Starting phenix.real_space_refine on Sat Jun 14 07:10:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byz_45049/06_2025/9byz_45049_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byz_45049/06_2025/9byz_45049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9byz_45049/06_2025/9byz_45049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byz_45049/06_2025/9byz_45049.map" model { file = "/net/cci-nas-00/data/ceres_data/9byz_45049/06_2025/9byz_45049_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byz_45049/06_2025/9byz_45049_neut.cif" } resolution = 3.94 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): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 12.23, per 1000 atoms: 0.76 Number of scatterers: 16038 At special positions: 0 Unit cell: (95.598, 134.244, 133.227, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.33 Conformation dependent library (CDL) restraints added in 2.1 seconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.985A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.954A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.665A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.126A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.694A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.628A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.677A 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: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.646A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.730A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.026A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A 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: 4.069A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.669A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.359A 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: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 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: 7.184A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.709A 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: 7.229A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.049A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.906A 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: 8.344A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.66 Time building geometry restraints manager: 5.35 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: 4770 1.34 - 1.46: 3070 1.46 - 1.58: 8365 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 2.33e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.039 1.20e-02 6.94e+03 1.04e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.032 1.08e-02 8.57e+03 9.05e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.569 -0.032 1.17e-02 7.31e+03 7.41e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.573 -0.033 1.25e-02 6.40e+03 6.86e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21576 2.09 - 4.18: 515 4.18 - 6.27: 37 6.27 - 8.36: 2 8.36 - 10.45: 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 110.54 116.62 -6.08 1.36e+00 5.41e-01 2.00e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.18 -4.47 1.15e+00 7.56e-01 1.51e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.83 -4.33 1.23e+00 6.61e-01 1.24e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.72 -4.01 1.15e+00 7.56e-01 1.21e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.53 3.66 1.06e+00 8.90e-01 1.19e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 9470 35.81 - 71.61: 337 71.61 - 107.42: 37 107.42 - 143.22: 3 143.22 - 179.03: 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 -58.32 120.71 -179.03 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 301.68 151.10 150.58 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 31.91 148.06 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: 2146 0.093 - 0.186: 179 0.186 - 0.278: 30 0.278 - 0.371: 3 0.371 - 0.464: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.38e+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 4.63e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO D 75 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " 0.017 2.00e-02 2.50e+03 1.10e-02 2.11e+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 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 179 " -0.016 2.00e-02 2.50e+03 9.81e-03 1.93e+00 pdb=" CG TYR D 179 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR D 179 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR D 179 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR D 179 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 179 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 179 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 179 " -0.005 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 129 2.51 - 3.11: 11559 3.11 - 3.70: 27048 3.70 - 4.30: 41564 4.30 - 4.90: 65457 Nonbonded interactions: 145757 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 145752 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: 0.08 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 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: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 42.640 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6780 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 16386 Z= 0.315 Angle : 0.740 10.448 22134 Z= 0.463 Chirality : 0.057 0.464 2360 Planarity : 0.003 0.042 2818 Dihedral : 17.908 179.029 6154 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.40 % Allowed : 15.21 % Favored : 83.39 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.18), residues: 1932 helix: 0.58 (0.14), residues: 1151 sheet: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE C 227 TYR 0.021 0.002 TYR D 179 ARG 0.004 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.15420 ( 871) hydrogen bonds : angle 6.51780 ( 2571) covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74014 (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 902 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 878 time to evaluate : 1.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.8819 (mt) cc_final: 0.8557 (mt) REVERT: A 37 PHE cc_start: 0.7949 (m-80) cc_final: 0.7498 (m-10) REVERT: A 144 MET cc_start: 0.6905 (mtm) cc_final: 0.6669 (mtm) REVERT: A 157 LEU cc_start: 0.9004 (tp) cc_final: 0.8742 (tt) REVERT: A 183 SER cc_start: 0.8618 (p) cc_final: 0.8382 (p) REVERT: A 186 ILE cc_start: 0.9440 (mt) cc_final: 0.9090 (mt) REVERT: A 188 ILE cc_start: 0.8765 (mt) cc_final: 0.8505 (mt) REVERT: A 202 ASN cc_start: 0.9018 (t0) cc_final: 0.8817 (t0) REVERT: A 218 ASN cc_start: 0.7691 (t0) cc_final: 0.7263 (t0) REVERT: A 257 ASP cc_start: 0.8040 (m-30) cc_final: 0.7731 (m-30) REVERT: A 267 ILE cc_start: 0.7996 (mp) cc_final: 0.7481 (tp) REVERT: A 362 ASP cc_start: 0.6663 (m-30) cc_final: 0.5919 (m-30) REVERT: A 390 GLN cc_start: 0.7453 (mt0) cc_final: 0.7132 (mt0) REVERT: A 405 LEU cc_start: 0.8644 (mt) cc_final: 0.8396 (mt) REVERT: A 433 THR cc_start: 0.8995 (m) cc_final: 0.8784 (m) REVERT: A 502 ARG cc_start: 0.8204 (tpt170) cc_final: 0.7741 (tpt170) REVERT: A 640 MET cc_start: 0.8149 (tpp) cc_final: 0.7871 (tpp) REVERT: A 644 ILE cc_start: 0.8792 (mt) cc_final: 0.8439 (mt) REVERT: B 51 LEU cc_start: 0.8149 (tp) cc_final: 0.7904 (tp) REVERT: B 157 LEU cc_start: 0.8341 (tp) cc_final: 0.8030 (tp) REVERT: B 177 ASP cc_start: 0.8219 (t0) cc_final: 0.6665 (p0) REVERT: B 180 ASN cc_start: 0.7454 (m-40) cc_final: 0.7251 (m110) REVERT: B 184 ARG cc_start: 0.8306 (tpp-160) cc_final: 0.8095 (tpp-160) REVERT: B 322 MET cc_start: 0.7732 (mmm) cc_final: 0.7433 (mmm) REVERT: B 425 ILE cc_start: 0.8674 (mt) cc_final: 0.8112 (mt) REVERT: B 485 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7803 (mtm-85) REVERT: B 597 ILE cc_start: 0.9135 (pt) cc_final: 0.8840 (pt) REVERT: B 605 THR cc_start: 0.7858 (m) cc_final: 0.7573 (t) REVERT: B 658 LEU cc_start: 0.8924 (mt) cc_final: 0.8385 (mt) REVERT: C 85 GLN cc_start: 0.4929 (mt0) cc_final: 0.4086 (pt0) REVERT: C 112 LEU cc_start: 0.3484 (mt) cc_final: 0.3056 (mp) REVERT: C 130 TYR cc_start: 0.3400 (m-80) cc_final: 0.3141 (m-80) REVERT: C 287 LEU cc_start: 0.2172 (OUTLIER) cc_final: 0.1844 (mp) REVERT: D 256 VAL cc_start: 0.6874 (t) cc_final: 0.6171 (t) REVERT: D 260 ILE cc_start: 0.6984 (mt) cc_final: 0.6360 (tp) outliers start: 24 outliers final: 8 residues processed: 885 average time/residue: 0.3028 time to fit residues: 381.4953 Evaluate side-chains 581 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 572 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 232 ASN 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 C residue 220 LYS Chi-restraints excluded: chain C residue 287 LEU Chi-restraints excluded: chain D residue 59 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 8.9990 chunk 145 optimal weight: 9.9990 chunk 80 optimal weight: 0.0270 chunk 49 optimal weight: 0.6980 chunk 98 optimal weight: 0.6980 chunk 77 optimal weight: 4.9990 chunk 150 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 overall best weight: 2.0842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN A 320 ASN A 387 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN B 329 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 84 HIS ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN C 263 ASN C 270 ASN D 23 ASN D 25 ASN D 28 GLN D 71 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.133316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.094750 restraints weight = 34542.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.098074 restraints weight = 16786.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.100286 restraints weight = 9978.408| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 16386 Z= 0.209 Angle : 0.684 9.066 22134 Z= 0.358 Chirality : 0.045 0.205 2360 Planarity : 0.004 0.048 2818 Dihedral : 11.607 174.550 2259 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.66 % Allowed : 19.06 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.19), residues: 1932 helix: 1.33 (0.15), residues: 1130 sheet: 0.12 (0.41), residues: 142 loop : 0.65 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 30 HIS 0.006 0.001 HIS A 438 PHE 0.033 0.002 PHE B 261 TYR 0.021 0.002 TYR D 177 ARG 0.008 0.001 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.04725 ( 871) hydrogen bonds : angle 5.21145 ( 2571) covalent geometry : bond 0.00464 (16386) covalent geometry : angle 0.68408 (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 681 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 601 time to evaluate : 1.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.8541 (t80) cc_final: 0.8248 (t80) REVERT: A 87 LYS cc_start: 0.9112 (tptm) cc_final: 0.8897 (tptm) REVERT: A 99 LYS cc_start: 0.9234 (mmmm) cc_final: 0.8736 (mmmm) REVERT: A 102 ASN cc_start: 0.9128 (OUTLIER) cc_final: 0.8749 (m110) REVERT: A 103 ASP cc_start: 0.8824 (m-30) cc_final: 0.8593 (m-30) REVERT: A 150 GLN cc_start: 0.8652 (tp40) cc_final: 0.8439 (tm-30) REVERT: A 161 ARG cc_start: 0.8119 (ttm170) cc_final: 0.7608 (mmm-85) REVERT: A 202 ASN cc_start: 0.9397 (t0) cc_final: 0.9111 (t0) REVERT: A 214 LYS cc_start: 0.8528 (ttmm) cc_final: 0.8226 (mttm) REVERT: A 218 ASN cc_start: 0.9027 (t0) cc_final: 0.8502 (t0) REVERT: A 256 ARG cc_start: 0.9127 (ttp80) cc_final: 0.8858 (ttp80) REVERT: A 335 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7581 (mt-10) REVERT: A 381 LEU cc_start: 0.9024 (tp) cc_final: 0.8589 (pt) REVERT: A 384 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.7570 (pm20) REVERT: A 385 VAL cc_start: 0.8865 (t) cc_final: 0.8291 (t) REVERT: A 402 GLU cc_start: 0.8004 (mp0) cc_final: 0.7798 (mp0) REVERT: A 409 CYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7617 (p) REVERT: A 467 ASN cc_start: 0.9203 (t0) cc_final: 0.8970 (m-40) REVERT: A 483 GLU cc_start: 0.9069 (mp0) cc_final: 0.8318 (pm20) REVERT: A 505 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7758 (mt-10) REVERT: A 548 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8430 (mm-30) REVERT: A 628 GLU cc_start: 0.9030 (mt-10) cc_final: 0.8661 (mt-10) REVERT: A 640 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8357 (tpp) REVERT: A 644 ILE cc_start: 0.9573 (mt) cc_final: 0.9344 (mt) REVERT: B 95 MET cc_start: 0.8555 (tpp) cc_final: 0.8266 (tpp) REVERT: B 177 ASP cc_start: 0.8039 (t0) cc_final: 0.7669 (t70) REVERT: B 184 ARG cc_start: 0.9141 (tpp-160) cc_final: 0.8641 (tpp-160) REVERT: B 190 MET cc_start: 0.9185 (mtm) cc_final: 0.8840 (mtm) REVERT: B 202 ASN cc_start: 0.8892 (t0) cc_final: 0.8479 (t0) REVERT: B 290 GLU cc_start: 0.9009 (tt0) cc_final: 0.8596 (tm-30) REVERT: B 312 GLN cc_start: 0.8426 (tt0) cc_final: 0.8049 (tt0) REVERT: B 322 MET cc_start: 0.9012 (mmm) cc_final: 0.8378 (mmm) REVERT: B 348 MET cc_start: 0.8133 (tpp) cc_final: 0.7931 (tpp) REVERT: B 362 ASP cc_start: 0.7781 (m-30) cc_final: 0.7511 (m-30) REVERT: B 374 SER cc_start: 0.9473 (t) cc_final: 0.9224 (t) REVERT: B 375 LYS cc_start: 0.8931 (mtmm) cc_final: 0.8488 (mtpp) REVERT: B 384 GLU cc_start: 0.8339 (pm20) cc_final: 0.7549 (pm20) REVERT: B 467 ASN cc_start: 0.9253 (t0) cc_final: 0.8927 (m-40) REVERT: B 493 MET cc_start: 0.9416 (tmm) cc_final: 0.9063 (tmm) REVERT: B 515 ASP cc_start: 0.8919 (m-30) cc_final: 0.8694 (m-30) REVERT: B 550 MET cc_start: 0.7869 (mtm) cc_final: 0.7474 (mtp) REVERT: B 583 SER cc_start: 0.8076 (OUTLIER) cc_final: 0.7794 (t) REVERT: B 640 MET cc_start: 0.9071 (tpp) cc_final: 0.8768 (tpp) REVERT: B 669 ARG cc_start: 0.8923 (mtp85) cc_final: 0.8653 (mmm-85) REVERT: B 683 TYR cc_start: 0.8903 (t80) cc_final: 0.8390 (t80) REVERT: C 68 GLU cc_start: 0.9394 (mm-30) cc_final: 0.9127 (mm-30) REVERT: C 85 GLN cc_start: 0.4084 (mt0) cc_final: 0.3418 (pt0) REVERT: C 93 MET cc_start: 0.8475 (mtt) cc_final: 0.8188 (mtt) REVERT: C 154 PHE cc_start: 0.8746 (t80) cc_final: 0.8405 (t80) REVERT: C 157 MET cc_start: 0.9017 (mtt) cc_final: 0.8735 (mtt) REVERT: C 158 VAL cc_start: 0.9521 (t) cc_final: 0.8956 (t) REVERT: C 162 TYR cc_start: 0.9308 (m-10) cc_final: 0.8850 (m-10) REVERT: C 266 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.9116 (tppt) REVERT: C 271 LEU cc_start: 0.8660 (mm) cc_final: 0.8161 (mm) REVERT: C 315 LEU cc_start: 0.9116 (mm) cc_final: 0.8911 (mm) REVERT: C 320 PHE cc_start: 0.9475 (m-80) cc_final: 0.9239 (m-10) REVERT: D 44 TRP cc_start: 0.7882 (t-100) cc_final: 0.7576 (t-100) REVERT: D 92 PHE cc_start: 0.7085 (t80) cc_final: 0.6768 (t80) REVERT: D 96 MET cc_start: 0.5900 (mmm) cc_final: 0.5685 (mmt) REVERT: D 174 TYR cc_start: 0.8169 (OUTLIER) cc_final: 0.7343 (t80) REVERT: D 184 LEU cc_start: 0.8688 (mt) cc_final: 0.8418 (mt) REVERT: D 195 LEU cc_start: 0.8795 (tt) cc_final: 0.8513 (mm) outliers start: 80 outliers final: 39 residues processed: 640 average time/residue: 0.2841 time to fit residues: 269.4296 Evaluate side-chains 553 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 506 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 216 VAL 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 260 ASP Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 664 THR Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 266 LYS Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 254 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 4.9990 chunk 168 optimal weight: 9.9990 chunk 175 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 191 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 171 optimal weight: 9.9990 chunk 189 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 42 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN D 25 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.126018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.088562 restraints weight = 34902.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.091723 restraints weight = 16917.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.093798 restraints weight = 10116.686| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 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 = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16386 Z= 0.259 Angle : 0.676 10.426 22134 Z= 0.356 Chirality : 0.045 0.212 2360 Planarity : 0.004 0.036 2818 Dihedral : 11.427 174.445 2255 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 5.07 % Allowed : 20.10 % Favored : 74.83 % 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: 1.14 (0.19), residues: 1932 helix: 1.17 (0.15), residues: 1136 sheet: -0.04 (0.41), residues: 144 loop : 0.43 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 30 HIS 0.006 0.001 HIS C 201 PHE 0.042 0.002 PHE C 168 TYR 0.037 0.002 TYR A 498 ARG 0.006 0.001 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 871) hydrogen bonds : angle 5.23033 ( 2571) covalent geometry : bond 0.00568 (16386) covalent geometry : angle 0.67640 (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 620 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 533 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.8578 (t80) cc_final: 0.8344 (t80) REVERT: A 99 LYS cc_start: 0.9166 (mmmm) cc_final: 0.8709 (mmmm) REVERT: A 102 ASN cc_start: 0.9084 (OUTLIER) cc_final: 0.8850 (m110) REVERT: A 103 ASP cc_start: 0.9007 (m-30) cc_final: 0.8720 (m-30) REVERT: A 117 ARG cc_start: 0.8145 (mtt-85) cc_final: 0.7855 (mtt-85) REVERT: A 150 GLN cc_start: 0.8906 (tp40) cc_final: 0.8358 (tm-30) REVERT: A 202 ASN cc_start: 0.9414 (t0) cc_final: 0.9209 (t0) REVERT: A 218 ASN cc_start: 0.8994 (t0) cc_final: 0.8523 (t0) REVERT: A 359 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8055 (ttp) REVERT: A 384 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7635 (pm20) REVERT: A 385 VAL cc_start: 0.8883 (t) cc_final: 0.8632 (t) REVERT: A 393 SER cc_start: 0.9155 (m) cc_final: 0.8853 (m) REVERT: A 402 GLU cc_start: 0.8202 (mp0) cc_final: 0.7961 (mp0) REVERT: A 467 ASN cc_start: 0.9123 (t0) cc_final: 0.8901 (m-40) REVERT: A 483 GLU cc_start: 0.9054 (mp0) cc_final: 0.8590 (pm20) REVERT: A 505 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7815 (mt-10) REVERT: A 527 TYR cc_start: 0.8620 (t80) cc_final: 0.8386 (t80) REVERT: A 548 GLU cc_start: 0.8678 (OUTLIER) cc_final: 0.8430 (mm-30) REVERT: A 628 GLU cc_start: 0.9064 (mt-10) cc_final: 0.8437 (mm-30) REVERT: A 640 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8297 (tpp) REVERT: A 645 GLN cc_start: 0.9112 (tp40) cc_final: 0.8884 (tp-100) REVERT: A 666 ASP cc_start: 0.8544 (m-30) cc_final: 0.8274 (m-30) REVERT: B 95 MET cc_start: 0.8625 (tpp) cc_final: 0.8230 (tpp) REVERT: B 178 SER cc_start: 0.8454 (OUTLIER) cc_final: 0.8227 (p) REVERT: B 184 ARG cc_start: 0.9141 (tpp-160) cc_final: 0.8683 (tpp-160) REVERT: B 190 MET cc_start: 0.9178 (mtm) cc_final: 0.8892 (mtm) REVERT: B 202 ASN cc_start: 0.8889 (t0) cc_final: 0.8451 (t0) REVERT: B 252 ASN cc_start: 0.9171 (t0) cc_final: 0.8877 (t0) REVERT: B 290 GLU cc_start: 0.8983 (tt0) cc_final: 0.8702 (tm-30) REVERT: B 312 GLN cc_start: 0.8497 (tt0) cc_final: 0.7842 (tt0) REVERT: B 335 GLU cc_start: 0.8392 (mt-10) cc_final: 0.8068 (mt-10) REVERT: B 348 MET cc_start: 0.8083 (tpp) cc_final: 0.7855 (tpp) REVERT: B 362 ASP cc_start: 0.7755 (m-30) cc_final: 0.7455 (m-30) REVERT: B 375 LYS cc_start: 0.8980 (mtmm) cc_final: 0.8658 (mtpp) REVERT: B 394 TYR cc_start: 0.9017 (m-80) cc_final: 0.8745 (m-80) REVERT: B 467 ASN cc_start: 0.9326 (t0) cc_final: 0.8928 (m-40) REVERT: B 493 MET cc_start: 0.9421 (tmm) cc_final: 0.9195 (tmm) REVERT: B 515 ASP cc_start: 0.8924 (m-30) cc_final: 0.8556 (m-30) REVERT: B 550 MET cc_start: 0.7956 (mtm) cc_final: 0.7613 (mtp) REVERT: B 669 ARG cc_start: 0.8877 (mtp85) cc_final: 0.8579 (mmm-85) REVERT: C 56 MET cc_start: 0.4898 (ptp) cc_final: 0.4630 (ptp) REVERT: C 69 GLN cc_start: 0.9016 (tp-100) cc_final: 0.8778 (pt0) REVERT: C 72 THR cc_start: 0.8917 (OUTLIER) cc_final: 0.8697 (p) REVERT: C 74 MET cc_start: 0.7148 (mtt) cc_final: 0.6392 (mtm) REVERT: C 76 ILE cc_start: 0.8476 (mm) cc_final: 0.8019 (tp) REVERT: C 85 GLN cc_start: 0.4076 (mt0) cc_final: 0.3321 (pt0) REVERT: C 93 MET cc_start: 0.8739 (mtt) cc_final: 0.8473 (mtt) REVERT: C 155 LYS cc_start: 0.8569 (mttm) cc_final: 0.8196 (mmtt) REVERT: C 157 MET cc_start: 0.9128 (mtt) cc_final: 0.8790 (mtt) REVERT: C 158 VAL cc_start: 0.9719 (t) cc_final: 0.9136 (t) REVERT: C 162 TYR cc_start: 0.9345 (m-10) cc_final: 0.8841 (m-10) REVERT: C 174 TYR cc_start: 0.8391 (OUTLIER) cc_final: 0.7958 (t80) REVERT: C 201 HIS cc_start: 0.8664 (m90) cc_final: 0.8186 (m90) REVERT: C 212 ILE cc_start: 0.8576 (mm) cc_final: 0.7744 (mm) REVERT: C 259 PHE cc_start: 0.7442 (t80) cc_final: 0.7163 (t80) REVERT: C 271 LEU cc_start: 0.8697 (mm) cc_final: 0.8085 (mm) REVERT: C 317 ASP cc_start: 0.8391 (m-30) cc_final: 0.8050 (m-30) REVERT: D 96 MET cc_start: 0.6224 (mmm) cc_final: 0.5970 (mmm) REVERT: D 174 TYR cc_start: 0.8193 (OUTLIER) cc_final: 0.7387 (t80) outliers start: 87 outliers final: 51 residues processed: 578 average time/residue: 0.2796 time to fit residues: 240.1698 Evaluate side-chains 535 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 475 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 638 VAL Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 178 SER Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 561 LEU Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 180 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 148 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN A 259 ASN A 312 GLN A 365 ASN A 410 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.127835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.090333 restraints weight = 35004.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.093451 restraints weight = 16972.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.095549 restraints weight = 10451.160| |-----------------------------------------------------------------------------| r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.5258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16386 Z= 0.178 Angle : 0.628 10.194 22134 Z= 0.326 Chirality : 0.043 0.172 2360 Planarity : 0.003 0.034 2818 Dihedral : 11.126 173.441 2255 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.20 % Allowed : 22.38 % 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: 1.09 (0.19), residues: 1932 helix: 1.17 (0.15), residues: 1138 sheet: -0.32 (0.41), residues: 146 loop : 0.39 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP D 30 HIS 0.006 0.001 HIS A 568 PHE 0.036 0.002 PHE C 168 TYR 0.023 0.001 TYR C 169 ARG 0.006 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.04061 ( 871) hydrogen bonds : angle 5.07976 ( 2571) covalent geometry : bond 0.00396 (16386) covalent geometry : angle 0.62767 (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 597 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 525 time to evaluate : 1.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.8628 (t80) cc_final: 0.8401 (t80) REVERT: A 65 GLU cc_start: 0.8625 (mm-30) cc_final: 0.7939 (mp0) REVERT: A 99 LYS cc_start: 0.9147 (mmmm) cc_final: 0.8855 (mmmm) REVERT: A 107 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8216 (mmmm) REVERT: A 117 ARG cc_start: 0.8082 (mtt-85) cc_final: 0.7819 (mtt-85) REVERT: A 150 GLN cc_start: 0.8833 (tp40) cc_final: 0.8352 (tm-30) REVERT: A 161 ARG cc_start: 0.8115 (ttm170) cc_final: 0.7540 (mmm-85) REVERT: A 188 ILE cc_start: 0.9373 (mt) cc_final: 0.9102 (mm) REVERT: A 202 ASN cc_start: 0.9414 (t0) cc_final: 0.9206 (t0) REVERT: A 218 ASN cc_start: 0.9006 (t0) cc_final: 0.8525 (t0) REVERT: A 232 ASN cc_start: 0.9461 (OUTLIER) cc_final: 0.9122 (m-40) REVERT: A 341 LYS cc_start: 0.9376 (mmtm) cc_final: 0.8872 (mmpt) REVERT: A 344 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8617 (mt-10) REVERT: A 359 MET cc_start: 0.8379 (OUTLIER) cc_final: 0.7929 (ttp) REVERT: A 381 LEU cc_start: 0.9162 (tp) cc_final: 0.8524 (pt) REVERT: A 384 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7489 (pm20) REVERT: A 385 VAL cc_start: 0.8856 (t) cc_final: 0.8565 (t) REVERT: A 390 GLN cc_start: 0.8463 (mt0) cc_final: 0.8124 (mt0) REVERT: A 393 SER cc_start: 0.9115 (m) cc_final: 0.8700 (m) REVERT: A 402 GLU cc_start: 0.8187 (mp0) cc_final: 0.7915 (mp0) REVERT: A 406 ASP cc_start: 0.8161 (m-30) cc_final: 0.7909 (t0) REVERT: A 467 ASN cc_start: 0.9056 (t0) cc_final: 0.8778 (m-40) REVERT: A 483 GLU cc_start: 0.9069 (mp0) cc_final: 0.8282 (pm20) REVERT: A 505 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7837 (mt-10) REVERT: A 527 TYR cc_start: 0.8621 (t80) cc_final: 0.8410 (t80) REVERT: A 548 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.8501 (mm-30) REVERT: A 590 SER cc_start: 0.9371 (OUTLIER) cc_final: 0.8733 (m) REVERT: A 628 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8486 (mm-30) REVERT: A 640 MET cc_start: 0.9281 (OUTLIER) cc_final: 0.8183 (tpp) REVERT: A 645 GLN cc_start: 0.9067 (tp40) cc_final: 0.8822 (tp-100) REVERT: A 662 MET cc_start: 0.8478 (ptp) cc_final: 0.8120 (ptp) REVERT: B 95 MET cc_start: 0.8672 (tpp) cc_final: 0.8233 (tpp) REVERT: B 184 ARG cc_start: 0.9157 (tpp-160) cc_final: 0.8619 (tpp-160) REVERT: B 190 MET cc_start: 0.9179 (mtm) cc_final: 0.8910 (mtm) REVERT: B 252 ASN cc_start: 0.9243 (t0) cc_final: 0.8872 (t0) REVERT: B 257 ASP cc_start: 0.8702 (m-30) cc_final: 0.8347 (m-30) REVERT: B 290 GLU cc_start: 0.8989 (tt0) cc_final: 0.8680 (tm-30) REVERT: B 312 GLN cc_start: 0.8629 (tt0) cc_final: 0.8337 (tt0) REVERT: B 322 MET cc_start: 0.9037 (mmm) cc_final: 0.8325 (mmm) REVERT: B 335 GLU cc_start: 0.8269 (mt-10) cc_final: 0.8018 (mt-10) REVERT: B 348 MET cc_start: 0.8089 (tpp) cc_final: 0.7817 (tpp) REVERT: B 362 ASP cc_start: 0.7729 (m-30) cc_final: 0.7318 (m-30) REVERT: B 375 LYS cc_start: 0.8910 (mtmm) cc_final: 0.8620 (mtpp) REVERT: B 394 TYR cc_start: 0.9009 (m-80) cc_final: 0.8788 (m-80) REVERT: B 467 ASN cc_start: 0.9267 (t0) cc_final: 0.8896 (m-40) REVERT: B 493 MET cc_start: 0.9434 (tmm) cc_final: 0.9053 (tmm) REVERT: B 515 ASP cc_start: 0.8970 (m-30) cc_final: 0.8633 (m-30) REVERT: B 576 LEU cc_start: 0.9478 (mt) cc_final: 0.9247 (mt) REVERT: B 668 ASN cc_start: 0.8460 (m110) cc_final: 0.8112 (m110) REVERT: C 17 PHE cc_start: 0.8514 (p90) cc_final: 0.7740 (p90) REVERT: C 56 MET cc_start: 0.4871 (ptp) cc_final: 0.4654 (ptp) REVERT: C 76 ILE cc_start: 0.8570 (mm) cc_final: 0.8213 (tp) REVERT: C 85 GLN cc_start: 0.4336 (mt0) cc_final: 0.3497 (pt0) REVERT: C 93 MET cc_start: 0.8960 (mtt) cc_final: 0.8710 (mtt) REVERT: C 155 LYS cc_start: 0.8597 (mttm) cc_final: 0.8200 (mmtt) REVERT: C 157 MET cc_start: 0.9217 (mtt) cc_final: 0.8909 (mtt) REVERT: C 162 TYR cc_start: 0.9376 (m-10) cc_final: 0.8785 (m-10) REVERT: C 174 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.7845 (t80) REVERT: C 177 TYR cc_start: 0.8463 (t80) cc_final: 0.8108 (t80) REVERT: C 196 ARG cc_start: 0.9046 (mmm-85) cc_final: 0.8824 (mmm-85) REVERT: C 201 HIS cc_start: 0.8743 (m90) cc_final: 0.8202 (m90) REVERT: C 212 ILE cc_start: 0.8678 (mm) cc_final: 0.7972 (mm) REVERT: C 271 LEU cc_start: 0.8596 (mm) cc_final: 0.7933 (mm) REVERT: D 28 GLN cc_start: 0.8350 (mt0) cc_final: 0.8146 (tt0) REVERT: D 96 MET cc_start: 0.6092 (mmm) cc_final: 0.5821 (mmm) REVERT: D 174 TYR cc_start: 0.8134 (OUTLIER) cc_final: 0.7324 (t80) outliers start: 72 outliers final: 43 residues processed: 561 average time/residue: 0.2796 time to fit residues: 233.0824 Evaluate side-chains 530 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 478 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 243 ARG Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 605 THR Chi-restraints excluded: chain B residue 624 PHE Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 55 TYR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 220 LYS Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 223 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 67 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 182 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 62 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 259 ASN A 312 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.129844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.092682 restraints weight = 35579.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.095758 restraints weight = 17050.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.097911 restraints weight = 10413.526| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.5587 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= 0.198 Angle : 0.641 10.423 22134 Z= 0.331 Chirality : 0.043 0.204 2360 Planarity : 0.003 0.036 2818 Dihedral : 11.109 175.490 2253 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.02 % Allowed : 23.48 % Favored : 72.49 % 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: 1.03 (0.19), residues: 1932 helix: 1.16 (0.15), residues: 1134 sheet: -0.49 (0.41), residues: 146 loop : 0.34 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP D 44 HIS 0.005 0.001 HIS C 201 PHE 0.033 0.002 PHE C 168 TYR 0.025 0.001 TYR B 626 ARG 0.006 0.001 ARG B 164 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 871) hydrogen bonds : angle 5.05736 ( 2571) covalent geometry : bond 0.00441 (16386) covalent geometry : angle 0.64147 (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 580 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 511 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 PHE cc_start: 0.8617 (t80) cc_final: 0.8396 (t80) REVERT: A 65 GLU cc_start: 0.8699 (mm-30) cc_final: 0.7972 (mp0) REVERT: A 99 LYS cc_start: 0.9114 (mmmm) cc_final: 0.8889 (mmmm) REVERT: A 107 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8289 (mmmm) REVERT: A 117 ARG cc_start: 0.8144 (mtt-85) cc_final: 0.7916 (mtt-85) REVERT: A 119 GLU cc_start: 0.8545 (mp0) cc_final: 0.8322 (mp0) REVERT: A 161 ARG cc_start: 0.8131 (ttm170) cc_final: 0.7449 (mmm-85) REVERT: A 164 ARG cc_start: 0.8761 (ptt90) cc_final: 0.8499 (ptt90) REVERT: A 202 ASN cc_start: 0.9420 (t0) cc_final: 0.9178 (t0) REVERT: A 218 ASN cc_start: 0.9017 (t0) cc_final: 0.8586 (t0) REVERT: A 341 LYS cc_start: 0.9381 (mmtm) cc_final: 0.8881 (mmpt) REVERT: A 344 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8662 (mt-10) REVERT: A 359 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.7943 (ttp) REVERT: A 381 LEU cc_start: 0.9180 (tp) cc_final: 0.8523 (pt) REVERT: A 384 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7494 (pm20) REVERT: A 385 VAL cc_start: 0.8868 (t) cc_final: 0.8521 (t) REVERT: A 390 GLN cc_start: 0.8467 (mt0) cc_final: 0.8117 (mt0) REVERT: A 393 SER cc_start: 0.9164 (m) cc_final: 0.8769 (m) REVERT: A 402 GLU cc_start: 0.8216 (mp0) cc_final: 0.7941 (mp0) REVERT: A 406 ASP cc_start: 0.8053 (m-30) cc_final: 0.7831 (t0) REVERT: A 427 LYS cc_start: 0.9070 (ttpp) cc_final: 0.8749 (ttpp) REVERT: A 467 ASN cc_start: 0.9093 (t0) cc_final: 0.8695 (m-40) REVERT: A 505 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7804 (mt-10) REVERT: A 548 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8524 (mm-30) REVERT: A 550 MET cc_start: 0.8679 (mmt) cc_final: 0.8383 (mmt) REVERT: A 590 SER cc_start: 0.9365 (OUTLIER) cc_final: 0.8539 (m) REVERT: A 628 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8533 (mm-30) REVERT: A 640 MET cc_start: 0.9311 (OUTLIER) cc_final: 0.8083 (tpp) REVERT: A 645 GLN cc_start: 0.9025 (tp40) cc_final: 0.8798 (tp-100) REVERT: B 95 MET cc_start: 0.8607 (tpp) cc_final: 0.8223 (tpp) REVERT: B 184 ARG cc_start: 0.9147 (tpp-160) cc_final: 0.8556 (tpp-160) REVERT: B 190 MET cc_start: 0.9115 (mtm) cc_final: 0.8829 (mtm) REVERT: B 257 ASP cc_start: 0.8612 (m-30) cc_final: 0.8273 (m-30) REVERT: B 312 GLN cc_start: 0.8681 (tt0) cc_final: 0.8396 (tt0) REVERT: B 322 MET cc_start: 0.9106 (mmm) cc_final: 0.8411 (mmm) REVERT: B 348 MET cc_start: 0.8111 (tpp) cc_final: 0.7877 (tpp) REVERT: B 362 ASP cc_start: 0.7639 (m-30) cc_final: 0.7175 (m-30) REVERT: B 375 LYS cc_start: 0.8912 (mtmm) cc_final: 0.8629 (mtpp) REVERT: B 394 TYR cc_start: 0.9021 (m-80) cc_final: 0.8787 (m-80) REVERT: B 467 ASN cc_start: 0.9265 (t0) cc_final: 0.8882 (m-40) REVERT: B 493 MET cc_start: 0.9421 (tmm) cc_final: 0.9009 (tmm) REVERT: B 515 ASP cc_start: 0.8945 (m-30) cc_final: 0.8540 (m-30) REVERT: B 628 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7956 (mm-30) REVERT: B 668 ASN cc_start: 0.8460 (m110) cc_final: 0.8116 (m110) REVERT: C 17 PHE cc_start: 0.8702 (p90) cc_final: 0.7883 (p90) REVERT: C 69 GLN cc_start: 0.8893 (tm-30) cc_final: 0.8543 (tm-30) REVERT: C 76 ILE cc_start: 0.8690 (mm) cc_final: 0.8403 (tp) REVERT: C 85 GLN cc_start: 0.4635 (mt0) cc_final: 0.3749 (pt0) REVERT: C 93 MET cc_start: 0.9017 (mtt) cc_final: 0.8659 (mtt) REVERT: C 96 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8564 (tpp) REVERT: C 155 LYS cc_start: 0.8709 (mttm) cc_final: 0.7842 (pttp) REVERT: C 157 MET cc_start: 0.9280 (mtt) cc_final: 0.9032 (mtt) REVERT: C 158 VAL cc_start: 0.9749 (t) cc_final: 0.9296 (m) REVERT: C 162 TYR cc_start: 0.9314 (m-10) cc_final: 0.8807 (m-10) REVERT: C 201 HIS cc_start: 0.8797 (m90) cc_final: 0.8262 (m90) REVERT: C 211 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8071 (pp20) REVERT: C 212 ILE cc_start: 0.8848 (mm) cc_final: 0.8262 (mm) REVERT: C 260 ILE cc_start: 0.8007 (pt) cc_final: 0.7779 (pt) REVERT: C 271 LEU cc_start: 0.8650 (mm) cc_final: 0.8067 (mm) REVERT: D 25 ASN cc_start: 0.9354 (m110) cc_final: 0.8792 (m110) REVERT: D 76 ILE cc_start: 0.5400 (tt) cc_final: 0.5062 (pt) REVERT: D 174 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.7279 (t80) outliers start: 69 outliers final: 42 residues processed: 547 average time/residue: 0.2821 time to fit residues: 232.2507 Evaluate side-chains 536 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 485 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 425 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR 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 598 MET Chi-restraints excluded: chain B residue 624 PHE Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 223 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 31 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 177 optimal weight: 8.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN A 438 HIS ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.124222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.087392 restraints weight = 35579.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.090493 restraints weight = 16801.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.092510 restraints weight = 9998.730| |-----------------------------------------------------------------------------| 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) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.5881 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= 0.286 Angle : 0.710 10.564 22134 Z= 0.366 Chirality : 0.045 0.247 2360 Planarity : 0.004 0.040 2818 Dihedral : 10.961 176.081 2249 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 17.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.60 % Allowed : 24.71 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.19), residues: 1932 helix: 1.06 (0.15), residues: 1130 sheet: -0.47 (0.42), residues: 142 loop : 0.30 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.003 TRP D 30 HIS 0.005 0.001 HIS A 647 PHE 0.029 0.002 PHE C 172 TYR 0.017 0.002 TYR B 626 ARG 0.007 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.04194 ( 871) hydrogen bonds : angle 5.18104 ( 2571) covalent geometry : bond 0.00628 (16386) covalent geometry : angle 0.71037 (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 571 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 492 time to evaluate : 1.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8086 (mp0) REVERT: A 87 LYS cc_start: 0.9195 (tptm) cc_final: 0.8961 (tptm) REVERT: A 99 LYS cc_start: 0.9116 (mmmm) cc_final: 0.8857 (mmmm) REVERT: A 102 ASN cc_start: 0.9172 (OUTLIER) cc_final: 0.8785 (m-40) REVERT: A 139 GLU cc_start: 0.8619 (mp0) cc_final: 0.8406 (mp0) REVERT: A 150 GLN cc_start: 0.9051 (tp40) cc_final: 0.8736 (tm-30) REVERT: A 161 ARG cc_start: 0.8125 (ttm170) cc_final: 0.7562 (mmm-85) REVERT: A 164 ARG cc_start: 0.8820 (ptt90) cc_final: 0.8492 (ptt90) REVERT: A 172 LEU cc_start: 0.9181 (mp) cc_final: 0.8551 (mp) REVERT: A 218 ASN cc_start: 0.9055 (t0) cc_final: 0.8661 (t0) REVERT: A 335 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7592 (mt-10) REVERT: A 344 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8556 (mt-10) REVERT: A 359 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.8104 (ttp) REVERT: A 366 LYS cc_start: 0.9222 (mtmt) cc_final: 0.8894 (ptpp) REVERT: A 384 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7568 (pm20) REVERT: A 385 VAL cc_start: 0.8921 (t) cc_final: 0.8603 (t) REVERT: A 390 GLN cc_start: 0.8515 (mt0) cc_final: 0.8187 (mt0) REVERT: A 393 SER cc_start: 0.9224 (m) cc_final: 0.8868 (m) REVERT: A 402 GLU cc_start: 0.8257 (mp0) cc_final: 0.8032 (mp0) REVERT: A 505 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7693 (mt-10) REVERT: A 548 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8549 (mm-30) REVERT: A 628 GLU cc_start: 0.8947 (mt-10) cc_final: 0.8543 (mm-30) REVERT: A 640 MET cc_start: 0.9307 (OUTLIER) cc_final: 0.8119 (tpp) REVERT: B 95 MET cc_start: 0.8625 (tpp) cc_final: 0.8245 (tpp) REVERT: B 184 ARG cc_start: 0.9139 (tpp-160) cc_final: 0.8672 (tpp-160) REVERT: B 190 MET cc_start: 0.9175 (mtm) cc_final: 0.8900 (mtm) REVERT: B 257 ASP cc_start: 0.8631 (m-30) cc_final: 0.8322 (m-30) REVERT: B 290 GLU cc_start: 0.9074 (OUTLIER) cc_final: 0.8711 (pp20) REVERT: B 322 MET cc_start: 0.9052 (mmm) cc_final: 0.8664 (mmm) REVERT: B 384 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.6883 (pm20) REVERT: B 441 GLU cc_start: 0.8622 (pt0) cc_final: 0.8247 (pt0) REVERT: B 467 ASN cc_start: 0.9323 (t0) cc_final: 0.8910 (m-40) REVERT: B 493 MET cc_start: 0.9379 (tmm) cc_final: 0.8970 (tmm) REVERT: B 515 ASP cc_start: 0.9003 (m-30) cc_final: 0.8678 (m-30) REVERT: B 550 MET cc_start: 0.8366 (mtt) cc_final: 0.8135 (mtt) REVERT: B 628 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8180 (mm-30) REVERT: B 668 ASN cc_start: 0.8585 (m110) cc_final: 0.8179 (m110) REVERT: C 69 GLN cc_start: 0.8944 (tm-30) cc_final: 0.8673 (tm-30) REVERT: C 76 ILE cc_start: 0.8819 (mm) cc_final: 0.8555 (tp) REVERT: C 85 GLN cc_start: 0.4932 (mt0) cc_final: 0.4098 (pt0) REVERT: C 93 MET cc_start: 0.9018 (mtt) cc_final: 0.8688 (mtt) REVERT: C 155 LYS cc_start: 0.8822 (mttm) cc_final: 0.7977 (pttp) REVERT: C 157 MET cc_start: 0.9277 (mtt) cc_final: 0.9043 (mtt) REVERT: C 158 VAL cc_start: 0.9700 (t) cc_final: 0.9308 (m) REVERT: C 162 TYR cc_start: 0.9303 (m-10) cc_final: 0.8838 (m-10) REVERT: C 174 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.7796 (t80) REVERT: C 201 HIS cc_start: 0.8835 (m90) cc_final: 0.8242 (m90) REVERT: C 260 ILE cc_start: 0.8053 (pt) cc_final: 0.7831 (pt) REVERT: C 271 LEU cc_start: 0.8781 (mm) cc_final: 0.8226 (mm) REVERT: D 25 ASN cc_start: 0.9361 (m110) cc_final: 0.8851 (m110) REVERT: D 28 GLN cc_start: 0.8626 (tt0) cc_final: 0.8023 (tt0) REVERT: D 76 ILE cc_start: 0.5493 (tt) cc_final: 0.5107 (pt) REVERT: D 143 LYS cc_start: 0.8406 (mmmt) cc_final: 0.8153 (mmmt) REVERT: D 172 PHE cc_start: 0.7057 (OUTLIER) cc_final: 0.6065 (m-80) REVERT: D 174 TYR cc_start: 0.8179 (OUTLIER) cc_final: 0.7482 (t80) outliers start: 79 outliers final: 56 residues processed: 529 average time/residue: 0.2656 time to fit residues: 210.7054 Evaluate side-chains 537 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 470 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 102 ASN Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 433 THR Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 661 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 346 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 561 LEU 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 624 PHE Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 53 ASP Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 138 ILE Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 239 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 39 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 23 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 184 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 312 GLN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN B 668 ASN C 238 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.133297 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.095750 restraints weight = 35284.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.099105 restraints weight = 16470.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.101202 restraints weight = 9614.478| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3141 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3141 r_free = 0.3141 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3141 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.6084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16386 Z= 0.140 Angle : 0.666 11.285 22134 Z= 0.339 Chirality : 0.044 0.254 2360 Planarity : 0.003 0.039 2818 Dihedral : 10.530 173.030 2249 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.91 % Allowed : 26.86 % Favored : 70.22 % 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: 0.95 (0.19), residues: 1932 helix: 1.17 (0.15), residues: 1127 sheet: -0.59 (0.42), residues: 146 loop : 0.18 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 30 HIS 0.005 0.001 HIS C 201 PHE 0.054 0.002 PHE C 172 TYR 0.016 0.001 TYR C 242 ARG 0.009 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.03903 ( 871) hydrogen bonds : angle 5.05144 ( 2571) covalent geometry : bond 0.00318 (16386) covalent geometry : angle 0.66629 (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 564 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 514 time to evaluate : 1.944 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 29 ASP cc_start: 0.9091 (OUTLIER) cc_final: 0.8881 (t70) REVERT: A 65 GLU cc_start: 0.8738 (mm-30) cc_final: 0.7810 (mp0) REVERT: A 139 GLU cc_start: 0.8544 (mp0) cc_final: 0.8235 (mm-30) REVERT: A 161 ARG cc_start: 0.8170 (ttm170) cc_final: 0.7570 (mmm-85) REVERT: A 164 ARG cc_start: 0.8727 (ptt90) cc_final: 0.8448 (ptt90) REVERT: A 202 ASN cc_start: 0.9446 (t0) cc_final: 0.9174 (t0) REVERT: A 218 ASN cc_start: 0.9030 (t0) cc_final: 0.8451 (t0) REVERT: A 236 TYR cc_start: 0.9284 (t80) cc_final: 0.9041 (t80) REVERT: A 341 LYS cc_start: 0.9344 (mmtm) cc_final: 0.8842 (mmpt) REVERT: A 344 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8590 (mt-10) REVERT: A 359 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.7948 (ttp) REVERT: A 366 LYS cc_start: 0.9088 (mtmt) cc_final: 0.8775 (ptpp) REVERT: A 381 LEU cc_start: 0.9139 (tp) cc_final: 0.8485 (pt) REVERT: A 384 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7439 (pm20) REVERT: A 385 VAL cc_start: 0.8983 (t) cc_final: 0.8615 (t) REVERT: A 390 GLN cc_start: 0.8395 (mt0) cc_final: 0.8008 (mt0) REVERT: A 505 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7755 (mt-10) REVERT: A 548 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.8529 (mm-30) REVERT: A 628 GLU cc_start: 0.8908 (mt-10) cc_final: 0.8600 (mm-30) REVERT: A 640 MET cc_start: 0.9294 (OUTLIER) cc_final: 0.7997 (tpp) REVERT: A 645 GLN cc_start: 0.9176 (tp-100) cc_final: 0.8943 (tp40) REVERT: B 95 MET cc_start: 0.8555 (tpp) cc_final: 0.8263 (tpp) REVERT: B 99 LYS cc_start: 0.9214 (OUTLIER) cc_final: 0.8662 (tptp) REVERT: B 143 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8754 (tt) REVERT: B 190 MET cc_start: 0.9134 (mtm) cc_final: 0.8832 (mtm) REVERT: B 257 ASP cc_start: 0.8543 (m-30) cc_final: 0.8209 (m-30) REVERT: B 290 GLU cc_start: 0.9095 (pt0) cc_final: 0.8741 (pp20) REVERT: B 322 MET cc_start: 0.9026 (mmm) cc_final: 0.8422 (mmm) REVERT: B 384 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.7077 (pm20) REVERT: B 467 ASN cc_start: 0.9074 (t0) cc_final: 0.8812 (m-40) REVERT: B 493 MET cc_start: 0.9400 (tmm) cc_final: 0.9067 (tmm) REVERT: B 515 ASP cc_start: 0.8890 (m-30) cc_final: 0.8515 (m-30) REVERT: B 576 LEU cc_start: 0.9474 (mt) cc_final: 0.9247 (mt) REVERT: B 664 THR cc_start: 0.8923 (p) cc_final: 0.8261 (t) REVERT: B 668 ASN cc_start: 0.8374 (m-40) cc_final: 0.8074 (m110) REVERT: C 69 GLN cc_start: 0.8867 (tm-30) cc_final: 0.8343 (pp30) REVERT: C 74 MET cc_start: 0.6931 (mtt) cc_final: 0.6186 (mtm) REVERT: C 76 ILE cc_start: 0.8831 (mm) cc_final: 0.8546 (tp) REVERT: C 85 GLN cc_start: 0.5203 (mt0) cc_final: 0.4412 (pt0) REVERT: C 93 MET cc_start: 0.9036 (mtt) cc_final: 0.8770 (mtt) REVERT: C 143 LYS cc_start: 0.8371 (tptp) cc_final: 0.8154 (tmtt) REVERT: C 157 MET cc_start: 0.9351 (mtt) cc_final: 0.9129 (mtt) REVERT: C 158 VAL cc_start: 0.9707 (t) cc_final: 0.9227 (m) REVERT: C 162 TYR cc_start: 0.9318 (m-10) cc_final: 0.8841 (m-10) REVERT: C 201 HIS cc_start: 0.8815 (m90) cc_final: 0.8198 (m90) REVERT: C 260 ILE cc_start: 0.7893 (pt) cc_final: 0.7641 (pt) REVERT: C 271 LEU cc_start: 0.8699 (mm) cc_final: 0.8037 (mm) REVERT: D 25 ASN cc_start: 0.9355 (m110) cc_final: 0.8687 (m110) REVERT: D 28 GLN cc_start: 0.8535 (tt0) cc_final: 0.8131 (tt0) REVERT: D 76 ILE cc_start: 0.5744 (tt) cc_final: 0.5368 (pt) REVERT: D 174 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.7312 (t80) outliers start: 50 outliers final: 28 residues processed: 534 average time/residue: 0.2993 time to fit residues: 239.2421 Evaluate side-chains 522 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 485 time to evaluate : 1.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 624 PHE Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 208 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 159 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 180 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 233 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.129543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.092621 restraints weight = 35260.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.095908 restraints weight = 16523.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.098044 restraints weight = 9617.224| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.6234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 16386 Z= 0.205 Angle : 0.723 14.342 22134 Z= 0.365 Chirality : 0.045 0.245 2360 Planarity : 0.004 0.038 2818 Dihedral : 10.272 173.723 2247 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.21 % Allowed : 28.09 % Favored : 68.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.19), residues: 1932 helix: 1.05 (0.15), residues: 1138 sheet: -0.55 (0.43), residues: 142 loop : 0.21 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 30 HIS 0.004 0.001 HIS A 255 PHE 0.042 0.002 PHE C 172 TYR 0.031 0.002 TYR B 394 ARG 0.008 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.03996 ( 871) hydrogen bonds : angle 5.12932 ( 2571) covalent geometry : bond 0.00462 (16386) covalent geometry : angle 0.72251 (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 527 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 472 time to evaluate : 1.850 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: 0.8671 (mm-30) cc_final: 0.8262 (mm-30) REVERT: A 139 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8269 (mm-30) REVERT: A 150 GLN cc_start: 0.8974 (tp40) cc_final: 0.8747 (tm-30) REVERT: A 161 ARG cc_start: 0.8160 (ttm170) cc_final: 0.7875 (mmm-85) REVERT: A 164 ARG cc_start: 0.8852 (ptt90) cc_final: 0.8525 (ptt90) REVERT: A 213 ILE cc_start: 0.8664 (OUTLIER) cc_final: 0.8432 (tp) REVERT: A 218 ASN cc_start: 0.9063 (t0) cc_final: 0.8500 (t0) REVERT: A 236 TYR cc_start: 0.9354 (t80) cc_final: 0.9066 (t80) REVERT: A 341 LYS cc_start: 0.9386 (mmtm) cc_final: 0.9089 (mmpt) REVERT: A 344 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8486 (mt-10) REVERT: A 359 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8089 (ttp) REVERT: A 366 LYS cc_start: 0.9130 (mtmt) cc_final: 0.8825 (ptpp) REVERT: A 384 GLU cc_start: 0.8211 (OUTLIER) cc_final: 0.7495 (pm20) REVERT: A 385 VAL cc_start: 0.8986 (t) cc_final: 0.8622 (t) REVERT: A 390 GLN cc_start: 0.8453 (mt0) cc_final: 0.8078 (mt0) REVERT: A 483 GLU cc_start: 0.9141 (mp0) cc_final: 0.8821 (mp0) REVERT: A 548 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8541 (mm-30) REVERT: A 590 SER cc_start: 0.9386 (m) cc_final: 0.9153 (m) REVERT: A 628 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8612 (mm-30) REVERT: A 640 MET cc_start: 0.9297 (OUTLIER) cc_final: 0.7997 (tpp) REVERT: A 645 GLN cc_start: 0.9163 (tp-100) cc_final: 0.8874 (tp40) REVERT: B 95 MET cc_start: 0.8590 (tpp) cc_final: 0.8260 (tpp) REVERT: B 99 LYS cc_start: 0.9231 (OUTLIER) cc_final: 0.8681 (tptp) REVERT: B 143 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9099 (tt) REVERT: B 184 ARG cc_start: 0.9086 (tpp-160) cc_final: 0.8749 (tpp-160) REVERT: B 190 MET cc_start: 0.9158 (mtm) cc_final: 0.8827 (mtm) REVERT: B 257 ASP cc_start: 0.8567 (m-30) cc_final: 0.8207 (m-30) REVERT: B 290 GLU cc_start: 0.9113 (pt0) cc_final: 0.8732 (pp20) REVERT: B 322 MET cc_start: 0.9086 (mmm) cc_final: 0.8471 (mmm) REVERT: B 357 TYR cc_start: 0.8384 (m-80) cc_final: 0.7970 (m-10) REVERT: B 384 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.7000 (pm20) REVERT: B 467 ASN cc_start: 0.9104 (t0) cc_final: 0.8823 (m-40) REVERT: B 493 MET cc_start: 0.9418 (tmm) cc_final: 0.9037 (tmm) REVERT: B 515 ASP cc_start: 0.8915 (m-30) cc_final: 0.8613 (m-30) REVERT: B 576 LEU cc_start: 0.9468 (mt) cc_final: 0.9257 (mt) REVERT: B 628 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8173 (mm-30) REVERT: B 632 MET cc_start: 0.8514 (mtp) cc_final: 0.7880 (mtt) REVERT: B 668 ASN cc_start: 0.8550 (m-40) cc_final: 0.8292 (m-40) REVERT: C 74 MET cc_start: 0.6957 (mtt) cc_final: 0.6614 (mtm) REVERT: C 76 ILE cc_start: 0.8858 (mm) cc_final: 0.8561 (tp) REVERT: C 85 GLN cc_start: 0.5252 (mt0) cc_final: 0.4491 (pt0) REVERT: C 93 MET cc_start: 0.9053 (mtt) cc_final: 0.8781 (mtt) REVERT: C 151 ILE cc_start: 0.8355 (mp) cc_final: 0.8058 (mt) REVERT: C 158 VAL cc_start: 0.9652 (t) cc_final: 0.9140 (m) REVERT: C 162 TYR cc_start: 0.9329 (OUTLIER) cc_final: 0.8790 (m-10) REVERT: C 201 HIS cc_start: 0.8796 (m90) cc_final: 0.8153 (m90) REVERT: C 260 ILE cc_start: 0.7996 (pt) cc_final: 0.7745 (pt) REVERT: C 271 LEU cc_start: 0.8751 (mm) cc_final: 0.7859 (mm) REVERT: D 18 THR cc_start: 0.8034 (m) cc_final: 0.7710 (m) REVERT: D 25 ASN cc_start: 0.9387 (m110) cc_final: 0.8735 (m110) REVERT: D 28 GLN cc_start: 0.8602 (tt0) cc_final: 0.8229 (tt0) REVERT: D 172 PHE cc_start: 0.6957 (OUTLIER) cc_final: 0.6660 (m-10) REVERT: D 174 TYR cc_start: 0.8054 (OUTLIER) cc_final: 0.7493 (t80) REVERT: D 269 MET cc_start: 0.8613 (ppp) cc_final: 0.8185 (ppp) outliers start: 55 outliers final: 38 residues processed: 497 average time/residue: 0.2661 time to fit residues: 197.8410 Evaluate side-chains 514 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 463 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 403 ILE Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 599 GLU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 561 LEU 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 624 PHE Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 172 PHE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 208 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 111 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 27 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.129377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.091969 restraints weight = 35410.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.095218 restraints weight = 17032.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.097325 restraints weight = 10116.805| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.6423 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= 0.194 Angle : 0.717 12.792 22134 Z= 0.366 Chirality : 0.046 0.257 2360 Planarity : 0.004 0.039 2818 Dihedral : 10.099 171.755 2247 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 3.67 % Allowed : 27.74 % Favored : 68.59 % 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: 0.79 (0.19), residues: 1932 helix: 0.98 (0.15), residues: 1135 sheet: -0.56 (0.44), residues: 142 loop : 0.18 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 30 HIS 0.004 0.001 HIS B 438 PHE 0.044 0.002 PHE C 172 TYR 0.030 0.002 TYR A 571 ARG 0.008 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.04032 ( 871) hydrogen bonds : angle 5.17309 ( 2571) covalent geometry : bond 0.00437 (16386) covalent geometry : angle 0.71675 (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 540 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 477 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8677 (mm-30) cc_final: 0.8302 (mm-30) REVERT: A 139 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8242 (mm-30) REVERT: A 150 GLN cc_start: 0.8939 (tp40) cc_final: 0.8700 (tm-30) REVERT: A 161 ARG cc_start: 0.8155 (ttm170) cc_final: 0.7822 (mmm-85) REVERT: A 164 ARG cc_start: 0.8816 (ptt90) cc_final: 0.8497 (ptt90) REVERT: A 213 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8484 (tp) REVERT: A 218 ASN cc_start: 0.9048 (t0) cc_final: 0.8513 (t0) REVERT: A 236 TYR cc_start: 0.9348 (t80) cc_final: 0.9073 (t80) REVERT: A 341 LYS cc_start: 0.9366 (mmtm) cc_final: 0.9049 (mmpt) REVERT: A 344 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8504 (mt-10) REVERT: A 359 MET cc_start: 0.8590 (OUTLIER) cc_final: 0.8106 (ttp) REVERT: A 366 LYS cc_start: 0.9134 (mtmt) cc_final: 0.8832 (ptpp) REVERT: A 384 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7507 (pm20) REVERT: A 385 VAL cc_start: 0.8986 (t) cc_final: 0.8638 (t) REVERT: A 390 GLN cc_start: 0.8505 (mt0) cc_final: 0.8118 (mt0) REVERT: A 483 GLU cc_start: 0.9146 (mp0) cc_final: 0.8839 (mp0) REVERT: A 548 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8547 (mm-30) REVERT: A 590 SER cc_start: 0.9357 (m) cc_final: 0.9128 (m) REVERT: A 628 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8620 (mm-30) REVERT: A 640 MET cc_start: 0.9291 (OUTLIER) cc_final: 0.7990 (tpp) REVERT: A 645 GLN cc_start: 0.9174 (tp-100) cc_final: 0.8884 (tp40) REVERT: B 95 MET cc_start: 0.8557 (tpp) cc_final: 0.8229 (tpp) REVERT: B 99 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8714 (tptp) REVERT: B 104 TYR cc_start: 0.8975 (m-80) cc_final: 0.8443 (m-80) REVERT: B 143 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9091 (tt) REVERT: B 184 ARG cc_start: 0.9093 (tpp-160) cc_final: 0.8751 (tpp-160) REVERT: B 190 MET cc_start: 0.9172 (mtm) cc_final: 0.8816 (mtm) REVERT: B 257 ASP cc_start: 0.8583 (m-30) cc_final: 0.8211 (m-30) REVERT: B 290 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8705 (pp20) REVERT: B 322 MET cc_start: 0.9087 (mmm) cc_final: 0.8502 (mmm) REVERT: B 357 TYR cc_start: 0.8358 (m-80) cc_final: 0.8028 (m-10) REVERT: B 384 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.7073 (pm20) REVERT: B 467 ASN cc_start: 0.9087 (t0) cc_final: 0.8829 (m-40) REVERT: B 493 MET cc_start: 0.9416 (tmm) cc_final: 0.9045 (tmm) REVERT: B 515 ASP cc_start: 0.8898 (m-30) cc_final: 0.8633 (m-30) REVERT: B 576 LEU cc_start: 0.9468 (mt) cc_final: 0.9256 (mt) REVERT: B 628 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8184 (mm-30) REVERT: B 668 ASN cc_start: 0.8523 (m-40) cc_final: 0.8285 (m-40) REVERT: C 21 PHE cc_start: 0.9386 (m-80) cc_final: 0.9148 (m-80) REVERT: C 69 GLN cc_start: 0.8880 (tm-30) cc_final: 0.8526 (pp30) REVERT: C 72 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8709 (p) REVERT: C 74 MET cc_start: 0.7057 (mtt) cc_final: 0.6293 (mtm) REVERT: C 76 ILE cc_start: 0.8825 (mm) cc_final: 0.8523 (tp) REVERT: C 85 GLN cc_start: 0.5246 (mt0) cc_final: 0.4583 (pt0) REVERT: C 93 MET cc_start: 0.9053 (mtt) cc_final: 0.8777 (mtt) REVERT: C 158 VAL cc_start: 0.9542 (t) cc_final: 0.9176 (m) REVERT: C 162 TYR cc_start: 0.9320 (OUTLIER) cc_final: 0.8794 (m-10) REVERT: C 201 HIS cc_start: 0.8792 (m90) cc_final: 0.8145 (m90) REVERT: C 260 ILE cc_start: 0.7956 (pt) cc_final: 0.7736 (pt) REVERT: C 271 LEU cc_start: 0.8678 (mm) cc_final: 0.8064 (mm) REVERT: D 25 ASN cc_start: 0.9291 (m110) cc_final: 0.8620 (m110) REVERT: D 28 GLN cc_start: 0.8625 (tt0) cc_final: 0.8267 (tt0) REVERT: D 174 TYR cc_start: 0.8164 (OUTLIER) cc_final: 0.7670 (t80) REVERT: D 235 LEU cc_start: 0.9017 (mp) cc_final: 0.8753 (mp) REVERT: D 269 MET cc_start: 0.8603 (ppp) cc_final: 0.8182 (ppp) outliers start: 63 outliers final: 41 residues processed: 504 average time/residue: 0.2708 time to fit residues: 204.4004 Evaluate side-chains 507 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 452 time to evaluate : 2.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 148 GLU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR 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 624 PHE Chi-restraints excluded: chain B residue 628 GLU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 223 GLU 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: 10.0000 chunk 79 optimal weight: 4.9990 chunk 160 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 120 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 148 optimal weight: 7.9990 chunk 127 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 646 GLN C 23 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.127001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.090457 restraints weight = 35423.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.093632 restraints weight = 16799.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.095595 restraints weight = 9856.171| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3109 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3109 r_free = 0.3109 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3109 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.6591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16386 Z= 0.207 Angle : 0.745 12.996 22134 Z= 0.378 Chirality : 0.047 0.255 2360 Planarity : 0.004 0.043 2818 Dihedral : 10.080 171.647 2247 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.44 % Allowed : 27.80 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.19), residues: 1932 helix: 0.87 (0.15), residues: 1142 sheet: -0.65 (0.43), residues: 142 loop : 0.12 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 30 HIS 0.004 0.001 HIS A 647 PHE 0.040 0.002 PHE C 172 TYR 0.041 0.002 TYR A 571 ARG 0.008 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04122 ( 871) hydrogen bonds : angle 5.23588 ( 2571) covalent geometry : bond 0.00468 (16386) covalent geometry : angle 0.74481 (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 524 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 465 time to evaluate : 1.850 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: A 65 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8248 (mm-30) REVERT: A 139 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.8230 (mm-30) REVERT: A 150 GLN cc_start: 0.9156 (tp40) cc_final: 0.8726 (tm-30) REVERT: A 161 ARG cc_start: 0.8081 (ttm170) cc_final: 0.7669 (mmm-85) REVERT: A 164 ARG cc_start: 0.8837 (ptt90) cc_final: 0.8501 (ptt90) REVERT: A 202 ASN cc_start: 0.9441 (t0) cc_final: 0.9151 (t0) REVERT: A 213 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8475 (tp) REVERT: A 218 ASN cc_start: 0.9079 (t0) cc_final: 0.8526 (t0) REVERT: A 236 TYR cc_start: 0.9363 (t80) cc_final: 0.9041 (t80) REVERT: A 341 LYS cc_start: 0.9368 (mmtm) cc_final: 0.9041 (mmpt) REVERT: A 344 GLU cc_start: 0.9000 (mt-10) cc_final: 0.8495 (mt-10) REVERT: A 359 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8135 (ttp) REVERT: A 366 LYS cc_start: 0.9133 (mtmt) cc_final: 0.8830 (ptpp) REVERT: A 384 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7509 (pm20) REVERT: A 385 VAL cc_start: 0.8919 (t) cc_final: 0.8445 (t) REVERT: A 483 GLU cc_start: 0.9152 (mp0) cc_final: 0.8842 (mp0) REVERT: A 548 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8587 (mm-30) REVERT: A 628 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8405 (mp0) REVERT: A 640 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.7974 (tpp) REVERT: A 645 GLN cc_start: 0.9159 (tp-100) cc_final: 0.8825 (tp40) REVERT: B 95 MET cc_start: 0.8557 (tpp) cc_final: 0.8239 (tpp) REVERT: B 99 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8730 (tptp) REVERT: B 104 TYR cc_start: 0.8980 (m-80) cc_final: 0.8502 (m-80) REVERT: B 143 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9082 (tt) REVERT: B 184 ARG cc_start: 0.9101 (tpp-160) cc_final: 0.8753 (tpp-160) REVERT: B 190 MET cc_start: 0.9176 (mtm) cc_final: 0.8838 (mtm) REVERT: B 257 ASP cc_start: 0.8562 (m-30) cc_final: 0.8229 (m-30) REVERT: B 290 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8718 (pp20) REVERT: B 322 MET cc_start: 0.9072 (mmm) cc_final: 0.8482 (mmm) REVERT: B 357 TYR cc_start: 0.8393 (m-80) cc_final: 0.8108 (m-10) REVERT: B 384 GLU cc_start: 0.8853 (OUTLIER) cc_final: 0.7165 (pm20) REVERT: B 398 ASP cc_start: 0.8304 (t0) cc_final: 0.7964 (t0) REVERT: B 415 ASN cc_start: 0.9314 (t0) cc_final: 0.8806 (t0) REVERT: B 467 ASN cc_start: 0.9110 (t0) cc_final: 0.8856 (m-40) REVERT: B 493 MET cc_start: 0.9396 (tmm) cc_final: 0.9019 (tmm) REVERT: B 515 ASP cc_start: 0.8896 (m-30) cc_final: 0.8647 (m-30) REVERT: B 576 LEU cc_start: 0.9473 (mt) cc_final: 0.9258 (mt) REVERT: B 628 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7864 (mm-30) REVERT: B 668 ASN cc_start: 0.8449 (m-40) cc_final: 0.8214 (m-40) REVERT: C 21 PHE cc_start: 0.9389 (m-80) cc_final: 0.9152 (m-80) REVERT: C 74 MET cc_start: 0.7209 (mtt) cc_final: 0.6961 (mtm) REVERT: C 85 GLN cc_start: 0.5372 (mt0) cc_final: 0.4723 (pt0) REVERT: C 93 MET cc_start: 0.8984 (mtt) cc_final: 0.8696 (mtt) REVERT: C 154 PHE cc_start: 0.9022 (m-80) cc_final: 0.8820 (m-80) REVERT: C 158 VAL cc_start: 0.9464 (t) cc_final: 0.9058 (m) REVERT: C 162 TYR cc_start: 0.9271 (OUTLIER) cc_final: 0.8738 (m-10) REVERT: C 174 TYR cc_start: 0.7831 (OUTLIER) cc_final: 0.7364 (t80) REVERT: C 201 HIS cc_start: 0.8788 (m90) cc_final: 0.8139 (m90) REVERT: C 260 ILE cc_start: 0.8143 (pt) cc_final: 0.7930 (pt) REVERT: C 271 LEU cc_start: 0.8683 (mm) cc_final: 0.8052 (mm) REVERT: D 25 ASN cc_start: 0.9273 (m110) cc_final: 0.8609 (m110) REVERT: D 28 GLN cc_start: 0.8650 (tt0) cc_final: 0.8279 (tt0) REVERT: D 174 TYR cc_start: 0.8162 (OUTLIER) cc_final: 0.7878 (t80) REVERT: D 269 MET cc_start: 0.8595 (ppp) cc_final: 0.8155 (ppp) outliers start: 59 outliers final: 39 residues processed: 490 average time/residue: 0.2675 time to fit residues: 195.8367 Evaluate side-chains 511 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 458 time to evaluate : 1.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 180 ASN Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 215 ASP Chi-restraints excluded: chain A residue 257 ASP Chi-restraints excluded: chain A residue 317 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 548 GLU Chi-restraints excluded: chain A residue 565 VAL Chi-restraints excluded: chain A residue 587 VAL Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 621 ASN Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 49 HIS Chi-restraints excluded: chain B residue 99 LYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 143 LEU Chi-restraints excluded: chain B residue 200 SER Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 290 GLU Chi-restraints excluded: chain B residue 317 MET Chi-restraints excluded: chain B residue 374 SER Chi-restraints excluded: chain B residue 381 LEU Chi-restraints excluded: chain B residue 384 GLU Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR 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 628 GLU Chi-restraints excluded: chain C residue 43 THR Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 162 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 227 PHE Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 67 THR Chi-restraints excluded: chain D residue 74 MET Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 239 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 81 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 179 optimal weight: 20.0000 chunk 190 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 180 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 ASN A 645 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.132037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.094446 restraints weight = 35405.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.097762 restraints weight = 17067.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.099947 restraints weight = 10140.294| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3168 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.6773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16386 Z= 0.150 Angle : 0.725 13.447 22134 Z= 0.366 Chirality : 0.046 0.258 2360 Planarity : 0.004 0.043 2818 Dihedral : 9.911 170.091 2247 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.51 % Allowed : 28.50 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.19), residues: 1932 helix: 0.89 (0.15), residues: 1142 sheet: -0.37 (0.45), residues: 134 loop : 0.01 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 30 HIS 0.004 0.001 HIS C 201 PHE 0.045 0.002 PHE C 172 TYR 0.037 0.001 TYR A 571 ARG 0.011 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.03971 ( 871) hydrogen bonds : angle 5.18199 ( 2571) covalent geometry : bond 0.00347 (16386) covalent geometry : angle 0.72477 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6411.84 seconds wall clock time: 112 minutes 45.67 seconds (6765.67 seconds total)