m-80) cc_final: 0.8373 (m-80) REVERT: A 640 MET cc_start: 0.9490 (tpp) cc_final: 0.9180 (tpp) REVERT: A 645 GLN cc_start: 0.8872 (tp40) cc_final: 0.8613 (tp-100) REVERT: A 667 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8979 (tt) REVERT: B 41 ILE cc_start: 0.9561 (mm) cc_final: 0.9360 (mm) REVERT: B 65 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8139 (mp0) REVERT: B 99 LYS cc_start: 0.9542 (mmmm) cc_final: 0.9289 (mmmm) REVERT: B 106 LEU cc_start: 0.9166 (tp) cc_final: 0.8738 (tt) REVERT: B 109 ASN cc_start: 0.9129 (m-40) cc_final: 0.8446 (p0) REVERT: B 147 GLN cc_start: 0.8873 (mt0) cc_final: 0.8102 (mm-40) REVERT: B 184 ARG cc_start: 0.9238 (mmm-85) cc_final: 0.8950 (tpp80) REVERT: B 202 ASN cc_start: 0.9278 (t0) cc_final: 0.8731 (t0) REVERT: B 246 SER cc_start: 0.7800 (m) cc_final: 0.7553 (p) REVERT: B 257 ASP cc_start: 0.8902 (m-30) cc_final: 0.8508 (m-30) REVERT: B 286 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7383 (m-30) REVERT: B 288 PHE cc_start: 0.9424 (t80) cc_final: 0.9214 (t80) REVERT: B 290 GLU cc_start: 0.8868 (tm-30) cc_final: 0.7778 (tm-30) REVERT: B 312 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8517 (pm20) REVERT: B 317 MET cc_start: 0.8691 (ptp) cc_final: 0.8353 (pmm) REVERT: B 322 MET cc_start: 0.9325 (mmm) cc_final: 0.8961 (mmm) REVERT: B 348 MET cc_start: 0.9002 (ttp) cc_final: 0.8528 (ttp) REVERT: B 362 ASP cc_start: 0.8603 (m-30) cc_final: 0.7450 (m-30) REVERT: B 366 LYS cc_start: 0.9241 (ptpp) cc_final: 0.9014 (ptpp) REVERT: B 374 SER cc_start: 0.9035 (t) cc_final: 0.8659 (t) REVERT: B 447 ASN cc_start: 0.8543 (m-40) cc_final: 0.7874 (t0) REVERT: B 471 TYR cc_start: 0.9442 (t80) cc_final: 0.9159 (t80) REVERT: B 477 ILE cc_start: 0.9300 (mp) cc_final: 0.9066 (pt) REVERT: B 480 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8637 (mt-10) REVERT: B 492 PHE cc_start: 0.9525 (m-80) cc_final: 0.9077 (m-10) REVERT: B 493 MET cc_start: 0.9690 (tmm) cc_final: 0.9082 (tmm) REVERT: B 515 ASP cc_start: 0.9228 (m-30) cc_final: 0.8791 (m-30) REVERT: B 526 GLU cc_start: 0.9043 (tt0) cc_final: 0.8840 (tt0) REVERT: B 558 TRP cc_start: 0.9366 (m100) cc_final: 0.8856 (m100) REVERT: B 588 GLN cc_start: 0.9446 (mm-40) cc_final: 0.8960 (mm110) REVERT: B 610 LYS cc_start: 0.8690 (mmmt) cc_final: 0.8383 (mmmt) REVERT: B 612 TYR cc_start: 0.8744 (m-80) cc_final: 0.8208 (m-80) REVERT: B 640 MET cc_start: 0.9355 (tpp) cc_final: 0.9112 (tpp) REVERT: B 664 THR cc_start: 0.9333 (p) cc_final: 0.9014 (p) REVERT: B 668 ASN cc_start: 0.9249 (m-40) cc_final: 0.8883 (m110) REVERT: C 41 LEU cc_start: 0.8497 (mm) cc_final: 0.8260 (mm) REVERT: C 47 LEU cc_start: 0.8163 (mt) cc_final: 0.7822 (tp) REVERT: C 55 TYR cc_start: 0.8214 (t80) cc_final: 0.7509 (t80) REVERT: C 56 MET cc_start: 0.5647 (ttt) cc_final: 0.5418 (ttt) REVERT: C 93 MET cc_start: 0.9347 (mtt) cc_final: 0.9021 (mtt) REVERT: C 96 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8597 (mmm) REVERT: C 97 GLU cc_start: 0.6973 (mm-30) cc_final: 0.6302 (mm-30) REVERT: C 111 THR cc_start: 0.8293 (m) cc_final: 0.8014 (p) REVERT: C 130 TYR cc_start: 0.9431 (m-10) cc_final: 0.9231 (m-10) REVERT: C 164 GLU cc_start: 0.9429 (mm-30) cc_final: 0.8720 (mm-30) REVERT: C 178 PHE cc_start: 0.9037 (m-80) cc_final: 0.7912 (m-80) REVERT: C 185 MET cc_start: 0.8269 (pmm) cc_final: 0.6943 (pmm) REVERT: C 186 GLN cc_start: 0.9443 (mm110) cc_final: 0.8967 (mp10) REVERT: C 198 GLU cc_start: 0.9490 (mm-30) cc_final: 0.9020 (mm-30) REVERT: C 259 PHE cc_start: 0.8995 (t80) cc_final: 0.8715 (t80) REVERT: C 270 ASN cc_start: 0.7881 (m110) cc_final: 0.7512 (m110) REVERT: D 46 TYR cc_start: 0.9212 (m-80) cc_final: 0.8861 (m-80) REVERT: D 96 MET cc_start: 0.8552 (mmt) cc_final: 0.8323 (mmt) REVERT: D 105 TYR cc_start: 0.7613 (m-10) cc_final: 0.7409 (m-10) REVERT: D 178 PHE cc_start: 0.9131 (m-10) cc_final: 0.8275 (m-80) REVERT: D 186 GLN cc_start: 0.9109 (mm-40) cc_final: 0.8870 (mm110) REVERT: D 200 ILE cc_start: 0.8027 (tt) cc_final: 0.7498 (tt) REVERT: D 212 ILE cc_start: 0.9065 (mt) cc_final: 0.8473 (tp) REVERT: D 247 TYR cc_start: 0.8714 (m-10) cc_final: 0.8468 (m-10) REVERT: D 282 ILE cc_start: 0.4681 (OUTLIER) cc_final: 0.4275 (pt) outliers start: 69 outliers final: 34 residues processed: 798 average time/residue: 0.2628 time to fit residues: 311.5316 Evaluate side-chains 741 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 697 time to evaluate : 1.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 6.9990 chunk 168 optimal weight: 0.8980 chunk 175 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 57 optimal weight: 0.4980 chunk 52 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 189 optimal weight: 0.9990 chunk 141 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN B 232 ASN B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN D 23 ASN D 128 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.124151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.088718 restraints weight = 35223.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.092218 restraints weight = 16376.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.094595 restraints weight = 9765.616| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3085 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.5069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16386 Z= 0.152 Angle : 0.685 14.423 22134 Z= 0.352 Chirality : 0.045 0.234 2360 Planarity : 0.004 0.041 2818 Dihedral : 11.073 172.128 2253 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.44 % Allowed : 25.64 % Favored : 70.92 % 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: 1.25 (0.19), residues: 1932 helix: 1.34 (0.15), residues: 1137 sheet: 0.79 (0.48), residues: 104 loop : 0.13 (0.22), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 30 HIS 0.006 0.001 HIS B 438 PHE 0.052 0.002 PHE C 168 TYR 0.023 0.001 TYR D 242 ARG 0.006 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04415 ( 871) hydrogen bonds : angle 5.06749 ( 2571) covalent geometry : bond 0.00336 (16386) covalent geometry : angle 0.68454 (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 814 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 755 time to evaluate : 1.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.9083 (m-10) cc_final: 0.8383 (m-10) REVERT: A 65 GLU cc_start: 0.8589 (mm-30) cc_final: 0.7874 (mp0) REVERT: A 82 LYS cc_start: 0.9641 (mmmm) cc_final: 0.9307 (mmmm) REVERT: A 144 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8648 (mtm) REVERT: A 163 ARG cc_start: 0.8400 (mmp80) cc_final: 0.8165 (mmm-85) REVERT: A 181 ASP cc_start: 0.8807 (m-30) cc_final: 0.8476 (m-30) REVERT: A 187 ASP cc_start: 0.9062 (t70) cc_final: 0.8753 (t70) REVERT: A 202 ASN cc_start: 0.9454 (t0) cc_final: 0.9028 (t0) REVERT: A 220 THR cc_start: 0.8926 (m) cc_final: 0.8670 (p) REVERT: A 243 ARG cc_start: 0.7804 (ttp80) cc_final: 0.7559 (tmm-80) REVERT: A 257 ASP cc_start: 0.9343 (m-30) cc_final: 0.8756 (m-30) REVERT: A 274 ARG cc_start: 0.7830 (ttp80) cc_final: 0.6834 (ptp90) REVERT: A 286 ASP cc_start: 0.8492 (m-30) cc_final: 0.8220 (m-30) REVERT: A 321 GLU cc_start: 0.8741 (tp30) cc_final: 0.8325 (tp30) REVERT: A 335 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8623 (mm-30) REVERT: A 341 LYS cc_start: 0.9247 (mmmm) cc_final: 0.9046 (mmtt) REVERT: A 344 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8565 (mt-10) REVERT: A 348 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7529 (tmm) REVERT: A 352 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7452 (mt-10) REVERT: A 362 ASP cc_start: 0.8565 (m-30) cc_final: 0.8047 (m-30) REVERT: A 370 ASN cc_start: 0.9089 (m-40) cc_final: 0.8778 (m-40) REVERT: A 384 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.7245 (pm20) REVERT: A 415 ASN cc_start: 0.9281 (t0) cc_final: 0.9009 (t0) REVERT: A 420 MET cc_start: 0.9365 (mmm) cc_final: 0.9088 (mmm) REVERT: A 447 ASN cc_start: 0.8409 (m-40) cc_final: 0.7946 (t0) REVERT: A 493 MET cc_start: 0.9037 (tmm) cc_final: 0.8570 (tmm) REVERT: A 505 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8595 (mt-10) REVERT: A 510 LYS cc_start: 0.9079 (mtpt) cc_final: 0.8511 (mtpt) REVERT: A 512 GLU cc_start: 0.8454 (pt0) cc_final: 0.8158 (pm20) REVERT: A 527 TYR cc_start: 0.8836 (t80) cc_final: 0.8559 (t80) REVERT: A 586 TYR cc_start: 0.8744 (m-80) cc_final: 0.8455 (m-10) REVERT: A 598 MET cc_start: 0.8796 (mtm) cc_final: 0.8541 (mtp) REVERT: A 599 GLU cc_start: 0.8401 (mp0) cc_final: 0.8104 (mp0) REVERT: A 602 GLU cc_start: 0.7544 (pt0) cc_final: 0.6516 (pt0) REVERT: A 604 ARG cc_start: 0.8879 (mmp80) cc_final: 0.8229 (mmt90) REVERT: A 640 MET cc_start: 0.9524 (tpp) cc_final: 0.9021 (tpp) REVERT: A 667 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9054 (tt) REVERT: A 686 ARG cc_start: 0.8572 (mmm-85) cc_final: 0.8259 (ttm-80) REVERT: B 15 GLU cc_start: 0.8963 (mt-10) cc_final: 0.8560 (tm-30) REVERT: B 17 MET cc_start: 0.8604 (mmm) cc_final: 0.8188 (mmm) REVERT: B 27 ASP cc_start: 0.9090 (p0) cc_final: 0.8685 (p0) REVERT: B 99 LYS cc_start: 0.9585 (mmmm) cc_final: 0.9351 (mmmm) REVERT: B 106 LEU cc_start: 0.9281 (tp) cc_final: 0.8997 (tt) REVERT: B 109 ASN cc_start: 0.9101 (m-40) cc_final: 0.8586 (p0) REVERT: B 184 ARG cc_start: 0.9285 (mmm-85) cc_final: 0.8964 (tpp80) REVERT: B 202 ASN cc_start: 0.9216 (t0) cc_final: 0.8124 (t0) REVERT: B 218 ASN cc_start: 0.8948 (OUTLIER) cc_final: 0.8358 (m-40) REVERT: B 257 ASP cc_start: 0.9091 (m-30) cc_final: 0.8524 (m-30) REVERT: B 271 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8596 (mm-30) REVERT: B 286 ASP cc_start: 0.8309 (OUTLIER) cc_final: 0.7474 (m-30) REVERT: B 290 GLU cc_start: 0.8641 (tm-30) cc_final: 0.8318 (tm-30) REVERT: B 312 GLN cc_start: 0.8929 (OUTLIER) cc_final: 0.8613 (pm20) REVERT: B 317 MET cc_start: 0.8616 (ptp) cc_final: 0.8187 (pmm) REVERT: B 322 MET cc_start: 0.9321 (mmm) cc_final: 0.9118 (mmm) REVERT: B 335 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7849 (mt-10) REVERT: B 362 ASP cc_start: 0.8649 (m-30) cc_final: 0.7593 (m-30) REVERT: B 366 LYS cc_start: 0.9216 (ptpp) cc_final: 0.8905 (ptpp) REVERT: B 374 SER cc_start: 0.9091 (t) cc_final: 0.8689 (t) REVERT: B 399 GLU cc_start: 0.8162 (mp0) cc_final: 0.7895 (mp0) REVERT: B 434 ASP cc_start: 0.8929 (m-30) cc_final: 0.8436 (m-30) REVERT: B 447 ASN cc_start: 0.8498 (m-40) cc_final: 0.8295 (m-40) REVERT: B 467 ASN cc_start: 0.9403 (t0) cc_final: 0.9160 (m-40) REVERT: B 471 TYR cc_start: 0.9358 (t80) cc_final: 0.9033 (t80) REVERT: B 477 ILE cc_start: 0.9314 (mp) cc_final: 0.9103 (pt) REVERT: B 493 MET cc_start: 0.9668 (tmm) cc_final: 0.9070 (tmm) REVERT: B 515 ASP cc_start: 0.9218 (m-30) cc_final: 0.8805 (m-30) REVERT: B 558 TRP cc_start: 0.9534 (m100) cc_final: 0.8936 (m100) REVERT: B 602 GLU cc_start: 0.8718 (tt0) cc_final: 0.8514 (tm-30) REVERT: B 610 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8303 (mmmt) REVERT: B 612 TYR cc_start: 0.8769 (m-80) cc_final: 0.8343 (m-80) REVERT: C 19 GLN cc_start: 0.7817 (mp10) cc_final: 0.7455 (pm20) REVERT: C 20 MET cc_start: 0.9069 (tpp) cc_final: 0.8863 (tpp) REVERT: C 55 TYR cc_start: 0.8279 (t80) cc_final: 0.7967 (t80) REVERT: C 56 MET cc_start: 0.5771 (ttt) cc_final: 0.5282 (ttt) REVERT: C 97 GLU cc_start: 0.6588 (mm-30) cc_final: 0.5796 (mm-30) REVERT: C 164 GLU cc_start: 0.9513 (mm-30) cc_final: 0.8938 (mm-30) REVERT: C 166 PHE cc_start: 0.7961 (t80) cc_final: 0.7590 (t80) REVERT: C 169 TYR cc_start: 0.8033 (m-80) cc_final: 0.7799 (m-80) REVERT: C 178 PHE cc_start: 0.9129 (m-80) cc_final: 0.8300 (m-10) REVERT: C 185 MET cc_start: 0.8431 (pmm) cc_final: 0.7394 (pmm) REVERT: C 186 GLN cc_start: 0.9385 (mm110) cc_final: 0.8913 (mp10) REVERT: C 198 GLU cc_start: 0.9360 (mm-30) cc_final: 0.9061 (mm-30) REVERT: C 220 LYS cc_start: 0.9150 (tppt) cc_final: 0.8712 (ptpt) REVERT: C 259 PHE cc_start: 0.8863 (t80) cc_final: 0.8493 (t80) REVERT: C 268 LEU cc_start: 0.9013 (tp) cc_final: 0.8471 (pp) REVERT: C 270 ASN cc_start: 0.7838 (m110) cc_final: 0.7573 (m110) REVERT: C 274 ASP cc_start: 0.7503 (p0) cc_final: 0.7288 (p0) REVERT: C 313 GLU cc_start: 0.8850 (tt0) cc_final: 0.8583 (tt0) REVERT: D 30 TRP cc_start: 0.8687 (p-90) cc_final: 0.8345 (p-90) REVERT: D 46 TYR cc_start: 0.9241 (m-80) cc_final: 0.8832 (m-80) REVERT: D 56 MET cc_start: 0.7413 (mmm) cc_final: 0.6898 (ptp) REVERT: D 59 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7911 (mm) REVERT: D 96 MET cc_start: 0.8534 (mmt) cc_final: 0.8332 (mmt) REVERT: D 105 TYR cc_start: 0.7715 (m-10) cc_final: 0.7390 (m-10) REVERT: D 178 PHE cc_start: 0.8953 (m-10) cc_final: 0.8085 (m-80) REVERT: D 186 GLN cc_start: 0.9195 (mm-40) cc_final: 0.8805 (mp10) REVERT: D 212 ILE cc_start: 0.9263 (mt) cc_final: 0.8946 (mm) REVERT: D 227 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.7634 (m-80) REVERT: D 287 LEU cc_start: 0.6986 (OUTLIER) cc_final: 0.6700 (mt) outliers start: 59 outliers final: 36 residues processed: 778 average time/residue: 0.2657 time to fit residues: 307.6248 Evaluate side-chains 748 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 701 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 214 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 287 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 180 optimal weight: 3.9990 chunk 99 optimal weight: 8.9990 chunk 1 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN B 232 ASN B 304 HIS ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.120180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.084762 restraints weight = 36059.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.088061 restraints weight = 17119.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.090310 restraints weight = 10270.786| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3007 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3007 r_free = 0.3007 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3007 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 16386 Z= 0.216 Angle : 0.705 14.985 22134 Z= 0.360 Chirality : 0.046 0.232 2360 Planarity : 0.004 0.049 2818 Dihedral : 10.996 171.109 2247 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.66 % Allowed : 27.33 % Favored : 68.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.18), residues: 1932 helix: 1.21 (0.15), residues: 1151 sheet: 0.78 (0.48), residues: 100 loop : 0.04 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 44 HIS 0.008 0.001 HIS A 438 PHE 0.037 0.002 PHE C 168 TYR 0.023 0.002 TYR D 242 ARG 0.006 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04271 ( 871) hydrogen bonds : angle 5.10995 ( 2571) covalent geometry : bond 0.00477 (16386) covalent geometry : angle 0.70495 (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 805 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 725 time to evaluate : 1.932 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.9193 (m-10) cc_final: 0.8543 (m-10) REVERT: A 65 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8027 (mp0) REVERT: A 66 GLU cc_start: 0.8544 (tp30) cc_final: 0.8260 (tp30) REVERT: A 82 LYS cc_start: 0.9651 (mmmm) cc_final: 0.9343 (mmmm) REVERT: A 134 THR cc_start: 0.9507 (OUTLIER) cc_final: 0.9189 (t) REVERT: A 144 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8750 (mtm) REVERT: A 181 ASP cc_start: 0.8857 (m-30) cc_final: 0.8555 (m-30) REVERT: A 187 ASP cc_start: 0.9092 (t70) cc_final: 0.8756 (t70) REVERT: A 218 ASN cc_start: 0.9207 (t0) cc_final: 0.8856 (t0) REVERT: A 257 ASP cc_start: 0.9427 (m-30) cc_final: 0.8881 (m-30) REVERT: A 321 GLU cc_start: 0.8863 (tp30) cc_final: 0.8490 (tp30) REVERT: A 359 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8367 (ttp) REVERT: A 370 ASN cc_start: 0.9229 (m-40) cc_final: 0.8929 (m-40) REVERT: A 384 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.7650 (pm20) REVERT: A 415 ASN cc_start: 0.9281 (t0) cc_final: 0.9053 (t0) REVERT: A 420 MET cc_start: 0.9353 (mmm) cc_final: 0.9038 (mmm) REVERT: A 447 ASN cc_start: 0.8499 (m-40) cc_final: 0.7927 (t0) REVERT: A 493 MET cc_start: 0.9058 (tmm) cc_final: 0.8516 (tmm) REVERT: A 505 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8783 (mt-10) REVERT: A 527 TYR cc_start: 0.9021 (t80) cc_final: 0.8734 (t80) REVERT: A 598 MET cc_start: 0.8764 (mtm) cc_final: 0.7851 (mtp) REVERT: A 602 GLU cc_start: 0.7746 (pt0) cc_final: 0.7075 (pt0) REVERT: A 603 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8296 (tp30) REVERT: A 604 ARG cc_start: 0.8903 (mmp80) cc_final: 0.8359 (mmt-90) REVERT: A 610 LYS cc_start: 0.8098 (tppt) cc_final: 0.7568 (tppt) REVERT: A 612 TYR cc_start: 0.9231 (m-80) cc_final: 0.8788 (m-80) REVERT: A 640 MET cc_start: 0.9639 (tpp) cc_final: 0.8790 (tpp) REVERT: A 647 HIS cc_start: 0.9000 (m90) cc_final: 0.8800 (m170) REVERT: A 667 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9142 (tt) REVERT: A 686 ARG cc_start: 0.8787 (mmm-85) cc_final: 0.8082 (mmm-85) REVERT: B 15 GLU cc_start: 0.8977 (mt-10) cc_final: 0.8699 (tm-30) REVERT: B 21 ASP cc_start: 0.8928 (m-30) cc_final: 0.8424 (t0) REVERT: B 27 ASP cc_start: 0.8986 (p0) cc_final: 0.8664 (p0) REVERT: B 65 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8154 (mp0) REVERT: B 99 LYS cc_start: 0.9584 (mmmm) cc_final: 0.9329 (mmmm) REVERT: B 106 LEU cc_start: 0.9274 (tp) cc_final: 0.8973 (tt) REVERT: B 108 THR cc_start: 0.8284 (OUTLIER) cc_final: 0.8069 (p) REVERT: B 109 ASN cc_start: 0.9233 (m-40) cc_final: 0.8639 (p0) REVERT: B 161 ARG cc_start: 0.8821 (ttm170) cc_final: 0.7934 (ttm170) REVERT: B 174 GLU cc_start: 0.8686 (mm-30) cc_final: 0.8369 (mm-30) REVERT: B 202 ASN cc_start: 0.9494 (t0) cc_final: 0.8977 (t0) REVERT: B 243 ARG cc_start: 0.7154 (tmm-80) cc_final: 0.6883 (ttp80) REVERT: B 257 ASP cc_start: 0.9006 (m-30) cc_final: 0.8667 (m-30) REVERT: B 286 ASP cc_start: 0.8455 (OUTLIER) cc_final: 0.7584 (m-30) REVERT: B 290 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8450 (tm-30) REVERT: B 312 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8476 (pt0) REVERT: B 316 GLU cc_start: 0.8625 (tm-30) cc_final: 0.7575 (tm-30) REVERT: B 317 MET cc_start: 0.8704 (ptp) cc_final: 0.7914 (pmm) REVERT: B 335 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7894 (mt-10) REVERT: B 362 ASP cc_start: 0.8730 (m-30) cc_final: 0.7544 (m-30) REVERT: B 366 LYS cc_start: 0.9360 (ptpp) cc_final: 0.9049 (ptpp) REVERT: B 374 SER cc_start: 0.9257 (t) cc_final: 0.8908 (t) REVERT: B 415 ASN cc_start: 0.9253 (t0) cc_final: 0.8887 (t0) REVERT: B 434 ASP cc_start: 0.9052 (m-30) cc_final: 0.8477 (m-30) REVERT: B 467 ASN cc_start: 0.9461 (t0) cc_final: 0.9233 (m-40) REVERT: B 471 TYR cc_start: 0.9429 (t80) cc_final: 0.9083 (t80) REVERT: B 493 MET cc_start: 0.9701 (tmm) cc_final: 0.8874 (tmm) REVERT: B 515 ASP cc_start: 0.9146 (m-30) cc_final: 0.8834 (m-30) REVERT: B 574 TYR cc_start: 0.9200 (m-80) cc_final: 0.8821 (m-80) REVERT: B 602 GLU cc_start: 0.8699 (tt0) cc_final: 0.8378 (tt0) REVERT: B 610 LYS cc_start: 0.8744 (mmmt) cc_final: 0.8452 (mmmt) REVERT: B 612 TYR cc_start: 0.8750 (m-80) cc_final: 0.8136 (m-80) REVERT: B 640 MET cc_start: 0.9241 (tpp) cc_final: 0.9015 (tpp) REVERT: C 19 GLN cc_start: 0.7721 (mp10) cc_final: 0.7411 (pm20) REVERT: C 20 MET cc_start: 0.9090 (tpp) cc_final: 0.8760 (tmm) REVERT: C 55 TYR cc_start: 0.8373 (t80) cc_final: 0.7902 (t80) REVERT: C 56 MET cc_start: 0.5919 (ttt) cc_final: 0.5495 (ttt) REVERT: C 80 HIS cc_start: 0.8610 (m90) cc_final: 0.8385 (m90) REVERT: C 164 GLU cc_start: 0.9427 (mm-30) cc_final: 0.8883 (mm-30) REVERT: C 178 PHE cc_start: 0.9306 (m-80) cc_final: 0.8335 (m-80) REVERT: C 185 MET cc_start: 0.8485 (pmm) cc_final: 0.7334 (pmm) REVERT: C 186 GLN cc_start: 0.9395 (mm110) cc_final: 0.8853 (mp10) REVERT: C 220 LYS cc_start: 0.9025 (tppt) cc_final: 0.8823 (mtmt) REVERT: C 242 TYR cc_start: 0.9455 (t80) cc_final: 0.8944 (t80) REVERT: C 259 PHE cc_start: 0.8917 (t80) cc_final: 0.8455 (t80) REVERT: C 268 LEU cc_start: 0.9056 (tp) cc_final: 0.8805 (tp) REVERT: C 270 ASN cc_start: 0.8047 (m110) cc_final: 0.7758 (m110) REVERT: D 17 PHE cc_start: 0.7437 (m-80) cc_final: 0.7165 (t80) REVERT: D 30 TRP cc_start: 0.8723 (p-90) cc_final: 0.8210 (p-90) REVERT: D 34 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8410 (mm-30) REVERT: D 46 TYR cc_start: 0.9183 (m-80) cc_final: 0.8810 (m-80) REVERT: D 96 MET cc_start: 0.8655 (mmt) cc_final: 0.8249 (mmt) REVERT: D 105 TYR cc_start: 0.7939 (m-10) cc_final: 0.7686 (m-10) REVERT: D 153 LEU cc_start: 0.9174 (pp) cc_final: 0.8934 (pp) REVERT: D 178 PHE cc_start: 0.9194 (m-10) cc_final: 0.8481 (m-80) REVERT: D 186 GLN cc_start: 0.9188 (mm-40) cc_final: 0.8774 (mp10) REVERT: D 207 LEU cc_start: 0.9168 (mm) cc_final: 0.8763 (mm) REVERT: D 210 GLN cc_start: 0.9340 (tm-30) cc_final: 0.9103 (pt0) outliers start: 80 outliers final: 54 residues processed: 755 average time/residue: 0.2703 time to fit residues: 302.7759 Evaluate side-chains 739 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 677 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 244 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 67 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 73 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 175 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 6.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN B 232 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.122780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.088107 restraints weight = 36215.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.091651 restraints weight = 16943.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.093981 restraints weight = 10016.941| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3069 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3069 r_free = 0.3069 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3069 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.6173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16386 Z= 0.143 Angle : 0.728 15.425 22134 Z= 0.360 Chirality : 0.045 0.279 2360 Planarity : 0.004 0.048 2818 Dihedral : 10.660 167.005 2247 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.14 % Allowed : 30.13 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.19), residues: 1932 helix: 1.18 (0.15), residues: 1139 sheet: 0.57 (0.48), residues: 114 loop : 0.08 (0.22), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 44 HIS 0.005 0.001 HIS A 255 PHE 0.032 0.002 PHE D 172 TYR 0.021 0.001 TYR D 242 ARG 0.007 0.001 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 871) hydrogen bonds : angle 5.04137 ( 2571) covalent geometry : bond 0.00323 (16386) covalent geometry : angle 0.72780 (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 792 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 721 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.9200 (m-10) cc_final: 0.8750 (m-10) REVERT: A 65 GLU cc_start: 0.8672 (mm-30) cc_final: 0.8094 (mp0) REVERT: A 66 GLU cc_start: 0.8580 (tp30) cc_final: 0.8266 (tp30) REVERT: A 82 LYS cc_start: 0.9664 (mmmm) cc_final: 0.9303 (mmmm) REVERT: A 181 ASP cc_start: 0.8825 (m-30) cc_final: 0.8573 (m-30) REVERT: A 187 ASP cc_start: 0.9104 (t70) cc_final: 0.8739 (t70) REVERT: A 202 ASN cc_start: 0.9443 (t0) cc_final: 0.9082 (t0) REVERT: A 218 ASN cc_start: 0.9225 (t0) cc_final: 0.8780 (t0) REVERT: A 228 LYS cc_start: 0.9457 (mmmm) cc_final: 0.8866 (mmtt) REVERT: A 257 ASP cc_start: 0.9461 (m-30) cc_final: 0.8990 (m-30) REVERT: A 286 ASP cc_start: 0.8555 (m-30) cc_final: 0.8324 (m-30) REVERT: A 321 GLU cc_start: 0.8871 (tp30) cc_final: 0.8350 (tp30) REVERT: A 348 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8043 (tmm) REVERT: A 362 ASP cc_start: 0.8596 (m-30) cc_final: 0.8089 (m-30) REVERT: A 370 ASN cc_start: 0.9216 (m-40) cc_final: 0.8934 (m110) REVERT: A 384 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.7635 (pm20) REVERT: A 389 SER cc_start: 0.9422 (OUTLIER) cc_final: 0.9095 (p) REVERT: A 415 ASN cc_start: 0.9322 (t0) cc_final: 0.9104 (t0) REVERT: A 420 MET cc_start: 0.9363 (mmm) cc_final: 0.9118 (mmm) REVERT: A 447 ASN cc_start: 0.8437 (m-40) cc_final: 0.7968 (t0) REVERT: A 493 MET cc_start: 0.8989 (tmm) cc_final: 0.8318 (tmm) REVERT: A 505 GLU cc_start: 0.9089 (mt-10) cc_final: 0.8811 (mt-10) REVERT: A 510 LYS cc_start: 0.9421 (mtpt) cc_final: 0.9122 (mtpt) REVERT: A 527 TYR cc_start: 0.8984 (t80) cc_final: 0.8705 (t80) REVERT: A 588 GLN cc_start: 0.9290 (mm-40) cc_final: 0.9082 (tp40) REVERT: A 602 GLU cc_start: 0.7822 (pt0) cc_final: 0.6095 (pt0) REVERT: A 604 ARG cc_start: 0.8902 (mmp80) cc_final: 0.7998 (mmt90) REVERT: A 640 MET cc_start: 0.9628 (tpp) cc_final: 0.8880 (tpp) REVERT: A 686 ARG cc_start: 0.8854 (mmm-85) cc_final: 0.8282 (ttm-80) REVERT: B 15 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8715 (tm-30) REVERT: B 17 MET cc_start: 0.8750 (mmm) cc_final: 0.8319 (mmm) REVERT: B 21 ASP cc_start: 0.8941 (m-30) cc_final: 0.8455 (t0) REVERT: B 31 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8148 (mt-10) REVERT: B 65 GLU cc_start: 0.8785 (mm-30) cc_final: 0.8095 (mp0) REVERT: B 99 LYS cc_start: 0.9528 (mmmm) cc_final: 0.9250 (mmmm) REVERT: B 106 LEU cc_start: 0.9257 (tp) cc_final: 0.8987 (tt) REVERT: B 108 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8193 (p) REVERT: B 109 ASN cc_start: 0.9277 (m-40) cc_final: 0.8830 (p0) REVERT: B 112 LYS cc_start: 0.9151 (pttm) cc_final: 0.8942 (pttm) REVERT: B 181 ASP cc_start: 0.9127 (OUTLIER) cc_final: 0.8692 (t0) REVERT: B 202 ASN cc_start: 0.9500 (t0) cc_final: 0.9045 (t0) REVERT: B 257 ASP cc_start: 0.8982 (m-30) cc_final: 0.8487 (m-30) REVERT: B 286 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.7627 (m-30) REVERT: B 290 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8406 (tm-30) REVERT: B 319 MET cc_start: 0.9014 (tpp) cc_final: 0.8778 (tpp) REVERT: B 335 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7870 (mt-10) REVERT: B 362 ASP cc_start: 0.8745 (m-30) cc_final: 0.7598 (m-30) REVERT: B 366 LYS cc_start: 0.9341 (ptpp) cc_final: 0.9068 (ptpp) REVERT: B 374 SER cc_start: 0.9187 (t) cc_final: 0.8822 (t) REVERT: B 393 SER cc_start: 0.9320 (m) cc_final: 0.9026 (p) REVERT: B 394 TYR cc_start: 0.9011 (m-80) cc_final: 0.8671 (m-80) REVERT: B 415 ASN cc_start: 0.9244 (t0) cc_final: 0.8833 (t0) REVERT: B 434 ASP cc_start: 0.9066 (m-30) cc_final: 0.8839 (m-30) REVERT: B 447 ASN cc_start: 0.8131 (m-40) cc_final: 0.7849 (t0) REVERT: B 467 ASN cc_start: 0.9386 (t0) cc_final: 0.9095 (m-40) REVERT: B 471 TYR cc_start: 0.9407 (t80) cc_final: 0.9108 (t80) REVERT: B 483 GLU cc_start: 0.9465 (mp0) cc_final: 0.9241 (mp0) REVERT: B 493 MET cc_start: 0.9681 (tmm) cc_final: 0.8895 (tmm) REVERT: B 515 ASP cc_start: 0.9100 (m-30) cc_final: 0.8761 (m-30) REVERT: B 610 LYS cc_start: 0.8807 (mmmt) cc_final: 0.8486 (mmmt) REVERT: B 612 TYR cc_start: 0.8690 (m-80) cc_final: 0.8250 (m-80) REVERT: C 19 GLN cc_start: 0.7691 (mp10) cc_final: 0.7329 (pm20) REVERT: C 20 MET cc_start: 0.9030 (tpp) cc_final: 0.8714 (tmm) REVERT: C 55 TYR cc_start: 0.8338 (t80) cc_final: 0.7818 (t80) REVERT: C 56 MET cc_start: 0.5898 (ttt) cc_final: 0.5434 (ttt) REVERT: C 80 HIS cc_start: 0.8610 (m90) cc_final: 0.8100 (m90) REVERT: C 150 GLU cc_start: 0.9289 (OUTLIER) cc_final: 0.8809 (tp30) REVERT: C 164 GLU cc_start: 0.9300 (mm-30) cc_final: 0.9035 (mm-30) REVERT: C 178 PHE cc_start: 0.9311 (m-80) cc_final: 0.8319 (m-10) REVERT: C 185 MET cc_start: 0.8559 (pmm) cc_final: 0.7454 (pmm) REVERT: C 186 GLN cc_start: 0.9394 (mm110) cc_final: 0.8855 (mp10) REVERT: C 220 LYS cc_start: 0.8962 (tppt) cc_final: 0.8442 (mtpt) REVERT: C 242 TYR cc_start: 0.9361 (t80) cc_final: 0.9154 (t80) REVERT: C 259 PHE cc_start: 0.8831 (t80) cc_final: 0.8313 (t80) REVERT: C 268 LEU cc_start: 0.9023 (tp) cc_final: 0.8817 (tp) REVERT: C 270 ASN cc_start: 0.8024 (m110) cc_final: 0.7748 (m110) REVERT: C 313 GLU cc_start: 0.9024 (tt0) cc_final: 0.8773 (tt0) REVERT: D 28 GLN cc_start: 0.9125 (tt0) cc_final: 0.8840 (tp40) REVERT: D 30 TRP cc_start: 0.8607 (p-90) cc_final: 0.8235 (p-90) REVERT: D 34 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8319 (mm-30) REVERT: D 46 TYR cc_start: 0.9169 (m-80) cc_final: 0.8830 (m-10) REVERT: D 105 TYR cc_start: 0.8013 (m-10) cc_final: 0.7645 (m-10) REVERT: D 178 PHE cc_start: 0.9180 (m-10) cc_final: 0.8492 (m-80) REVERT: D 186 GLN cc_start: 0.9221 (mm-40) cc_final: 0.8816 (mp10) REVERT: D 207 LEU cc_start: 0.9177 (mm) cc_final: 0.8821 (mm) REVERT: D 210 GLN cc_start: 0.9335 (tm-30) cc_final: 0.9055 (pt0) REVERT: D 227 PHE cc_start: 0.8026 (OUTLIER) cc_final: 0.7584 (m-80) REVERT: D 244 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7450 (mp0) REVERT: D 252 LEU cc_start: 0.6181 (mt) cc_final: 0.5675 (mm) outliers start: 71 outliers final: 39 residues processed: 753 average time/residue: 0.2647 time to fit residues: 296.7949 Evaluate side-chains 724 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 676 time to evaluate : 1.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 321 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 31 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 69 optimal weight: 8.9990 chunk 156 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 113 optimal weight: 8.9990 chunk 177 optimal weight: 0.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 410 ASN B 418 ASN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS ** C 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.119220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.083840 restraints weight = 36448.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.087215 restraints weight = 17536.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.089401 restraints weight = 10604.933| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.6615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16386 Z= 0.240 Angle : 0.761 15.347 22134 Z= 0.383 Chirality : 0.047 0.322 2360 Planarity : 0.004 0.050 2818 Dihedral : 10.829 166.425 2247 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 17.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.37 % Allowed : 30.30 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.19), residues: 1932 helix: 1.10 (0.15), residues: 1146 sheet: -0.55 (0.41), residues: 148 loop : 0.08 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 44 HIS 0.006 0.001 HIS A 647 PHE 0.044 0.002 PHE B 261 TYR 0.020 0.002 TYR D 242 ARG 0.007 0.001 ARG C 86 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 871) hydrogen bonds : angle 5.19411 ( 2571) covalent geometry : bond 0.00527 (16386) covalent geometry : angle 0.76113 (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 760 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 685 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 55 LEU cc_start: 0.9754 (mt) cc_final: 0.9440 (pp) REVERT: A 65 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8155 (mp0) REVERT: A 66 GLU cc_start: 0.8570 (tp30) cc_final: 0.8270 (tp30) REVERT: A 82 LYS cc_start: 0.9668 (mmmm) cc_final: 0.9366 (mmmm) REVERT: A 144 MET cc_start: 0.9129 (mtm) cc_final: 0.8893 (mtm) REVERT: A 147 GLN cc_start: 0.9310 (mt0) cc_final: 0.8127 (mt0) REVERT: A 149 TYR cc_start: 0.9283 (t80) cc_final: 0.8829 (t80) REVERT: A 181 ASP cc_start: 0.8854 (m-30) cc_final: 0.8593 (m-30) REVERT: A 202 ASN cc_start: 0.9605 (t0) cc_final: 0.9360 (t0) REVERT: A 218 ASN cc_start: 0.9379 (t0) cc_final: 0.9050 (t0) REVERT: A 228 LYS cc_start: 0.9506 (mmmm) cc_final: 0.8946 (mmtt) REVERT: A 257 ASP cc_start: 0.9441 (m-30) cc_final: 0.8919 (m-30) REVERT: A 286 ASP cc_start: 0.8600 (m-30) cc_final: 0.8249 (m-30) REVERT: A 321 GLU cc_start: 0.8971 (tp30) cc_final: 0.8629 (tp30) REVERT: A 322 MET cc_start: 0.9258 (mmp) cc_final: 0.8957 (mmm) REVERT: A 348 MET cc_start: 0.8591 (OUTLIER) cc_final: 0.8142 (tmm) REVERT: A 359 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8371 (ttp) REVERT: A 362 ASP cc_start: 0.8716 (m-30) cc_final: 0.7971 (m-30) REVERT: A 384 GLU cc_start: 0.9051 (OUTLIER) cc_final: 0.7754 (pm20) REVERT: A 389 SER cc_start: 0.9503 (OUTLIER) cc_final: 0.9141 (p) REVERT: A 415 ASN cc_start: 0.9311 (t0) cc_final: 0.9069 (t0) REVERT: A 420 MET cc_start: 0.9409 (mmm) cc_final: 0.9204 (mmm) REVERT: A 447 ASN cc_start: 0.8519 (m-40) cc_final: 0.8223 (m-40) REVERT: A 493 MET cc_start: 0.9061 (tmm) cc_final: 0.8313 (tmm) REVERT: A 505 GLU cc_start: 0.9011 (mt-10) cc_final: 0.8472 (mt-10) REVERT: A 510 LYS cc_start: 0.9383 (mtpt) cc_final: 0.9160 (mtpt) REVERT: A 512 GLU cc_start: 0.8495 (pt0) cc_final: 0.8078 (pt0) REVERT: A 527 TYR cc_start: 0.9036 (t80) cc_final: 0.8795 (t80) REVERT: A 550 MET cc_start: 0.7997 (mtm) cc_final: 0.7532 (mtm) REVERT: A 583 SER cc_start: 0.9467 (m) cc_final: 0.8893 (t) REVERT: A 598 MET cc_start: 0.8749 (mtp) cc_final: 0.8474 (mtp) REVERT: A 602 GLU cc_start: 0.7820 (pt0) cc_final: 0.7594 (pt0) REVERT: A 603 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8433 (tp30) REVERT: A 610 LYS cc_start: 0.8208 (tppt) cc_final: 0.7759 (tppt) REVERT: A 640 MET cc_start: 0.9645 (tpp) cc_final: 0.8785 (tpp) REVERT: A 686 ARG cc_start: 0.8859 (mmm-85) cc_final: 0.8335 (mtp85) REVERT: B 15 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8732 (tm-30) REVERT: B 21 ASP cc_start: 0.8974 (m-30) cc_final: 0.8472 (t0) REVERT: B 27 ASP cc_start: 0.8849 (p0) cc_final: 0.8536 (p0) REVERT: B 31 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7891 (mt-10) REVERT: B 65 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8151 (mp0) REVERT: B 71 LEU cc_start: 0.9717 (mm) cc_final: 0.9442 (mp) REVERT: B 99 LYS cc_start: 0.9571 (mmmm) cc_final: 0.9309 (mmmm) REVERT: B 109 ASN cc_start: 0.9316 (m-40) cc_final: 0.8784 (p0) REVERT: B 161 ARG cc_start: 0.8683 (ttm-80) cc_final: 0.7784 (ttm170) REVERT: B 174 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8369 (mm-30) REVERT: B 181 ASP cc_start: 0.9249 (OUTLIER) cc_final: 0.8882 (t0) REVERT: B 202 ASN cc_start: 0.9459 (t0) cc_final: 0.8947 (t0) REVERT: B 257 ASP cc_start: 0.8919 (m-30) cc_final: 0.8445 (m-30) REVERT: B 263 ASP cc_start: 0.9151 (m-30) cc_final: 0.8800 (p0) REVERT: B 286 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.7666 (m-30) REVERT: B 290 GLU cc_start: 0.8745 (tm-30) cc_final: 0.8409 (tm-30) REVERT: B 335 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7934 (mt-10) REVERT: B 362 ASP cc_start: 0.8828 (m-30) cc_final: 0.7418 (m-30) REVERT: B 366 LYS cc_start: 0.9431 (ptpp) cc_final: 0.9092 (ptpp) REVERT: B 393 SER cc_start: 0.9298 (m) cc_final: 0.9010 (p) REVERT: B 434 ASP cc_start: 0.9108 (m-30) cc_final: 0.8904 (m-30) REVERT: B 447 ASN cc_start: 0.8152 (m-40) cc_final: 0.7850 (t0) REVERT: B 471 TYR cc_start: 0.9535 (t80) cc_final: 0.8936 (t80) REVERT: B 483 GLU cc_start: 0.9500 (mp0) cc_final: 0.9261 (mp0) REVERT: B 493 MET cc_start: 0.9704 (tmm) cc_final: 0.8909 (tmm) REVERT: B 515 ASP cc_start: 0.9186 (m-30) cc_final: 0.8880 (m-30) REVERT: B 546 LEU cc_start: 0.9757 (mt) cc_final: 0.9507 (mt) REVERT: B 610 LYS cc_start: 0.8885 (mmmt) cc_final: 0.8580 (mmmt) REVERT: B 612 TYR cc_start: 0.8687 (m-80) cc_final: 0.8167 (m-80) REVERT: C 19 GLN cc_start: 0.7698 (mp10) cc_final: 0.7315 (pm20) REVERT: C 20 MET cc_start: 0.9040 (tpp) cc_final: 0.8737 (tmm) REVERT: C 55 TYR cc_start: 0.8382 (t80) cc_final: 0.7761 (t80) REVERT: C 56 MET cc_start: 0.5912 (ttt) cc_final: 0.5483 (ttt) REVERT: C 80 HIS cc_start: 0.8609 (m90) cc_final: 0.8168 (m90) REVERT: C 96 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8260 (mmt) REVERT: C 164 GLU cc_start: 0.9340 (mm-30) cc_final: 0.9054 (mm-30) REVERT: C 174 TYR cc_start: 0.9342 (OUTLIER) cc_final: 0.8717 (t80) REVERT: C 185 MET cc_start: 0.8579 (pmm) cc_final: 0.7488 (pmm) REVERT: C 186 GLN cc_start: 0.9403 (mm110) cc_final: 0.8884 (mp10) REVERT: C 220 LYS cc_start: 0.8826 (tppt) cc_final: 0.8537 (mtpt) REVERT: C 242 TYR cc_start: 0.9428 (t80) cc_final: 0.9120 (t80) REVERT: C 268 LEU cc_start: 0.8921 (tp) cc_final: 0.8655 (tp) REVERT: C 270 ASN cc_start: 0.8263 (m110) cc_final: 0.8012 (m110) REVERT: C 313 GLU cc_start: 0.9079 (tt0) cc_final: 0.8824 (tt0) REVERT: D 21 PHE cc_start: 0.9473 (m-80) cc_final: 0.9153 (m-80) REVERT: D 30 TRP cc_start: 0.8653 (p-90) cc_final: 0.7612 (p-90) REVERT: D 46 TYR cc_start: 0.9094 (m-80) cc_final: 0.8822 (m-10) REVERT: D 96 MET cc_start: 0.8648 (mmt) cc_final: 0.8160 (mmm) REVERT: D 136 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8321 (mt0) REVERT: D 178 PHE cc_start: 0.9336 (m-10) cc_final: 0.8712 (m-80) REVERT: D 186 GLN cc_start: 0.9237 (mm-40) cc_final: 0.8817 (mp10) REVERT: D 207 LEU cc_start: 0.9199 (mm) cc_final: 0.8793 (mm) REVERT: D 210 GLN cc_start: 0.9382 (tm-30) cc_final: 0.9075 (pt0) REVERT: D 227 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7551 (m-80) REVERT: D 240 LEU cc_start: 0.8597 (mt) cc_final: 0.7731 (pp) REVERT: D 244 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: D 252 LEU cc_start: 0.6010 (mt) cc_final: 0.5604 (mm) REVERT: D 269 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8137 (ppp) outliers start: 75 outliers final: 57 residues processed: 712 average time/residue: 0.2665 time to fit residues: 283.6463 Evaluate side-chains 713 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 644 time to evaluate : 1.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 187 ASP Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 217 THR Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 192 ASN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 287 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 39 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 161 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 184 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 175 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.123489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.088138 restraints weight = 36126.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.091664 restraints weight = 17227.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.093946 restraints weight = 10254.822| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3080 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3080 r_free = 0.3080 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3080 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.6871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16386 Z= 0.147 Angle : 0.746 15.723 22134 Z= 0.369 Chirality : 0.046 0.325 2360 Planarity : 0.004 0.049 2818 Dihedral : 10.466 160.815 2246 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.50 % Allowed : 32.17 % Favored : 64.34 % 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: 0.75 (0.19), residues: 1932 helix: 1.03 (0.15), residues: 1154 sheet: -0.56 (0.41), residues: 148 loop : -0.05 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 44 HIS 0.007 0.001 HIS A 255 PHE 0.027 0.002 PHE C 172 TYR 0.023 0.001 TYR A 236 ARG 0.022 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 871) hydrogen bonds : angle 5.09574 ( 2571) covalent geometry : bond 0.00333 (16386) covalent geometry : angle 0.74577 (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 745 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 685 time to evaluate : 1.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.9231 (m-10) cc_final: 0.8885 (m-10) REVERT: A 65 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8197 (mp0) REVERT: A 66 GLU cc_start: 0.8509 (tp30) cc_final: 0.8173 (tp30) REVERT: A 82 LYS cc_start: 0.9656 (mmmm) cc_final: 0.9356 (mmmm) REVERT: A 144 MET cc_start: 0.9159 (OUTLIER) cc_final: 0.8664 (mtm) REVERT: A 149 TYR cc_start: 0.9333 (t80) cc_final: 0.8912 (t80) REVERT: A 181 ASP cc_start: 0.8835 (m-30) cc_final: 0.8605 (m-30) REVERT: A 184 ARG cc_start: 0.9170 (tpp80) cc_final: 0.8965 (tpp80) REVERT: A 187 ASP cc_start: 0.9058 (t70) cc_final: 0.8769 (t70) REVERT: A 202 ASN cc_start: 0.9555 (t0) cc_final: 0.9237 (t0) REVERT: A 218 ASN cc_start: 0.9318 (t0) cc_final: 0.8930 (t0) REVERT: A 228 LYS cc_start: 0.9477 (mmmm) cc_final: 0.8980 (mmtt) REVERT: A 257 ASP cc_start: 0.9408 (m-30) cc_final: 0.9006 (m-30) REVERT: A 321 GLU cc_start: 0.8863 (tp30) cc_final: 0.8446 (tp30) REVERT: A 322 MET cc_start: 0.9229 (mmp) cc_final: 0.9000 (mmm) REVERT: A 362 ASP cc_start: 0.8677 (m-30) cc_final: 0.7953 (m-30) REVERT: A 384 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.7608 (pm20) REVERT: A 389 SER cc_start: 0.9464 (OUTLIER) cc_final: 0.9166 (p) REVERT: A 415 ASN cc_start: 0.9257 (t0) cc_final: 0.8992 (t0) REVERT: A 435 SER cc_start: 0.9464 (OUTLIER) cc_final: 0.9202 (t) REVERT: A 447 ASN cc_start: 0.8442 (m-40) cc_final: 0.7975 (t0) REVERT: A 493 MET cc_start: 0.9023 (tmm) cc_final: 0.8268 (tmm) REVERT: A 494 MET cc_start: 0.9220 (mtm) cc_final: 0.8811 (mtt) REVERT: A 505 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8741 (mt-10) REVERT: A 510 LYS cc_start: 0.9368 (mtpt) cc_final: 0.9077 (mtpt) REVERT: A 512 GLU cc_start: 0.8418 (pt0) cc_final: 0.8176 (pt0) REVERT: A 583 SER cc_start: 0.9431 (m) cc_final: 0.8855 (t) REVERT: A 595 MET cc_start: 0.8773 (mmp) cc_final: 0.8496 (mmp) REVERT: A 598 MET cc_start: 0.8738 (mtp) cc_final: 0.8401 (mtp) REVERT: A 602 GLU cc_start: 0.7726 (pt0) cc_final: 0.6423 (pt0) REVERT: A 604 ARG cc_start: 0.8913 (mmp80) cc_final: 0.8110 (mmt90) REVERT: A 640 MET cc_start: 0.9661 (tpp) cc_final: 0.8789 (tpp) REVERT: A 645 GLN cc_start: 0.8960 (tp40) cc_final: 0.8298 (tp-100) REVERT: A 665 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8732 (ttp80) REVERT: A 686 ARG cc_start: 0.8847 (mmm-85) cc_final: 0.8299 (mtp85) REVERT: B 12 LEU cc_start: 0.9652 (mt) cc_final: 0.9452 (mt) REVERT: B 15 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8663 (tm-30) REVERT: B 17 MET cc_start: 0.8750 (mmm) cc_final: 0.8346 (mmm) REVERT: B 21 ASP cc_start: 0.8958 (m-30) cc_final: 0.8441 (t0) REVERT: B 31 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8149 (mt-10) REVERT: B 99 LYS cc_start: 0.9536 (mmmm) cc_final: 0.9307 (mmmm) REVERT: B 181 ASP cc_start: 0.9192 (OUTLIER) cc_final: 0.8680 (t0) REVERT: B 202 ASN cc_start: 0.9457 (t0) cc_final: 0.9060 (t0) REVERT: B 257 ASP cc_start: 0.8945 (m-30) cc_final: 0.8429 (m-30) REVERT: B 286 ASP cc_start: 0.8567 (OUTLIER) cc_final: 0.7735 (m-30) REVERT: B 290 GLU cc_start: 0.8727 (tm-30) cc_final: 0.8320 (tm-30) REVERT: B 321 GLU cc_start: 0.8724 (pp20) cc_final: 0.8455 (pp20) REVERT: B 322 MET cc_start: 0.9283 (mmm) cc_final: 0.9008 (mmm) REVERT: B 335 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7864 (mt-10) REVERT: B 362 ASP cc_start: 0.8680 (m-30) cc_final: 0.7575 (m-30) REVERT: B 366 LYS cc_start: 0.9388 (ptpp) cc_final: 0.9066 (ptpp) REVERT: B 374 SER cc_start: 0.9230 (t) cc_final: 0.8993 (t) REVERT: B 378 PHE cc_start: 0.9285 (p90) cc_final: 0.9009 (p90) REVERT: B 393 SER cc_start: 0.9305 (m) cc_final: 0.9087 (p) REVERT: B 394 TYR cc_start: 0.8957 (m-80) cc_final: 0.8449 (m-80) REVERT: B 415 ASN cc_start: 0.9170 (t0) cc_final: 0.8898 (t0) REVERT: B 447 ASN cc_start: 0.8052 (m-40) cc_final: 0.7815 (t0) REVERT: B 467 ASN cc_start: 0.9298 (m-40) cc_final: 0.9069 (m-40) REVERT: B 471 TYR cc_start: 0.9456 (t80) cc_final: 0.9069 (t80) REVERT: B 483 GLU cc_start: 0.9480 (mp0) cc_final: 0.9251 (mp0) REVERT: B 493 MET cc_start: 0.9676 (tmm) cc_final: 0.8894 (tmm) REVERT: B 515 ASP cc_start: 0.9133 (m-30) cc_final: 0.8818 (m-30) REVERT: B 595 MET cc_start: 0.8940 (mmm) cc_final: 0.8021 (mmm) REVERT: B 610 LYS cc_start: 0.8997 (mmmt) cc_final: 0.8719 (mmmt) REVERT: B 612 TYR cc_start: 0.8656 (m-80) cc_final: 0.8265 (m-80) REVERT: B 668 ASN cc_start: 0.9277 (m110) cc_final: 0.9039 (m110) REVERT: C 19 GLN cc_start: 0.7634 (mp10) cc_final: 0.7202 (pm20) REVERT: C 20 MET cc_start: 0.9021 (tpp) cc_final: 0.8739 (tmm) REVERT: C 55 TYR cc_start: 0.8258 (t80) cc_final: 0.7391 (t80) REVERT: C 56 MET cc_start: 0.5796 (ttt) cc_final: 0.5496 (ttt) REVERT: C 80 HIS cc_start: 0.8609 (m90) cc_final: 0.8172 (m90) REVERT: C 86 ARG cc_start: 0.7390 (mmt180) cc_final: 0.7107 (mmp80) REVERT: C 154 PHE cc_start: 0.8648 (m-80) cc_final: 0.8010 (m-80) REVERT: C 164 GLU cc_start: 0.9281 (mm-30) cc_final: 0.8997 (mm-30) REVERT: C 169 TYR cc_start: 0.8379 (m-80) cc_final: 0.8082 (m-80) REVERT: C 178 PHE cc_start: 0.9333 (m-80) cc_final: 0.8349 (m-10) REVERT: C 185 MET cc_start: 0.8622 (pmm) cc_final: 0.7644 (pmm) REVERT: C 186 GLN cc_start: 0.9401 (mm110) cc_final: 0.8897 (mp10) REVERT: C 189 GLU cc_start: 0.8708 (tp30) cc_final: 0.8401 (mm-30) REVERT: C 220 LYS cc_start: 0.8768 (tppt) cc_final: 0.8457 (mtpt) REVERT: C 259 PHE cc_start: 0.8859 (t80) cc_final: 0.8371 (t80) REVERT: C 268 LEU cc_start: 0.8818 (tp) cc_final: 0.8550 (tp) REVERT: C 269 MET cc_start: 0.9103 (ppp) cc_final: 0.8847 (ppp) REVERT: C 270 ASN cc_start: 0.8141 (m110) cc_final: 0.7799 (m110) REVERT: C 316 LYS cc_start: 0.9202 (mmtt) cc_final: 0.8934 (mmtt) REVERT: D 30 TRP cc_start: 0.8614 (p-90) cc_final: 0.7644 (p-90) REVERT: D 41 LEU cc_start: 0.8910 (pp) cc_final: 0.8496 (mm) REVERT: D 42 LEU cc_start: 0.9443 (mp) cc_final: 0.9003 (mm) REVERT: D 46 TYR cc_start: 0.9006 (m-80) cc_final: 0.8738 (m-10) REVERT: D 130 TYR cc_start: 0.6341 (m-10) cc_final: 0.6008 (m-10) REVERT: D 178 PHE cc_start: 0.9318 (m-10) cc_final: 0.8721 (m-80) REVERT: D 186 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8702 (mp10) REVERT: D 207 LEU cc_start: 0.9222 (mm) cc_final: 0.8739 (mm) REVERT: D 210 GLN cc_start: 0.9355 (tm-30) cc_final: 0.9053 (pt0) REVERT: D 227 PHE cc_start: 0.8068 (OUTLIER) cc_final: 0.7533 (m-80) REVERT: D 240 LEU cc_start: 0.8699 (mt) cc_final: 0.7855 (pp) REVERT: D 244 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: D 252 LEU cc_start: 0.6032 (mt) cc_final: 0.5566 (mm) REVERT: D 269 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8121 (ppp) outliers start: 60 outliers final: 43 residues processed: 710 average time/residue: 0.2679 time to fit residues: 283.8000 Evaluate side-chains 709 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 656 time to evaluate : 1.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 665 ARG Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 287 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 51 optimal weight: 0.0980 chunk 159 optimal weight: 0.3980 chunk 72 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 183 optimal weight: 6.9990 chunk 52 optimal weight: 0.8980 chunk 180 optimal weight: 8.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN A 588 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 216 GLN C 233 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.123740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.088768 restraints weight = 35650.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.092376 restraints weight = 16813.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.094650 restraints weight = 10039.610| |-----------------------------------------------------------------------------| r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3114 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.7142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16386 Z= 0.144 Angle : 0.785 15.370 22134 Z= 0.382 Chirality : 0.047 0.384 2360 Planarity : 0.004 0.045 2818 Dihedral : 10.211 153.484 2246 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.90 % Allowed : 32.52 % Favored : 63.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.19), residues: 1932 helix: 0.96 (0.15), residues: 1155 sheet: -0.51 (0.42), residues: 148 loop : -0.14 (0.23), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 44 HIS 0.006 0.001 HIS B 438 PHE 0.042 0.002 PHE C 227 TYR 0.022 0.001 TYR D 242 ARG 0.011 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 871) hydrogen bonds : angle 5.16511 ( 2571) covalent geometry : bond 0.00325 (16386) covalent geometry : angle 0.78505 (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 753 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 686 time to evaluate : 1.876 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9267 (mtpp) cc_final: 0.9017 (ttpp) REVERT: A 64 TYR cc_start: 0.9215 (m-10) cc_final: 0.8922 (m-10) REVERT: A 65 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8198 (mp0) REVERT: A 66 GLU cc_start: 0.8542 (tp30) cc_final: 0.8197 (tp30) REVERT: A 82 LYS cc_start: 0.9648 (mmmm) cc_final: 0.9323 (mmmm) REVERT: A 102 ASN cc_start: 0.9311 (m110) cc_final: 0.8860 (m-40) REVERT: A 144 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8630 (mtm) REVERT: A 149 TYR cc_start: 0.9317 (t80) cc_final: 0.8731 (t80) REVERT: A 181 ASP cc_start: 0.8840 (m-30) cc_final: 0.8600 (m-30) REVERT: A 187 ASP cc_start: 0.9001 (t70) cc_final: 0.8686 (t70) REVERT: A 202 ASN cc_start: 0.9542 (t0) cc_final: 0.9153 (t0) REVERT: A 218 ASN cc_start: 0.9255 (t0) cc_final: 0.8909 (t0) REVERT: A 228 LYS cc_start: 0.9483 (mmmm) cc_final: 0.8826 (mmtt) REVERT: A 232 ASN cc_start: 0.9407 (OUTLIER) cc_final: 0.8759 (m-40) REVERT: A 243 ARG cc_start: 0.8286 (tmm-80) cc_final: 0.7938 (ttt180) REVERT: A 257 ASP cc_start: 0.9374 (m-30) cc_final: 0.9044 (m-30) REVERT: A 321 GLU cc_start: 0.8815 (tp30) cc_final: 0.8393 (tp30) REVERT: A 322 MET cc_start: 0.9189 (mmp) cc_final: 0.8939 (mmm) REVERT: A 350 ARG cc_start: 0.9191 (mtp180) cc_final: 0.8971 (mtp180) REVERT: A 357 TYR cc_start: 0.9094 (m-10) cc_final: 0.8487 (m-10) REVERT: A 384 GLU cc_start: 0.8905 (OUTLIER) cc_final: 0.7572 (pm20) REVERT: A 389 SER cc_start: 0.9399 (OUTLIER) cc_final: 0.9096 (p) REVERT: A 415 ASN cc_start: 0.9245 (t0) cc_final: 0.9041 (t0) REVERT: A 435 SER cc_start: 0.9481 (p) cc_final: 0.9222 (t) REVERT: A 447 ASN cc_start: 0.8358 (m-40) cc_final: 0.7923 (t0) REVERT: A 493 MET cc_start: 0.8999 (tmm) cc_final: 0.8280 (tmm) REVERT: A 494 MET cc_start: 0.9159 (mtm) cc_final: 0.8650 (mtt) REVERT: A 505 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8754 (mt-10) REVERT: A 510 LYS cc_start: 0.9274 (mtpt) cc_final: 0.9033 (mtpt) REVERT: A 583 SER cc_start: 0.9422 (m) cc_final: 0.8832 (t) REVERT: A 595 MET cc_start: 0.8763 (mmp) cc_final: 0.8546 (mmp) REVERT: A 598 MET cc_start: 0.8756 (mtp) cc_final: 0.8356 (mtp) REVERT: A 602 GLU cc_start: 0.7722 (pt0) cc_final: 0.6420 (pt0) REVERT: A 604 ARG cc_start: 0.8956 (mmp80) cc_final: 0.8055 (mmt-90) REVERT: A 606 TYR cc_start: 0.8122 (m-80) cc_final: 0.7914 (m-80) REVERT: A 640 MET cc_start: 0.9660 (tpp) cc_final: 0.8799 (tpp) REVERT: A 645 GLN cc_start: 0.9000 (tp40) cc_final: 0.8339 (tp-100) REVERT: A 686 ARG cc_start: 0.8835 (mmm-85) cc_final: 0.8248 (mtp85) REVERT: B 17 MET cc_start: 0.8778 (mmm) cc_final: 0.8406 (mmm) REVERT: B 21 ASP cc_start: 0.8903 (m-30) cc_final: 0.8422 (t0) REVERT: B 31 GLU cc_start: 0.8353 (mt-10) cc_final: 0.8110 (mt-10) REVERT: B 65 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8254 (mp0) REVERT: B 99 LYS cc_start: 0.9519 (mmmm) cc_final: 0.9290 (mmmm) REVERT: B 107 LYS cc_start: 0.9544 (mmmm) cc_final: 0.8920 (mmmm) REVERT: B 108 THR cc_start: 0.8718 (OUTLIER) cc_final: 0.8424 (p) REVERT: B 119 GLU cc_start: 0.8691 (mp0) cc_final: 0.8373 (mp0) REVERT: B 161 ARG cc_start: 0.9004 (mmm-85) cc_final: 0.8630 (mmm-85) REVERT: B 181 ASP cc_start: 0.9157 (OUTLIER) cc_final: 0.8649 (t0) REVERT: B 202 ASN cc_start: 0.9460 (t0) cc_final: 0.9070 (t0) REVERT: B 232 ASN cc_start: 0.9253 (m-40) cc_final: 0.8762 (m-40) REVERT: B 257 ASP cc_start: 0.8906 (m-30) cc_final: 0.8442 (m-30) REVERT: B 263 ASP cc_start: 0.9142 (m-30) cc_final: 0.8654 (p0) REVERT: B 286 ASP cc_start: 0.8583 (OUTLIER) cc_final: 0.7853 (m-30) REVERT: B 290 GLU cc_start: 0.8687 (tm-30) cc_final: 0.8280 (tm-30) REVERT: B 321 GLU cc_start: 0.8715 (pp20) cc_final: 0.8507 (pp20) REVERT: B 335 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7861 (mt-10) REVERT: B 348 MET cc_start: 0.8998 (ttp) cc_final: 0.8792 (ttp) REVERT: B 362 ASP cc_start: 0.8634 (m-30) cc_final: 0.7507 (m-30) REVERT: B 366 LYS cc_start: 0.9399 (ptpp) cc_final: 0.9098 (ptpp) REVERT: B 446 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7553 (ttm-80) REVERT: B 447 ASN cc_start: 0.8075 (m-40) cc_final: 0.7827 (t0) REVERT: B 483 GLU cc_start: 0.9469 (mp0) cc_final: 0.9239 (mp0) REVERT: B 493 MET cc_start: 0.9662 (tmm) cc_final: 0.8867 (tmm) REVERT: B 515 ASP cc_start: 0.9083 (m-30) cc_final: 0.8798 (m-30) REVERT: B 610 LYS cc_start: 0.9034 (mmmt) cc_final: 0.8774 (mmmt) REVERT: B 612 TYR cc_start: 0.8614 (m-80) cc_final: 0.8177 (m-80) REVERT: C 19 GLN cc_start: 0.7599 (mp10) cc_final: 0.7165 (pm20) REVERT: C 20 MET cc_start: 0.8959 (tpp) cc_final: 0.8642 (tmm) REVERT: C 55 TYR cc_start: 0.8152 (t80) cc_final: 0.7372 (t80) REVERT: C 56 MET cc_start: 0.5739 (ttt) cc_final: 0.5370 (ttt) REVERT: C 80 HIS cc_start: 0.8673 (m90) cc_final: 0.8250 (m90) REVERT: C 96 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8100 (mmt) REVERT: C 154 PHE cc_start: 0.8722 (m-80) cc_final: 0.8080 (m-80) REVERT: C 164 GLU cc_start: 0.9294 (mm-30) cc_final: 0.8989 (mm-30) REVERT: C 178 PHE cc_start: 0.9333 (m-80) cc_final: 0.8470 (m-10) REVERT: C 185 MET cc_start: 0.8627 (pmm) cc_final: 0.7547 (pmm) REVERT: C 186 GLN cc_start: 0.9396 (mm110) cc_final: 0.8901 (mp10) REVERT: C 220 LYS cc_start: 0.8729 (tppt) cc_final: 0.8419 (mtpt) REVERT: C 229 ILE cc_start: 0.8633 (mm) cc_final: 0.8288 (mm) REVERT: C 259 PHE cc_start: 0.8885 (t80) cc_final: 0.8349 (t80) REVERT: C 268 LEU cc_start: 0.8783 (tp) cc_final: 0.8518 (tp) REVERT: C 269 MET cc_start: 0.9058 (ppp) cc_final: 0.8788 (ppp) REVERT: C 270 ASN cc_start: 0.8193 (m110) cc_final: 0.7867 (m110) REVERT: D 28 GLN cc_start: 0.9230 (tt0) cc_final: 0.8636 (tt0) REVERT: D 30 TRP cc_start: 0.8526 (p-90) cc_final: 0.7587 (p-90) REVERT: D 41 LEU cc_start: 0.8966 (pp) cc_final: 0.8570 (mm) REVERT: D 42 LEU cc_start: 0.9429 (mp) cc_final: 0.9033 (mm) REVERT: D 46 TYR cc_start: 0.8942 (m-80) cc_final: 0.8687 (m-10) REVERT: D 96 MET cc_start: 0.8598 (mmt) cc_final: 0.8172 (mmm) REVERT: D 136 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8477 (mt0) REVERT: D 178 PHE cc_start: 0.9316 (m-10) cc_final: 0.8804 (m-80) REVERT: D 186 GLN cc_start: 0.9176 (mm-40) cc_final: 0.8695 (mp10) REVERT: D 207 LEU cc_start: 0.9169 (mm) cc_final: 0.8723 (mm) REVERT: D 210 GLN cc_start: 0.9346 (tm-30) cc_final: 0.9028 (pt0) REVERT: D 240 LEU cc_start: 0.8763 (mt) cc_final: 0.7937 (pp) REVERT: D 244 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7625 (mp0) REVERT: D 252 LEU cc_start: 0.5986 (mt) cc_final: 0.5597 (mm) REVERT: D 269 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7960 (ppp) outliers start: 67 outliers final: 46 residues processed: 712 average time/residue: 0.2585 time to fit residues: 273.6321 Evaluate side-chains 718 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 660 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 181 ASP Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 21 PHE Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 111 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 182 optimal weight: 10.0000 chunk 107 optimal weight: 0.4980 chunk 77 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 127 optimal weight: 0.6980 chunk 188 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.121641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.087165 restraints weight = 35984.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.090646 restraints weight = 17149.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.092949 restraints weight = 10345.015| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.7314 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= 0.179 Angle : 0.826 15.014 22134 Z= 0.404 Chirality : 0.048 0.361 2360 Planarity : 0.004 0.044 2818 Dihedral : 10.205 148.052 2246 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.73 % Allowed : 33.92 % Favored : 62.35 % 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: 0.52 (0.19), residues: 1932 helix: 0.86 (0.15), residues: 1156 sheet: -0.45 (0.43), residues: 148 loop : -0.22 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 44 HIS 0.006 0.001 HIS A 255 PHE 0.036 0.002 PHE B 378 TYR 0.022 0.002 TYR B 527 ARG 0.027 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.04226 ( 871) hydrogen bonds : angle 5.28687 ( 2571) covalent geometry : bond 0.00408 (16386) covalent geometry : angle 0.82607 (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 729 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 665 time to evaluate : 1.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9294 (mtpp) cc_final: 0.9059 (ttpp) REVERT: A 55 LEU cc_start: 0.9738 (mt) cc_final: 0.9426 (pp) REVERT: A 64 TYR cc_start: 0.9242 (m-10) cc_final: 0.8911 (m-10) REVERT: A 65 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8235 (mp0) REVERT: A 66 GLU cc_start: 0.8533 (tp30) cc_final: 0.8187 (tp30) REVERT: A 82 LYS cc_start: 0.9650 (mmmm) cc_final: 0.9303 (mmmm) REVERT: A 102 ASN cc_start: 0.9290 (m110) cc_final: 0.8808 (m110) REVERT: A 144 MET cc_start: 0.9121 (OUTLIER) cc_final: 0.8639 (mtm) REVERT: A 181 ASP cc_start: 0.8776 (m-30) cc_final: 0.8531 (m-30) REVERT: A 187 ASP cc_start: 0.9046 (t70) cc_final: 0.8692 (t70) REVERT: A 218 ASN cc_start: 0.9324 (t0) cc_final: 0.8841 (t0) REVERT: A 228 LYS cc_start: 0.9503 (mmmm) cc_final: 0.8772 (mmtt) REVERT: A 232 ASN cc_start: 0.9417 (OUTLIER) cc_final: 0.8716 (m-40) REVERT: A 243 ARG cc_start: 0.8317 (tmm-80) cc_final: 0.7925 (ttt180) REVERT: A 257 ASP cc_start: 0.9361 (m-30) cc_final: 0.9012 (m-30) REVERT: A 290 GLU cc_start: 0.8774 (tp30) cc_final: 0.8433 (tm-30) REVERT: A 321 GLU cc_start: 0.8880 (tp30) cc_final: 0.8136 (tp30) REVERT: A 359 MET cc_start: 0.9048 (OUTLIER) cc_final: 0.8237 (ttp) REVERT: A 384 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.7644 (pm20) REVERT: A 389 SER cc_start: 0.9417 (OUTLIER) cc_final: 0.9101 (p) REVERT: A 394 TYR cc_start: 0.9218 (m-80) cc_final: 0.8923 (m-80) REVERT: A 435 SER cc_start: 0.9501 (p) cc_final: 0.9265 (t) REVERT: A 447 ASN cc_start: 0.8389 (m-40) cc_final: 0.7906 (t0) REVERT: A 493 MET cc_start: 0.9011 (tmm) cc_final: 0.8272 (tmm) REVERT: A 505 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8557 (mt-10) REVERT: A 583 SER cc_start: 0.9446 (m) cc_final: 0.8865 (t) REVERT: A 595 MET cc_start: 0.8867 (mmp) cc_final: 0.8499 (mmp) REVERT: A 598 MET cc_start: 0.8736 (mtp) cc_final: 0.8347 (mtp) REVERT: A 602 GLU cc_start: 0.7630 (pt0) cc_final: 0.7233 (pt0) REVERT: A 604 ARG cc_start: 0.8934 (mmp80) cc_final: 0.8574 (mmp80) REVERT: A 640 MET cc_start: 0.9655 (tpp) cc_final: 0.8789 (tpp) REVERT: A 645 GLN cc_start: 0.9067 (tp40) cc_final: 0.8394 (tp-100) REVERT: A 686 ARG cc_start: 0.8831 (mmm-85) cc_final: 0.8281 (mtp85) REVERT: B 17 MET cc_start: 0.8983 (mmm) cc_final: 0.8616 (mmm) REVERT: B 21 ASP cc_start: 0.8943 (m-30) cc_final: 0.8449 (t0) REVERT: B 31 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8018 (mt-10) REVERT: B 65 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8191 (mp0) REVERT: B 99 LYS cc_start: 0.9524 (mmmm) cc_final: 0.9302 (mmmm) REVERT: B 119 GLU cc_start: 0.8807 (mp0) cc_final: 0.8493 (mp0) REVERT: B 232 ASN cc_start: 0.9271 (m-40) cc_final: 0.8744 (m-40) REVERT: B 257 ASP cc_start: 0.8861 (m-30) cc_final: 0.8385 (m-30) REVERT: B 263 ASP cc_start: 0.9174 (m-30) cc_final: 0.8692 (p0) REVERT: B 286 ASP cc_start: 0.8621 (OUTLIER) cc_final: 0.7887 (m-30) REVERT: B 290 GLU cc_start: 0.8697 (tm-30) cc_final: 0.8393 (tm-30) REVERT: B 362 ASP cc_start: 0.8680 (m-30) cc_final: 0.7502 (m-30) REVERT: B 366 LYS cc_start: 0.9416 (ptpp) cc_final: 0.9086 (ptpp) REVERT: B 415 ASN cc_start: 0.9268 (t0) cc_final: 0.8965 (t0) REVERT: B 447 ASN cc_start: 0.8048 (m-40) cc_final: 0.7811 (t0) REVERT: B 467 ASN cc_start: 0.9241 (m-40) cc_final: 0.8928 (m-40) REVERT: B 471 TYR cc_start: 0.9459 (t80) cc_final: 0.9090 (t80) REVERT: B 483 GLU cc_start: 0.9491 (mp0) cc_final: 0.9249 (mp0) REVERT: B 493 MET cc_start: 0.9674 (tmm) cc_final: 0.8889 (tmm) REVERT: B 515 ASP cc_start: 0.9090 (m-30) cc_final: 0.8817 (m-30) REVERT: B 606 TYR cc_start: 0.8661 (m-80) cc_final: 0.8228 (m-80) REVERT: B 610 LYS cc_start: 0.9030 (mmmt) cc_final: 0.8703 (mmmt) REVERT: B 612 TYR cc_start: 0.8628 (m-80) cc_final: 0.8277 (m-80) REVERT: C 20 MET cc_start: 0.8887 (tpp) cc_final: 0.8385 (tmm) REVERT: C 55 TYR cc_start: 0.8195 (t80) cc_final: 0.7372 (t80) REVERT: C 56 MET cc_start: 0.5792 (ttt) cc_final: 0.5458 (ttt) REVERT: C 80 HIS cc_start: 0.8736 (m90) cc_final: 0.8322 (m90) REVERT: C 96 MET cc_start: 0.8740 (mmt) cc_final: 0.8450 (mmm) REVERT: C 164 GLU cc_start: 0.9319 (mm-30) cc_final: 0.8911 (mm-30) REVERT: C 178 PHE cc_start: 0.9358 (m-80) cc_final: 0.8401 (m-10) REVERT: C 185 MET cc_start: 0.8687 (pmm) cc_final: 0.7761 (pmm) REVERT: C 186 GLN cc_start: 0.9395 (mm110) cc_final: 0.8895 (mp10) REVERT: C 189 GLU cc_start: 0.8611 (tp30) cc_final: 0.8232 (mm-30) REVERT: C 220 LYS cc_start: 0.8722 (tppt) cc_final: 0.8444 (mtpt) REVERT: C 259 PHE cc_start: 0.8920 (t80) cc_final: 0.8411 (t80) REVERT: C 268 LEU cc_start: 0.8744 (tp) cc_final: 0.8480 (tp) REVERT: C 269 MET cc_start: 0.9014 (ppp) cc_final: 0.8744 (ppp) REVERT: C 270 ASN cc_start: 0.8265 (m110) cc_final: 0.7957 (m110) REVERT: D 21 PHE cc_start: 0.9358 (OUTLIER) cc_final: 0.8660 (t80) REVERT: D 41 LEU cc_start: 0.9051 (pp) cc_final: 0.8591 (mm) REVERT: D 96 MET cc_start: 0.8725 (mmt) cc_final: 0.8367 (mmm) REVERT: D 136 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.8526 (mt0) REVERT: D 154 PHE cc_start: 0.9125 (t80) cc_final: 0.8594 (m-80) REVERT: D 186 GLN cc_start: 0.9170 (mm-40) cc_final: 0.8673 (mp10) REVERT: D 207 LEU cc_start: 0.9170 (mm) cc_final: 0.8705 (mm) REVERT: D 210 GLN cc_start: 0.9336 (tm-30) cc_final: 0.9039 (pt0) REVERT: D 240 LEU cc_start: 0.8713 (mt) cc_final: 0.7892 (pp) REVERT: D 244 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: D 252 LEU cc_start: 0.6290 (mt) cc_final: 0.5890 (mm) REVERT: D 269 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7914 (ppp) outliers start: 64 outliers final: 50 residues processed: 691 average time/residue: 0.2665 time to fit residues: 275.9257 Evaluate side-chains 706 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 646 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 21 PHE Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 215 LYS Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 137 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 160 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 135 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 70 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN D 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.122728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.088337 restraints weight = 36258.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.091770 restraints weight = 17338.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.094040 restraints weight = 10387.495| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.7476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16386 Z= 0.177 Angle : 0.849 14.995 22134 Z= 0.417 Chirality : 0.048 0.324 2360 Planarity : 0.004 0.044 2818 Dihedral : 10.078 145.314 2246 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.67 % Allowed : 34.44 % Favored : 61.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.19), residues: 1932 helix: 0.82 (0.15), residues: 1143 sheet: -0.45 (0.44), residues: 152 loop : -0.25 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 124 HIS 0.006 0.001 HIS A 255 PHE 0.043 0.002 PHE B 378 TYR 0.021 0.002 TYR D 46 ARG 0.020 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.04288 ( 871) hydrogen bonds : angle 5.32167 ( 2571) covalent geometry : bond 0.00406 (16386) covalent geometry : angle 0.84934 (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 715 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 652 time to evaluate : 1.890 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: A 8 LYS cc_start: 0.9261 (mtpp) cc_final: 0.8990 (ttpp) REVERT: A 55 LEU cc_start: 0.9732 (mt) cc_final: 0.9408 (pp) REVERT: A 64 TYR cc_start: 0.9238 (m-10) cc_final: 0.8867 (m-10) REVERT: A 65 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8266 (mp0) REVERT: A 66 GLU cc_start: 0.8484 (tp30) cc_final: 0.8166 (tp30) REVERT: A 82 LYS cc_start: 0.9638 (mmmm) cc_final: 0.9296 (mmmm) REVERT: A 102 ASN cc_start: 0.9280 (m110) cc_final: 0.8800 (m110) REVERT: A 144 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8622 (mtm) REVERT: A 181 ASP cc_start: 0.8768 (m-30) cc_final: 0.8540 (m-30) REVERT: A 187 ASP cc_start: 0.9016 (t70) cc_final: 0.8693 (t70) REVERT: A 218 ASN cc_start: 0.9340 (t0) cc_final: 0.8858 (t0) REVERT: A 228 LYS cc_start: 0.9501 (mmmm) cc_final: 0.8721 (mmtt) REVERT: A 232 ASN cc_start: 0.9400 (OUTLIER) cc_final: 0.8713 (m-40) REVERT: A 243 ARG cc_start: 0.8282 (tmm-80) cc_final: 0.7914 (ttt180) REVERT: A 257 ASP cc_start: 0.9373 (m-30) cc_final: 0.9001 (m-30) REVERT: A 321 GLU cc_start: 0.8882 (tp30) cc_final: 0.8162 (tp30) REVERT: A 384 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.7590 (pm20) REVERT: A 389 SER cc_start: 0.9370 (OUTLIER) cc_final: 0.9044 (p) REVERT: A 394 TYR cc_start: 0.9215 (m-80) cc_final: 0.8886 (m-80) REVERT: A 435 SER cc_start: 0.9514 (OUTLIER) cc_final: 0.9268 (t) REVERT: A 447 ASN cc_start: 0.8331 (m-40) cc_final: 0.7857 (t0) REVERT: A 458 MET cc_start: 0.9253 (mmm) cc_final: 0.8884 (tpp) REVERT: A 459 LYS cc_start: 0.9084 (OUTLIER) cc_final: 0.8656 (ttpp) REVERT: A 493 MET cc_start: 0.8969 (tmm) cc_final: 0.8341 (tmm) REVERT: A 494 MET cc_start: 0.9180 (mtm) cc_final: 0.8843 (mtt) REVERT: A 505 GLU cc_start: 0.9052 (mt-10) cc_final: 0.8773 (mt-10) REVERT: A 583 SER cc_start: 0.9428 (m) cc_final: 0.8852 (t) REVERT: A 595 MET cc_start: 0.8866 (mmp) cc_final: 0.8568 (mmp) REVERT: A 602 GLU cc_start: 0.7622 (pt0) cc_final: 0.6934 (pt0) REVERT: A 604 ARG cc_start: 0.8936 (mmp80) cc_final: 0.8325 (mmt-90) REVERT: A 640 MET cc_start: 0.9644 (tpp) cc_final: 0.8798 (tpp) REVERT: A 645 GLN cc_start: 0.9066 (tp40) cc_final: 0.8434 (tp-100) REVERT: A 686 ARG cc_start: 0.8862 (mmm-85) cc_final: 0.8525 (mmm-85) REVERT: B 17 MET cc_start: 0.9021 (mmm) cc_final: 0.8632 (mmm) REVERT: B 21 ASP cc_start: 0.8947 (m-30) cc_final: 0.8450 (t0) REVERT: B 31 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7813 (mt-10) REVERT: B 65 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8268 (mp0) REVERT: B 99 LYS cc_start: 0.9523 (mmmm) cc_final: 0.9304 (mmmm) REVERT: B 119 GLU cc_start: 0.8825 (mp0) cc_final: 0.8500 (mp0) REVERT: B 232 ASN cc_start: 0.9282 (m-40) cc_final: 0.8752 (m-40) REVERT: B 257 ASP cc_start: 0.8865 (m-30) cc_final: 0.8419 (m-30) REVERT: B 263 ASP cc_start: 0.9160 (m-30) cc_final: 0.8661 (p0) REVERT: B 274 ARG cc_start: 0.8800 (ttm-80) cc_final: 0.8582 (ttm-80) REVERT: B 286 ASP cc_start: 0.8634 (OUTLIER) cc_final: 0.7877 (m-30) REVERT: B 290 GLU cc_start: 0.8671 (tm-30) cc_final: 0.8358 (tm-30) REVERT: B 362 ASP cc_start: 0.8693 (m-30) cc_final: 0.7701 (m-30) REVERT: B 366 LYS cc_start: 0.9416 (ptpp) cc_final: 0.9082 (ptpp) REVERT: B 415 ASN cc_start: 0.9276 (t0) cc_final: 0.8960 (t0) REVERT: B 447 ASN cc_start: 0.8045 (m-40) cc_final: 0.7802 (t0) REVERT: B 467 ASN cc_start: 0.9343 (m-40) cc_final: 0.9024 (m-40) REVERT: B 471 TYR cc_start: 0.9479 (t80) cc_final: 0.9092 (t80) REVERT: B 483 GLU cc_start: 0.9470 (mp0) cc_final: 0.9243 (mp0) REVERT: B 493 MET cc_start: 0.9666 (tmm) cc_final: 0.8875 (tmm) REVERT: B 515 ASP cc_start: 0.9064 (m-30) cc_final: 0.8806 (m-30) REVERT: B 548 GLU cc_start: 0.8852 (mm-30) cc_final: 0.8292 (mm-30) REVERT: B 606 TYR cc_start: 0.8659 (m-80) cc_final: 0.8250 (m-80) REVERT: B 610 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8742 (mmmt) REVERT: B 612 TYR cc_start: 0.8611 (m-80) cc_final: 0.8196 (m-80) REVERT: C 25 ASN cc_start: 0.8963 (p0) cc_final: 0.8750 (p0) REVERT: C 29 PHE cc_start: 0.8273 (t80) cc_final: 0.7977 (t80) REVERT: C 56 MET cc_start: 0.5798 (ttt) cc_final: 0.5549 (ttt) REVERT: C 80 HIS cc_start: 0.8743 (m90) cc_final: 0.8376 (m90) REVERT: C 92 PHE cc_start: 0.7792 (t80) cc_final: 0.7468 (t80) REVERT: C 96 MET cc_start: 0.8824 (mmt) cc_final: 0.8246 (mmm) REVERT: C 154 PHE cc_start: 0.8881 (m-80) cc_final: 0.8190 (m-80) REVERT: C 178 PHE cc_start: 0.9331 (m-80) cc_final: 0.8531 (m-80) REVERT: C 185 MET cc_start: 0.8715 (pmm) cc_final: 0.7788 (pmm) REVERT: C 186 GLN cc_start: 0.9328 (mm110) cc_final: 0.8811 (mp10) REVERT: C 189 GLU cc_start: 0.8554 (tp30) cc_final: 0.8157 (mm-30) REVERT: C 220 LYS cc_start: 0.8750 (tppt) cc_final: 0.8466 (mtpt) REVERT: C 259 PHE cc_start: 0.8978 (t80) cc_final: 0.8446 (t80) REVERT: C 268 LEU cc_start: 0.8652 (tp) cc_final: 0.8388 (tp) REVERT: C 269 MET cc_start: 0.8969 (ppp) cc_final: 0.8713 (ppp) REVERT: C 270 ASN cc_start: 0.8311 (m110) cc_final: 0.8021 (m110) REVERT: C 309 LYS cc_start: 0.7291 (ptpt) cc_final: 0.6947 (ttmt) REVERT: D 21 PHE cc_start: 0.9312 (OUTLIER) cc_final: 0.8538 (t80) REVERT: D 28 GLN cc_start: 0.9259 (tt0) cc_final: 0.8746 (tt0) REVERT: D 41 LEU cc_start: 0.9086 (pp) cc_final: 0.8622 (mm) REVERT: D 96 MET cc_start: 0.8916 (mmt) cc_final: 0.8597 (mmm) REVERT: D 136 GLN cc_start: 0.9012 (OUTLIER) cc_final: 0.8500 (mt0) REVERT: D 154 PHE cc_start: 0.9138 (t80) cc_final: 0.8578 (m-80) REVERT: D 178 PHE cc_start: 0.9368 (m-10) cc_final: 0.8821 (m-80) REVERT: D 186 GLN cc_start: 0.9183 (mm110) cc_final: 0.8646 (mp10) REVERT: D 207 LEU cc_start: 0.9138 (mm) cc_final: 0.8683 (mm) REVERT: D 210 GLN cc_start: 0.9330 (tm-30) cc_final: 0.9035 (pt0) REVERT: D 240 LEU cc_start: 0.8709 (mt) cc_final: 0.7956 (pp) REVERT: D 244 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7580 (mp0) REVERT: D 252 LEU cc_start: 0.6426 (mt) cc_final: 0.6126 (mm) REVERT: D 269 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7936 (ppp) outliers start: 63 outliers final: 48 residues processed: 675 average time/residue: 0.2574 time to fit residues: 261.3084 Evaluate side-chains 704 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 645 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 459 LYS Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 106 LEU Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 451 VAL Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 91 ASN Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 21 PHE Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 244 GLU Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 81 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 190 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 180 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN ** A 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN D 28 GLN D 50 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.124496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.089405 restraints weight = 35580.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.092832 restraints weight = 16932.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.095123 restraints weight = 10184.446| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3097 r_free = 0.3097 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3097 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.7637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16386 Z= 0.162 Angle : 0.866 16.686 22134 Z= 0.422 Chirality : 0.049 0.385 2360 Planarity : 0.004 0.043 2818 Dihedral : 9.883 145.317 2246 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.55 % Allowed : 34.91 % Favored : 61.54 % 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: 0.43 (0.19), residues: 1932 helix: 0.81 (0.15), residues: 1145 sheet: -0.38 (0.44), residues: 152 loop : -0.30 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 124 HIS 0.006 0.001 HIS A 255 PHE 0.040 0.002 PHE B 74 TYR 0.022 0.002 TYR D 46 ARG 0.017 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.04305 ( 871) hydrogen bonds : angle 5.31653 ( 2571) covalent geometry : bond 0.00377 (16386) covalent geometry : angle 0.86649 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6726.70 seconds wall clock time: 118 minutes 18.30 seconds (7098.30 seconds total)