Starting phenix.real_space_refine on Sat May 17 16:58:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bza_45061/05_2025/9bza_45061_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bza_45061/05_2025/9bza_45061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bza_45061/05_2025/9bza_45061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bza_45061/05_2025/9bza_45061.map" model { file = "/net/cci-nas-00/data/ceres_data/9bza_45061/05_2025/9bza_45061_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bza_45061/05_2025/9bza_45061_neut.cif" } resolution = 3.93 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 9.05, per 1000 atoms: 0.56 Number of scatterers: 16038 At special positions: 0 Unit cell: (94.302, 128.778, 130.806, 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: 4.19 Conformation dependent library (CDL) restraints added in 2.0 seconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 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: 3.953A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.666A 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: 4.850A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.627A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.676A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.730A 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: 4.068A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.514A 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: 3.668A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.360A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.477A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A 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: 6.479A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.184A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.383A 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: 4.048A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.563A 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: 8.345A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A 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: 4.78 Time building geometry restraints manager: 4.87 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: 4960 1.34 - 1.46: 3015 1.46 - 1.58: 8230 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.060 1.25e-02 6.40e+03 2.34e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.579 -0.039 1.20e-02 6.94e+03 1.07e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.032 1.08e-02 8.57e+03 9.01e+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 7.57e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.574 -0.033 1.25e-02 6.40e+03 7.16e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21571 2.09 - 4.18: 521 4.18 - 6.27: 35 6.27 - 8.36: 3 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 110.54 116.64 -6.10 1.36e+00 5.41e-01 2.01e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.10 -4.39 1.15e+00 7.56e-01 1.46e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.85 -4.35 1.23e+00 6.61e-01 1.25e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.70 -3.99 1.15e+00 7.56e-01 1.21e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.54 3.65 1.06e+00 8.90e-01 1.19e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 9469 35.81 - 71.61: 338 71.61 - 107.42: 37 107.42 - 143.23: 3 143.23 - 179.04: 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 -58.32 120.72 -179.04 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 301.68 151.16 150.52 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 31.89 148.08 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 9847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2144 0.093 - 0.186: 184 0.186 - 0.280: 27 0.280 - 0.373: 3 0.373 - 0.466: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.43e+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 4.62e+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 2.16 0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.71e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.017 2.00e-02 2.50e+03 1.11e-02 2.15e+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 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 169 " 0.017 2.00e-02 2.50e+03 9.89e-03 1.95e+00 pdb=" CG TYR C 169 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 169 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 169 " 0.008 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 131 2.51 - 3.11: 11555 3.11 - 3.70: 27053 3.70 - 4.30: 41581 4.30 - 4.90: 65450 Nonbonded interactions: 145770 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 1.965 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 145765 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 0.560 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 35.840 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 16386 Z= 0.316 Angle : 0.740 10.446 22134 Z= 0.463 Chirality : 0.058 0.466 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.952 179.037 6154 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.40 % Allowed : 15.27 % Favored : 83.33 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.18), residues: 1932 helix: 0.58 (0.14), residues: 1151 sheet: 0.47 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE C 227 TYR 0.020 0.002 TYR C 169 ARG 0.004 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.15419 ( 871) hydrogen bonds : angle 6.51766 ( 2571) covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.73996 (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 1046 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 1022 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASP cc_start: 0.8196 (m-30) cc_final: 0.7884 (m-30) REVERT: A 127 LEU cc_start: 0.8792 (mt) cc_final: 0.8566 (mt) REVERT: A 172 LEU cc_start: 0.9195 (mp) cc_final: 0.8811 (mp) REVERT: A 191 GLN cc_start: 0.8607 (mm-40) cc_final: 0.7710 (mm-40) REVERT: A 259 ASN cc_start: 0.7879 (m-40) cc_final: 0.7592 (m-40) REVERT: A 322 MET cc_start: 0.7161 (mmp) cc_final: 0.6877 (mmm) REVERT: A 348 MET cc_start: 0.7365 (tmm) cc_final: 0.7124 (tmm) REVERT: A 361 GLN cc_start: 0.6593 (tt0) cc_final: 0.6379 (tt0) REVERT: A 362 ASP cc_start: 0.5889 (m-30) cc_final: 0.5605 (m-30) REVERT: A 381 LEU cc_start: 0.8959 (tp) cc_final: 0.8663 (tp) REVERT: A 407 ILE cc_start: 0.8805 (mt) cc_final: 0.8372 (mt) REVERT: A 430 LYS cc_start: 0.8845 (mttt) cc_final: 0.8629 (mttt) REVERT: A 435 SER cc_start: 0.9465 (p) cc_final: 0.9116 (p) REVERT: A 447 ASN cc_start: 0.7902 (m-40) cc_final: 0.7073 (m-40) REVERT: A 500 ILE cc_start: 0.8893 (mt) cc_final: 0.8665 (mt) REVERT: A 531 TYR cc_start: 0.7842 (m-80) cc_final: 0.7566 (m-10) REVERT: A 576 LEU cc_start: 0.8601 (mt) cc_final: 0.8351 (mt) REVERT: A 640 MET cc_start: 0.7640 (tpp) cc_final: 0.7432 (tpp) REVERT: A 644 ILE cc_start: 0.8567 (mt) cc_final: 0.8057 (mt) REVERT: B 12 LEU cc_start: 0.8440 (mt) cc_final: 0.8214 (mp) REVERT: B 109 ASN cc_start: 0.8288 (m-40) cc_final: 0.7488 (m-40) REVERT: B 129 PHE cc_start: 0.8312 (m-10) cc_final: 0.8066 (m-10) REVERT: B 147 GLN cc_start: 0.7673 (mt0) cc_final: 0.7248 (mm-40) REVERT: B 149 TYR cc_start: 0.8499 (t80) cc_final: 0.8222 (t80) REVERT: B 157 LEU cc_start: 0.8570 (tp) cc_final: 0.8366 (tp) REVERT: B 162 LYS cc_start: 0.8390 (tppt) cc_final: 0.8042 (tppt) REVERT: B 172 LEU cc_start: 0.9120 (mp) cc_final: 0.8902 (mp) REVERT: B 190 MET cc_start: 0.7935 (mtm) cc_final: 0.7664 (mtm) REVERT: B 202 ASN cc_start: 0.8476 (t0) cc_final: 0.8273 (t0) REVERT: B 203 LEU cc_start: 0.8470 (mt) cc_final: 0.8170 (mt) REVERT: B 204 SER cc_start: 0.8881 (m) cc_final: 0.8058 (t) REVERT: B 256 ARG cc_start: 0.8198 (ttp80) cc_final: 0.7817 (tpt90) REVERT: B 265 LYS cc_start: 0.8573 (mmtt) cc_final: 0.8354 (mmmt) REVERT: B 291 LEU cc_start: 0.9065 (mt) cc_final: 0.8861 (mt) REVERT: B 322 MET cc_start: 0.8200 (mmm) cc_final: 0.7003 (tpp) REVERT: B 366 LYS cc_start: 0.8483 (ptpp) cc_final: 0.8200 (ptpp) REVERT: B 376 VAL cc_start: 0.9555 (t) cc_final: 0.9243 (m) REVERT: B 379 SER cc_start: 0.8385 (t) cc_final: 0.8178 (t) REVERT: B 386 LEU cc_start: 0.9234 (mt) cc_final: 0.8965 (mt) REVERT: B 389 SER cc_start: 0.7863 (p) cc_final: 0.7560 (p) REVERT: B 413 SER cc_start: 0.8473 (m) cc_final: 0.8161 (m) REVERT: B 435 SER cc_start: 0.9382 (p) cc_final: 0.8995 (p) REVERT: B 453 ARG cc_start: 0.8818 (ttt90) cc_final: 0.8542 (ttt-90) REVERT: B 458 MET cc_start: 0.8418 (mmm) cc_final: 0.8051 (mmm) REVERT: B 480 GLU cc_start: 0.7497 (mt-10) cc_final: 0.7241 (mt-10) REVERT: B 496 ASN cc_start: 0.8022 (t0) cc_final: 0.7805 (t0) REVERT: B 500 ILE cc_start: 0.9019 (mt) cc_final: 0.8709 (mt) REVERT: B 550 MET cc_start: 0.8056 (mtm) cc_final: 0.7390 (mtp) REVERT: B 558 TRP cc_start: 0.8075 (m100) cc_final: 0.7768 (m100) REVERT: B 575 ARG cc_start: 0.7995 (mtm110) cc_final: 0.7776 (mtm-85) REVERT: B 585 SER cc_start: 0.8843 (p) cc_final: 0.8357 (t) REVERT: B 588 GLN cc_start: 0.7774 (mm-40) cc_final: 0.7083 (mm-40) REVERT: B 590 SER cc_start: 0.9042 (p) cc_final: 0.8732 (t) REVERT: B 597 ILE cc_start: 0.9232 (pt) cc_final: 0.9013 (pt) REVERT: B 658 LEU cc_start: 0.7920 (mt) cc_final: 0.7541 (mt) REVERT: B 667 LEU cc_start: 0.8536 (tp) cc_final: 0.8050 (tp) REVERT: D 153 LEU cc_start: 0.6334 (tp) cc_final: 0.5935 (tp) REVERT: D 158 VAL cc_start: 0.6262 (t) cc_final: 0.4739 (t) REVERT: D 320 PHE cc_start: 0.6635 (m-80) cc_final: 0.6309 (m-10) outliers start: 24 outliers final: 9 residues processed: 1034 average time/residue: 0.3073 time to fit residues: 449.4531 Evaluate side-chains 667 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 658 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 287 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 0.3980 chunk 145 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 49 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 150 optimal weight: 8.9990 chunk 58 optimal weight: 6.9990 chunk 91 optimal weight: 8.9990 chunk 112 optimal weight: 0.7980 chunk 174 optimal weight: 6.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 19 GLN B 43 GLN B 61 ASN B 158 ASN ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 329 ASN B 338 ASN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN B 410 ASN C 28 GLN C 214 ASN D 71 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN D 210 GLN D 214 ASN D 234 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.138079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.094641 restraints weight = 34930.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.098230 restraints weight = 17000.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.100478 restraints weight = 10291.275| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4536 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= 0.240 Angle : 0.734 10.829 22134 Z= 0.384 Chirality : 0.046 0.274 2360 Planarity : 0.004 0.032 2818 Dihedral : 11.789 170.128 2256 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 5.24 % Allowed : 19.81 % Favored : 74.94 % 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: 1.28 (0.19), residues: 1932 helix: 1.23 (0.15), residues: 1137 sheet: 0.20 (0.43), residues: 130 loop : 0.55 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 9 HIS 0.009 0.002 HIS A 438 PHE 0.036 0.003 PHE D 168 TYR 0.032 0.002 TYR D 162 ARG 0.008 0.001 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.04628 ( 871) hydrogen bonds : angle 5.16259 ( 2571) covalent geometry : bond 0.00518 (16386) covalent geometry : angle 0.73435 (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 780 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 690 time to evaluate : 1.810 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 15 GLU cc_start: 0.8727 (tp30) cc_final: 0.8477 (tp30) REVERT: A 54 LYS cc_start: 0.9742 (tttt) cc_final: 0.9521 (ttmt) REVERT: A 60 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8827 (pt0) REVERT: A 64 TYR cc_start: 0.9234 (m-10) cc_final: 0.8439 (m-80) REVERT: A 65 GLU cc_start: 0.8945 (mm-30) cc_final: 0.8525 (mm-30) REVERT: A 127 LEU cc_start: 0.9600 (mt) cc_final: 0.9390 (mt) REVERT: A 147 GLN cc_start: 0.8995 (mt0) cc_final: 0.8015 (mm-40) REVERT: A 172 LEU cc_start: 0.9580 (mp) cc_final: 0.8974 (mp) REVERT: A 191 GLN cc_start: 0.8972 (mm-40) cc_final: 0.8484 (mm-40) REVERT: A 202 ASN cc_start: 0.9612 (t0) cc_final: 0.9283 (t0) REVERT: A 251 LEU cc_start: 0.9542 (tp) cc_final: 0.9212 (tp) REVERT: A 259 ASN cc_start: 0.8843 (m-40) cc_final: 0.8601 (m-40) REVERT: A 263 ASP cc_start: 0.8734 (m-30) cc_final: 0.8426 (m-30) REVERT: A 270 ASP cc_start: 0.8850 (m-30) cc_final: 0.8609 (m-30) REVERT: A 286 ASP cc_start: 0.8697 (m-30) cc_final: 0.8244 (m-30) REVERT: A 321 GLU cc_start: 0.9021 (tp30) cc_final: 0.8720 (tp30) REVERT: A 348 MET cc_start: 0.8377 (OUTLIER) cc_final: 0.7808 (tmm) REVERT: A 352 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7714 (mt-10) REVERT: A 362 ASP cc_start: 0.8621 (m-30) cc_final: 0.7746 (m-30) REVERT: A 394 TYR cc_start: 0.9187 (m-80) cc_final: 0.8795 (m-10) REVERT: A 400 GLU cc_start: 0.8288 (pp20) cc_final: 0.7611 (pp20) REVERT: A 402 GLU cc_start: 0.8436 (mm-30) cc_final: 0.7713 (mm-30) REVERT: A 406 ASP cc_start: 0.8401 (m-30) cc_final: 0.7984 (m-30) REVERT: A 407 ILE cc_start: 0.9285 (mt) cc_final: 0.8764 (mt) REVERT: A 447 ASN cc_start: 0.8644 (m-40) cc_final: 0.7392 (t0) REVERT: A 493 MET cc_start: 0.9389 (tmm) cc_final: 0.9161 (tmm) REVERT: A 501 GLN cc_start: 0.9360 (OUTLIER) cc_final: 0.8934 (tt0) REVERT: A 515 ASP cc_start: 0.8971 (m-30) cc_final: 0.8456 (m-30) REVERT: A 595 MET cc_start: 0.9092 (mmp) cc_final: 0.8877 (mmp) REVERT: A 615 MET cc_start: 0.9087 (mmp) cc_final: 0.8622 (mmp) REVERT: A 640 MET cc_start: 0.9400 (OUTLIER) cc_final: 0.9075 (tpp) REVERT: A 647 HIS cc_start: 0.9252 (m-70) cc_final: 0.8912 (m-70) REVERT: A 659 LYS cc_start: 0.9153 (mttt) cc_final: 0.8950 (mmmt) REVERT: A 668 ASN cc_start: 0.9637 (m-40) cc_final: 0.9255 (m-40) REVERT: A 683 TYR cc_start: 0.8585 (t80) cc_final: 0.8054 (t80) REVERT: A 686 ARG cc_start: 0.8370 (mtp85) cc_final: 0.8159 (mtp-110) REVERT: B 27 ASP cc_start: 0.9422 (OUTLIER) cc_final: 0.9085 (p0) REVERT: B 31 GLU cc_start: 0.8933 (mp0) cc_final: 0.8494 (mp0) REVERT: B 95 MET cc_start: 0.9388 (tpp) cc_final: 0.9086 (tpp) REVERT: B 147 GLN cc_start: 0.9314 (mt0) cc_final: 0.8148 (mt0) REVERT: B 149 TYR cc_start: 0.9230 (t80) cc_final: 0.8583 (t80) REVERT: B 157 LEU cc_start: 0.9371 (tp) cc_final: 0.9115 (tp) REVERT: B 161 ARG cc_start: 0.8007 (ttm110) cc_final: 0.6879 (ttm110) REVERT: B 202 ASN cc_start: 0.9486 (t0) cc_final: 0.9171 (t0) REVERT: B 204 SER cc_start: 0.9367 (m) cc_final: 0.9146 (t) REVERT: B 214 LYS cc_start: 0.8820 (ttmm) cc_final: 0.8409 (mmtm) REVERT: B 236 TYR cc_start: 0.9198 (t80) cc_final: 0.8930 (t80) REVERT: B 250 TYR cc_start: 0.9183 (m-80) cc_final: 0.8935 (m-80) REVERT: B 296 LYS cc_start: 0.8818 (mttt) cc_final: 0.8613 (mmmt) REVERT: B 322 MET cc_start: 0.9460 (mmm) cc_final: 0.9244 (tpp) REVERT: B 348 MET cc_start: 0.8977 (ptp) cc_final: 0.8441 (ptp) REVERT: B 361 GLN cc_start: 0.9068 (tt0) cc_final: 0.8747 (tp40) REVERT: B 362 ASP cc_start: 0.8947 (m-30) cc_final: 0.8255 (m-30) REVERT: B 376 VAL cc_start: 0.9632 (t) cc_final: 0.9237 (t) REVERT: B 389 SER cc_start: 0.9132 (p) cc_final: 0.8817 (p) REVERT: B 392 SER cc_start: 0.9549 (m) cc_final: 0.9195 (p) REVERT: B 459 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.8729 (mtmm) REVERT: B 467 ASN cc_start: 0.9509 (t0) cc_final: 0.9205 (m-40) REVERT: B 483 GLU cc_start: 0.9340 (mp0) cc_final: 0.8948 (mp0) REVERT: B 493 MET cc_start: 0.9688 (tmm) cc_final: 0.9245 (tmm) REVERT: B 494 MET cc_start: 0.9625 (mtp) cc_final: 0.9382 (ttm) REVERT: B 505 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8430 (mt-10) REVERT: B 515 ASP cc_start: 0.9271 (m-30) cc_final: 0.9014 (m-30) REVERT: B 586 TYR cc_start: 0.9138 (m-80) cc_final: 0.8420 (m-10) REVERT: B 588 GLN cc_start: 0.9474 (mm-40) cc_final: 0.8884 (mm-40) REVERT: B 604 ARG cc_start: 0.9073 (tpp80) cc_final: 0.8865 (tpp80) REVERT: B 615 MET cc_start: 0.9286 (mmp) cc_final: 0.8844 (mmm) REVERT: B 634 MET cc_start: 0.9285 (mmm) cc_final: 0.9061 (mmt) REVERT: B 640 MET cc_start: 0.9468 (tpp) cc_final: 0.9202 (tpp) REVERT: B 667 LEU cc_start: 0.9093 (tp) cc_final: 0.8791 (tp) REVERT: B 671 ASP cc_start: 0.8720 (m-30) cc_final: 0.8517 (m-30) REVERT: C 96 MET cc_start: 0.6558 (mmm) cc_final: 0.6275 (mmm) REVERT: C 176 LEU cc_start: 0.9183 (mp) cc_final: 0.8879 (tp) REVERT: C 242 TYR cc_start: 0.2178 (t80) cc_final: 0.1676 (t80) REVERT: C 245 ASP cc_start: 0.8570 (t70) cc_final: 0.8224 (m-30) REVERT: C 246 LEU cc_start: 0.8279 (mp) cc_final: 0.7736 (mt) REVERT: D 72 THR cc_start: 0.8535 (OUTLIER) cc_final: 0.8322 (p) REVERT: D 96 MET cc_start: 0.7604 (mmt) cc_final: 0.7188 (mmt) REVERT: D 109 PHE cc_start: 0.8611 (m-10) cc_final: 0.8399 (m-80) REVERT: D 127 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8913 (mp10) REVERT: D 158 VAL cc_start: 0.9561 (t) cc_final: 0.9271 (t) REVERT: D 162 TYR cc_start: 0.9149 (m-10) cc_final: 0.8829 (m-80) REVERT: D 185 MET cc_start: 0.6636 (mmm) cc_final: 0.6335 (mmm) REVERT: D 224 LEU cc_start: 0.9183 (mt) cc_final: 0.8894 (mt) REVERT: D 227 PHE cc_start: 0.8353 (m-80) cc_final: 0.7994 (m-80) REVERT: D 236 TYR cc_start: 0.8882 (t80) cc_final: 0.8667 (t80) REVERT: D 268 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7680 (mm) outliers start: 90 outliers final: 48 residues processed: 742 average time/residue: 0.2618 time to fit residues: 291.9183 Evaluate side-chains 684 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 629 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 501 GLN Chi-restraints excluded: chain A residue 583 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 654 PHE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 264 THR Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 589 SER Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 18 THR Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 111 THR Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 268 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 5.9990 chunk 168 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 47 optimal weight: 1.9990 chunk 191 optimal weight: 10.0000 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 171 optimal weight: 0.8980 chunk 189 optimal weight: 6.9990 chunk 141 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN A 474 GLN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 HIS ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN C 24 GLN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.138330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.095096 restraints weight = 35061.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.098678 restraints weight = 16855.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.101019 restraints weight = 10181.856| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.5215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16386 Z= 0.167 Angle : 0.663 8.457 22134 Z= 0.344 Chirality : 0.044 0.197 2360 Planarity : 0.004 0.037 2818 Dihedral : 11.242 169.740 2251 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.79 % Allowed : 24.42 % Favored : 71.79 % 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: 1.22 (0.19), residues: 1932 helix: 1.18 (0.15), residues: 1132 sheet: 0.37 (0.43), residues: 128 loop : 0.47 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 124 HIS 0.006 0.001 HIS D 101 PHE 0.033 0.002 PHE D 172 TYR 0.046 0.002 TYR D 142 ARG 0.006 0.001 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.04284 ( 871) hydrogen bonds : angle 4.99258 ( 2571) covalent geometry : bond 0.00373 (16386) covalent geometry : angle 0.66323 (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 744 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 679 time to evaluate : 1.773 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 15 GLU cc_start: 0.8819 (tp30) cc_final: 0.8573 (tp30) REVERT: A 16 ILE cc_start: 0.9427 (mm) cc_final: 0.9174 (tp) REVERT: A 29 ASP cc_start: 0.9389 (t70) cc_final: 0.9071 (t70) REVERT: A 147 GLN cc_start: 0.8957 (mt0) cc_final: 0.7878 (mm-40) REVERT: A 150 GLN cc_start: 0.9072 (tm-30) cc_final: 0.7637 (tm-30) REVERT: A 161 ARG cc_start: 0.8576 (ttm110) cc_final: 0.8273 (ttm110) REVERT: A 172 LEU cc_start: 0.9544 (mp) cc_final: 0.8962 (mp) REVERT: A 191 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8116 (mm-40) REVERT: A 214 LYS cc_start: 0.8955 (tppt) cc_final: 0.8601 (mmtt) REVERT: A 228 LYS cc_start: 0.9481 (mmmm) cc_final: 0.8874 (tppt) REVERT: A 231 ASP cc_start: 0.8940 (OUTLIER) cc_final: 0.8622 (t0) REVERT: A 243 ARG cc_start: 0.7355 (tmt-80) cc_final: 0.7079 (tmt-80) REVERT: A 251 LEU cc_start: 0.9525 (tp) cc_final: 0.9109 (tp) REVERT: A 263 ASP cc_start: 0.8682 (m-30) cc_final: 0.8431 (m-30) REVERT: A 270 ASP cc_start: 0.8902 (m-30) cc_final: 0.8666 (m-30) REVERT: A 301 PHE cc_start: 0.9424 (m-80) cc_final: 0.9217 (m-10) REVERT: A 321 GLU cc_start: 0.9091 (tp30) cc_final: 0.8689 (tp30) REVERT: A 341 LYS cc_start: 0.9169 (OUTLIER) cc_final: 0.8903 (mmtm) REVERT: A 348 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8081 (tmm) REVERT: A 361 GLN cc_start: 0.9185 (tp40) cc_final: 0.8737 (tp-100) REVERT: A 400 GLU cc_start: 0.8311 (pp20) cc_final: 0.7691 (pp20) REVERT: A 402 GLU cc_start: 0.8443 (mm-30) cc_final: 0.7639 (mm-30) REVERT: A 406 ASP cc_start: 0.8365 (m-30) cc_final: 0.8034 (m-30) REVERT: A 407 ILE cc_start: 0.9255 (mt) cc_final: 0.8795 (mt) REVERT: A 436 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9269 (mm) REVERT: A 447 ASN cc_start: 0.8466 (m-40) cc_final: 0.7086 (t0) REVERT: A 493 MET cc_start: 0.9440 (tmm) cc_final: 0.9146 (tmm) REVERT: A 515 ASP cc_start: 0.9024 (m-30) cc_final: 0.8794 (m-30) REVERT: A 590 SER cc_start: 0.9404 (t) cc_final: 0.8719 (p) REVERT: A 615 MET cc_start: 0.9171 (mmp) cc_final: 0.8568 (mmp) REVERT: A 640 MET cc_start: 0.9561 (OUTLIER) cc_final: 0.9072 (tpp) REVERT: A 646 GLN cc_start: 0.8897 (pt0) cc_final: 0.8601 (pt0) REVERT: A 647 HIS cc_start: 0.9192 (m-70) cc_final: 0.8962 (m-70) REVERT: A 668 ASN cc_start: 0.9630 (m-40) cc_final: 0.9302 (m-40) REVERT: B 31 GLU cc_start: 0.8924 (mp0) cc_final: 0.8641 (mp0) REVERT: B 95 MET cc_start: 0.9371 (tpp) cc_final: 0.9049 (tpp) REVERT: B 119 GLU cc_start: 0.9009 (mp0) cc_final: 0.8470 (mp0) REVERT: B 147 GLN cc_start: 0.9340 (mt0) cc_final: 0.8808 (mm-40) REVERT: B 149 TYR cc_start: 0.9218 (t80) cc_final: 0.8689 (t80) REVERT: B 157 LEU cc_start: 0.9336 (tp) cc_final: 0.9094 (tp) REVERT: B 161 ARG cc_start: 0.7962 (ttm110) cc_final: 0.6891 (ttm110) REVERT: B 180 ASN cc_start: 0.8414 (m-40) cc_final: 0.7667 (m-40) REVERT: B 194 LYS cc_start: 0.9550 (OUTLIER) cc_final: 0.9313 (pttt) REVERT: B 202 ASN cc_start: 0.9449 (t0) cc_final: 0.9118 (t0) REVERT: B 204 SER cc_start: 0.9323 (m) cc_final: 0.9095 (t) REVERT: B 214 LYS cc_start: 0.8804 (ttmm) cc_final: 0.8208 (mmtp) REVERT: B 236 TYR cc_start: 0.9208 (t80) cc_final: 0.8805 (t80) REVERT: B 296 LYS cc_start: 0.9017 (mttt) cc_final: 0.8729 (mmmt) REVERT: B 361 GLN cc_start: 0.9036 (tt0) cc_final: 0.8629 (tp40) REVERT: B 362 ASP cc_start: 0.8791 (m-30) cc_final: 0.8277 (m-30) REVERT: B 376 VAL cc_start: 0.9649 (t) cc_final: 0.9211 (t) REVERT: B 389 SER cc_start: 0.9114 (p) cc_final: 0.8824 (p) REVERT: B 447 ASN cc_start: 0.8492 (m-40) cc_final: 0.8087 (m-40) REVERT: B 459 LYS cc_start: 0.9342 (OUTLIER) cc_final: 0.8756 (mtmm) REVERT: B 477 ILE cc_start: 0.9072 (mm) cc_final: 0.8758 (pt) REVERT: B 493 MET cc_start: 0.9693 (tmm) cc_final: 0.9128 (tmm) REVERT: B 494 MET cc_start: 0.9568 (mtp) cc_final: 0.9270 (mtp) REVERT: B 515 ASP cc_start: 0.9291 (m-30) cc_final: 0.9014 (m-30) REVERT: B 586 TYR cc_start: 0.9106 (m-80) cc_final: 0.8442 (m-10) REVERT: B 604 ARG cc_start: 0.9071 (tpp80) cc_final: 0.8720 (mmm-85) REVERT: B 615 MET cc_start: 0.9204 (mmp) cc_final: 0.8775 (mmm) REVERT: B 628 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8506 (mp0) REVERT: B 634 MET cc_start: 0.9329 (mmm) cc_final: 0.9022 (mmt) REVERT: B 640 MET cc_start: 0.9514 (tpp) cc_final: 0.9231 (tpp) REVERT: B 659 LYS cc_start: 0.7891 (tptt) cc_final: 0.7629 (tptt) REVERT: B 665 ARG cc_start: 0.9228 (OUTLIER) cc_final: 0.8992 (tmm-80) REVERT: B 667 LEU cc_start: 0.9112 (tp) cc_final: 0.8816 (tp) REVERT: C 96 MET cc_start: 0.7030 (mmm) cc_final: 0.6246 (mmm) REVERT: C 197 ASP cc_start: 0.7122 (t70) cc_final: 0.6834 (t70) REVERT: C 245 ASP cc_start: 0.8578 (t70) cc_final: 0.8198 (m-30) REVERT: C 246 LEU cc_start: 0.8148 (mp) cc_final: 0.7775 (mt) REVERT: D 68 GLU cc_start: 0.7229 (mm-30) cc_final: 0.7013 (mm-30) REVERT: D 90 LEU cc_start: 0.7827 (mt) cc_final: 0.7225 (mt) REVERT: D 96 MET cc_start: 0.7728 (mmt) cc_final: 0.7432 (mmt) REVERT: D 142 TYR cc_start: 0.7118 (m-80) cc_final: 0.6412 (m-80) REVERT: D 169 TYR cc_start: 0.8305 (m-80) cc_final: 0.8102 (m-80) REVERT: D 174 TYR cc_start: 0.8500 (OUTLIER) cc_final: 0.8295 (t80) REVERT: D 185 MET cc_start: 0.6833 (mmm) cc_final: 0.6592 (mmm) REVERT: D 223 GLU cc_start: 0.9269 (OUTLIER) cc_final: 0.8928 (pt0) REVERT: D 271 LEU cc_start: 0.8297 (mt) cc_final: 0.8090 (mt) outliers start: 65 outliers final: 43 residues processed: 708 average time/residue: 0.2581 time to fit residues: 274.7863 Evaluate side-chains 691 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 638 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 459 LYS Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 665 ARG Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 223 GLU Chi-restraints excluded: chain D residue 281 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 180 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 74 optimal weight: 8.9990 chunk 148 optimal weight: 20.0000 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN D 85 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN D 234 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.131131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.090018 restraints weight = 36596.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.093243 restraints weight = 17790.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.095446 restraints weight = 10772.908| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3061 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3061 r_free = 0.3061 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3061 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.5886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 16386 Z= 0.262 Angle : 0.695 9.974 22134 Z= 0.367 Chirality : 0.046 0.243 2360 Planarity : 0.004 0.062 2818 Dihedral : 11.156 172.660 2249 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 5.48 % Allowed : 24.18 % Favored : 70.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.19), residues: 1932 helix: 1.05 (0.15), residues: 1133 sheet: -0.59 (0.37), residues: 166 loop : 0.53 (0.25), residues: 633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C 124 HIS 0.006 0.001 HIS D 101 PHE 0.043 0.002 PHE D 227 TYR 0.029 0.002 TYR D 142 ARG 0.009 0.001 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.04337 ( 871) hydrogen bonds : angle 5.10753 ( 2571) covalent geometry : bond 0.00568 (16386) covalent geometry : angle 0.69515 (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 746 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 652 time to evaluate : 1.813 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 40 TYR cc_start: 0.9470 (t80) cc_final: 0.9227 (t80) REVERT: A 64 TYR cc_start: 0.9256 (m-10) cc_final: 0.9000 (m-10) REVERT: A 107 LYS cc_start: 0.9164 (OUTLIER) cc_final: 0.8919 (mmmm) REVERT: A 147 GLN cc_start: 0.9051 (mt0) cc_final: 0.7980 (mm-40) REVERT: A 161 ARG cc_start: 0.8539 (ttm110) cc_final: 0.8210 (ttm110) REVERT: A 172 LEU cc_start: 0.9557 (mp) cc_final: 0.9050 (mp) REVERT: A 191 GLN cc_start: 0.8932 (mm-40) cc_final: 0.8211 (mm-40) REVERT: A 251 LEU cc_start: 0.9545 (tp) cc_final: 0.9101 (tp) REVERT: A 263 ASP cc_start: 0.8731 (m-30) cc_final: 0.8449 (m-30) REVERT: A 286 ASP cc_start: 0.8801 (m-30) cc_final: 0.8302 (m-30) REVERT: A 321 GLU cc_start: 0.9190 (tp30) cc_final: 0.8850 (tp30) REVERT: A 341 LYS cc_start: 0.9172 (OUTLIER) cc_final: 0.8889 (mmtm) REVERT: A 348 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8259 (tmm) REVERT: A 361 GLN cc_start: 0.9274 (tt0) cc_final: 0.8712 (tp-100) REVERT: A 362 ASP cc_start: 0.8587 (m-30) cc_final: 0.7940 (m-30) REVERT: A 384 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.7781 (pm20) REVERT: A 400 GLU cc_start: 0.8439 (pp20) cc_final: 0.8057 (pp20) REVERT: A 402 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8188 (mm-30) REVERT: A 406 ASP cc_start: 0.8480 (m-30) cc_final: 0.8106 (m-30) REVERT: A 407 ILE cc_start: 0.9321 (mt) cc_final: 0.8858 (mt) REVERT: A 447 ASN cc_start: 0.8592 (m-40) cc_final: 0.7317 (t0) REVERT: A 458 MET cc_start: 0.9014 (mmp) cc_final: 0.8197 (mmp) REVERT: A 479 TYR cc_start: 0.9105 (t80) cc_final: 0.8762 (t80) REVERT: A 493 MET cc_start: 0.9419 (tmm) cc_final: 0.8987 (tmm) REVERT: A 515 ASP cc_start: 0.9023 (m-30) cc_final: 0.8521 (m-30) REVERT: A 590 SER cc_start: 0.9262 (t) cc_final: 0.8994 (m) REVERT: A 602 GLU cc_start: 0.8447 (tt0) cc_final: 0.8193 (tt0) REVERT: A 615 MET cc_start: 0.9211 (mmp) cc_final: 0.8616 (mmp) REVERT: A 640 MET cc_start: 0.9668 (OUTLIER) cc_final: 0.9129 (tpp) REVERT: A 646 GLN cc_start: 0.8969 (pt0) cc_final: 0.8677 (pt0) REVERT: A 647 HIS cc_start: 0.9294 (m-70) cc_final: 0.9054 (m-70) REVERT: A 668 ASN cc_start: 0.9661 (m-40) cc_final: 0.9436 (m-40) REVERT: B 30 LYS cc_start: 0.9489 (tptt) cc_final: 0.9268 (tptt) REVERT: B 31 GLU cc_start: 0.8877 (mp0) cc_final: 0.8604 (mt-10) REVERT: B 119 GLU cc_start: 0.9050 (mp0) cc_final: 0.8494 (mp0) REVERT: B 129 PHE cc_start: 0.9611 (m-10) cc_final: 0.9363 (m-10) REVERT: B 149 TYR cc_start: 0.9360 (t80) cc_final: 0.8353 (t80) REVERT: B 157 LEU cc_start: 0.9361 (tp) cc_final: 0.9107 (tp) REVERT: B 161 ARG cc_start: 0.8162 (ttm110) cc_final: 0.7126 (ttm110) REVERT: B 172 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9027 (mt) REVERT: B 180 ASN cc_start: 0.8520 (m-40) cc_final: 0.7872 (m-40) REVERT: B 194 LYS cc_start: 0.9574 (OUTLIER) cc_final: 0.9319 (pttt) REVERT: B 202 ASN cc_start: 0.9371 (t0) cc_final: 0.9110 (t0) REVERT: B 214 LYS cc_start: 0.8900 (ttmm) cc_final: 0.8373 (mmtp) REVERT: B 236 TYR cc_start: 0.9280 (t80) cc_final: 0.8996 (t80) REVERT: B 274 ARG cc_start: 0.9185 (ttm170) cc_final: 0.8971 (ttm-80) REVERT: B 296 LYS cc_start: 0.9147 (mttt) cc_final: 0.8873 (mmmt) REVERT: B 315 ASP cc_start: 0.8640 (p0) cc_final: 0.8376 (p0) REVERT: B 361 GLN cc_start: 0.9044 (tt0) cc_final: 0.8667 (tt0) REVERT: B 362 ASP cc_start: 0.8799 (m-30) cc_final: 0.8301 (m-30) REVERT: B 376 VAL cc_start: 0.9651 (t) cc_final: 0.9226 (t) REVERT: B 389 SER cc_start: 0.9139 (p) cc_final: 0.8906 (p) REVERT: B 394 TYR cc_start: 0.9431 (m-80) cc_final: 0.9216 (m-80) REVERT: B 467 ASN cc_start: 0.9402 (t0) cc_final: 0.9112 (m-40) REVERT: B 483 GLU cc_start: 0.9341 (mp0) cc_final: 0.9132 (mp0) REVERT: B 493 MET cc_start: 0.9693 (tmm) cc_final: 0.9124 (tmm) REVERT: B 494 MET cc_start: 0.9575 (mtp) cc_final: 0.9252 (mtp) REVERT: B 515 ASP cc_start: 0.9299 (m-30) cc_final: 0.9066 (m-30) REVERT: B 527 TYR cc_start: 0.9290 (t80) cc_final: 0.9051 (t80) REVERT: B 548 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8479 (mm-30) REVERT: B 560 LYS cc_start: 0.9521 (mmtm) cc_final: 0.9310 (mmtp) REVERT: B 586 TYR cc_start: 0.9145 (m-80) cc_final: 0.8560 (m-10) REVERT: B 604 ARG cc_start: 0.9053 (tpp80) cc_final: 0.8734 (mmm-85) REVERT: B 615 MET cc_start: 0.9201 (mmp) cc_final: 0.8831 (mmp) REVERT: B 628 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8662 (mp0) REVERT: B 640 MET cc_start: 0.9416 (tpp) cc_final: 0.9181 (tpp) REVERT: B 659 LYS cc_start: 0.8070 (tptt) cc_final: 0.7765 (tptt) REVERT: C 124 TRP cc_start: 0.6341 (t60) cc_final: 0.5993 (t60) REVERT: C 245 ASP cc_start: 0.8584 (t70) cc_final: 0.8218 (m-30) REVERT: C 246 LEU cc_start: 0.8248 (mp) cc_final: 0.8045 (mp) REVERT: D 93 MET cc_start: 0.6978 (ppp) cc_final: 0.6724 (ppp) REVERT: D 96 MET cc_start: 0.7506 (mmt) cc_final: 0.7079 (mmt) REVERT: D 110 MET cc_start: 0.8380 (ppp) cc_final: 0.7692 (ptt) REVERT: D 148 ASP cc_start: 0.7612 (t0) cc_final: 0.7357 (t0) REVERT: D 162 TYR cc_start: 0.8917 (m-10) cc_final: 0.8637 (m-80) REVERT: D 185 MET cc_start: 0.6981 (mmm) cc_final: 0.6628 (mmm) REVERT: D 219 GLU cc_start: 0.9274 (OUTLIER) cc_final: 0.9071 (pm20) REVERT: D 271 LEU cc_start: 0.8377 (mt) cc_final: 0.8084 (mt) outliers start: 94 outliers final: 62 residues processed: 693 average time/residue: 0.2666 time to fit residues: 279.1615 Evaluate side-chains 693 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 623 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 357 TYR 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 411 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 207 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 67 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 175 optimal weight: 0.4980 chunk 182 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 86 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 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 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN A 588 GLN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.136619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.094277 restraints weight = 36400.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.097790 restraints weight = 17538.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.100049 restraints weight = 10527.028| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3173 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3173 r_free = 0.3173 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3173 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.6267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16386 Z= 0.147 Angle : 0.653 8.850 22134 Z= 0.343 Chirality : 0.045 0.207 2360 Planarity : 0.004 0.050 2818 Dihedral : 10.682 169.252 2246 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.49 % Allowed : 26.69 % Favored : 68.82 % 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: 0.96 (0.19), residues: 1932 helix: 1.05 (0.15), residues: 1123 sheet: -0.57 (0.38), residues: 158 loop : 0.48 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 124 HIS 0.005 0.001 HIS D 101 PHE 0.056 0.002 PHE D 109 TYR 0.045 0.002 TYR D 142 ARG 0.007 0.001 ARG B 485 Details of bonding type rmsd hydrogen bonds : bond 0.04151 ( 871) hydrogen bonds : angle 5.04356 ( 2571) covalent geometry : bond 0.00330 (16386) covalent geometry : angle 0.65315 (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 741 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 664 time to evaluate : 1.801 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 29 ASP cc_start: 0.9267 (t70) cc_final: 0.8991 (t70) REVERT: A 40 TYR cc_start: 0.9466 (t80) cc_final: 0.9214 (t80) REVERT: A 107 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8894 (mmmm) REVERT: A 119 GLU cc_start: 0.8605 (mt-10) cc_final: 0.8055 (mt-10) REVERT: A 144 MET cc_start: 0.8909 (mtm) cc_final: 0.8383 (mtt) REVERT: A 147 GLN cc_start: 0.8965 (mt0) cc_final: 0.7858 (mm-40) REVERT: A 150 GLN cc_start: 0.9132 (tm-30) cc_final: 0.8884 (tm-30) REVERT: A 172 LEU cc_start: 0.9489 (mp) cc_final: 0.8991 (mp) REVERT: A 214 LYS cc_start: 0.8904 (tppt) cc_final: 0.8541 (mmtt) REVERT: A 228 LYS cc_start: 0.9434 (mmmm) cc_final: 0.8840 (tppt) REVERT: A 251 LEU cc_start: 0.9541 (tp) cc_final: 0.9107 (tp) REVERT: A 263 ASP cc_start: 0.8723 (m-30) cc_final: 0.8346 (m-30) REVERT: A 286 ASP cc_start: 0.8748 (m-30) cc_final: 0.8305 (m-30) REVERT: A 290 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8442 (tm-30) REVERT: A 321 GLU cc_start: 0.9152 (tp30) cc_final: 0.8845 (tp30) REVERT: A 348 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8168 (tmm) REVERT: A 361 GLN cc_start: 0.9189 (tt0) cc_final: 0.8924 (tp40) REVERT: A 362 ASP cc_start: 0.8459 (m-30) cc_final: 0.7697 (m-30) REVERT: A 384 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7689 (pm20) REVERT: A 389 SER cc_start: 0.9526 (OUTLIER) cc_final: 0.9184 (p) REVERT: A 400 GLU cc_start: 0.8373 (pp20) cc_final: 0.7998 (pp20) REVERT: A 402 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8077 (mm-30) REVERT: A 407 ILE cc_start: 0.9119 (mt) cc_final: 0.8683 (mt) REVERT: A 493 MET cc_start: 0.9410 (tmm) cc_final: 0.9155 (tmm) REVERT: A 515 ASP cc_start: 0.9032 (m-30) cc_final: 0.8550 (m-30) REVERT: A 550 MET cc_start: 0.8654 (ptp) cc_final: 0.8139 (ptp) REVERT: A 570 MET cc_start: 0.9127 (mtp) cc_final: 0.8921 (mtp) REVERT: A 602 GLU cc_start: 0.8236 (tt0) cc_final: 0.7407 (tt0) REVERT: A 604 ARG cc_start: 0.8859 (mmp80) cc_final: 0.8515 (mmt-90) REVERT: A 610 LYS cc_start: 0.9189 (ttpp) cc_final: 0.8932 (ttpp) REVERT: A 615 MET cc_start: 0.9262 (mmp) cc_final: 0.8844 (mmp) REVERT: A 640 MET cc_start: 0.9633 (OUTLIER) cc_final: 0.9008 (tpp) REVERT: A 668 ASN cc_start: 0.9697 (m-40) cc_final: 0.9426 (m110) REVERT: B 30 LYS cc_start: 0.9458 (tptt) cc_final: 0.9219 (tptt) REVERT: B 31 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8504 (mt-10) REVERT: B 54 LYS cc_start: 0.9620 (ttmt) cc_final: 0.9380 (ttmm) REVERT: B 65 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8071 (mm-30) REVERT: B 95 MET cc_start: 0.9343 (tpp) cc_final: 0.9074 (tpp) REVERT: B 106 LEU cc_start: 0.9226 (tt) cc_final: 0.8918 (tt) REVERT: B 112 LYS cc_start: 0.9577 (mmmt) cc_final: 0.9261 (mmmt) REVERT: B 119 GLU cc_start: 0.8998 (mp0) cc_final: 0.8393 (mp0) REVERT: B 129 PHE cc_start: 0.9563 (m-10) cc_final: 0.9293 (m-10) REVERT: B 149 TYR cc_start: 0.9376 (t80) cc_final: 0.8362 (t80) REVERT: B 157 LEU cc_start: 0.9340 (tp) cc_final: 0.9067 (tp) REVERT: B 161 ARG cc_start: 0.8143 (ttm110) cc_final: 0.7165 (ttm110) REVERT: B 164 ARG cc_start: 0.8786 (ptt90) cc_final: 0.8562 (ttp80) REVERT: B 172 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8357 (mt) REVERT: B 194 LYS cc_start: 0.9550 (OUTLIER) cc_final: 0.9280 (pttt) REVERT: B 202 ASN cc_start: 0.9463 (t0) cc_final: 0.9064 (t0) REVERT: B 214 LYS cc_start: 0.8879 (ttmm) cc_final: 0.8292 (mmtp) REVERT: B 221 LYS cc_start: 0.9353 (mmtp) cc_final: 0.9115 (mttm) REVERT: B 236 TYR cc_start: 0.9242 (t80) cc_final: 0.8969 (t80) REVERT: B 263 ASP cc_start: 0.9221 (m-30) cc_final: 0.8913 (m-30) REVERT: B 296 LYS cc_start: 0.9257 (mttt) cc_final: 0.8967 (mmmt) REVERT: B 344 GLU cc_start: 0.9218 (OUTLIER) cc_final: 0.8770 (mt-10) REVERT: B 348 MET cc_start: 0.8984 (ptp) cc_final: 0.8528 (ptp) REVERT: B 389 SER cc_start: 0.9084 (p) cc_final: 0.8588 (p) REVERT: B 394 TYR cc_start: 0.9401 (m-80) cc_final: 0.9147 (m-80) REVERT: B 406 ASP cc_start: 0.8437 (m-30) cc_final: 0.8018 (t0) REVERT: B 466 MET cc_start: 0.8997 (ptp) cc_final: 0.8784 (ptp) REVERT: B 471 TYR cc_start: 0.9278 (t80) cc_final: 0.8521 (t80) REVERT: B 493 MET cc_start: 0.9651 (tmm) cc_final: 0.9084 (tmm) REVERT: B 505 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8362 (mt-10) REVERT: B 515 ASP cc_start: 0.9265 (m-30) cc_final: 0.9001 (m-30) REVERT: B 527 TYR cc_start: 0.9297 (t80) cc_final: 0.9035 (t80) REVERT: B 548 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8349 (mm-30) REVERT: B 586 TYR cc_start: 0.9050 (m-80) cc_final: 0.8557 (m-10) REVERT: B 602 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.6762 (pt0) REVERT: B 615 MET cc_start: 0.9199 (mmp) cc_final: 0.8858 (mmp) REVERT: B 645 GLN cc_start: 0.9574 (tp40) cc_final: 0.9115 (tp-100) REVERT: B 659 LYS cc_start: 0.8001 (tptt) cc_final: 0.7629 (tptt) REVERT: C 96 MET cc_start: 0.7075 (mmm) cc_final: 0.6346 (mmm) REVERT: C 277 PHE cc_start: 0.7734 (m-80) cc_final: 0.7470 (m-80) REVERT: D 95 MET cc_start: 0.7674 (tmm) cc_final: 0.7245 (tmm) REVERT: D 110 MET cc_start: 0.8313 (ppp) cc_final: 0.7738 (ptt) REVERT: D 162 TYR cc_start: 0.8911 (m-10) cc_final: 0.8601 (m-80) REVERT: D 185 MET cc_start: 0.6887 (mmm) cc_final: 0.6560 (mmm) REVERT: D 219 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.9023 (pm20) REVERT: D 232 LEU cc_start: 0.8920 (mm) cc_final: 0.8711 (mm) REVERT: D 271 LEU cc_start: 0.8356 (mt) cc_final: 0.8060 (mt) outliers start: 77 outliers final: 52 residues processed: 692 average time/residue: 0.2706 time to fit residues: 283.9938 Evaluate side-chains 693 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 630 time to evaluate : 1.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 658 LEU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 344 GLU Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 219 GLU Chi-restraints excluded: chain D residue 281 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 31 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 156 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 115 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 169 optimal weight: 9.9990 chunk 113 optimal weight: 8.9990 chunk 177 optimal weight: 5.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 191 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN A 447 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.134042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.092891 restraints weight = 36958.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.096178 restraints weight = 18177.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.098507 restraints weight = 10975.922| |-----------------------------------------------------------------------------| r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.6571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 16386 Z= 0.262 Angle : 0.738 12.452 22134 Z= 0.383 Chirality : 0.048 0.264 2360 Planarity : 0.004 0.050 2818 Dihedral : 10.770 170.195 2246 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 5.42 % Allowed : 28.15 % Favored : 66.43 % 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: 0.72 (0.18), residues: 1932 helix: 0.85 (0.15), residues: 1146 sheet: -0.54 (0.39), residues: 162 loop : 0.34 (0.24), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 124 HIS 0.011 0.002 HIS A 469 PHE 0.044 0.002 PHE D 227 TYR 0.039 0.002 TYR D 142 ARG 0.006 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 871) hydrogen bonds : angle 5.20957 ( 2571) covalent geometry : bond 0.00580 (16386) covalent geometry : angle 0.73756 (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 721 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 628 time to evaluate : 1.941 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 51 LEU cc_start: 0.9212 (tp) cc_final: 0.8937 (mp) REVERT: A 103 ASP cc_start: 0.8882 (m-30) cc_final: 0.8639 (m-30) REVERT: A 119 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8175 (mt-10) REVERT: A 147 GLN cc_start: 0.9169 (mt0) cc_final: 0.8419 (mt0) REVERT: A 172 LEU cc_start: 0.9497 (mp) cc_final: 0.8717 (mp) REVERT: A 214 LYS cc_start: 0.8982 (tppt) cc_final: 0.8689 (mmtt) REVERT: A 251 LEU cc_start: 0.9560 (tp) cc_final: 0.9093 (tp) REVERT: A 263 ASP cc_start: 0.8654 (m-30) cc_final: 0.8307 (m-30) REVERT: A 286 ASP cc_start: 0.8759 (m-30) cc_final: 0.8221 (m-30) REVERT: A 290 GLU cc_start: 0.8723 (tm-30) cc_final: 0.8474 (tm-30) REVERT: A 321 GLU cc_start: 0.9182 (tp30) cc_final: 0.8892 (tp30) REVERT: A 341 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8749 (mmtm) REVERT: A 348 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.8273 (tmm) REVERT: A 355 TYR cc_start: 0.8711 (m-10) cc_final: 0.8459 (m-10) REVERT: A 361 GLN cc_start: 0.9281 (OUTLIER) cc_final: 0.8919 (tp-100) REVERT: A 362 ASP cc_start: 0.8433 (m-30) cc_final: 0.7538 (m-30) REVERT: A 384 GLU cc_start: 0.8755 (OUTLIER) cc_final: 0.7929 (pm20) REVERT: A 389 SER cc_start: 0.9506 (OUTLIER) cc_final: 0.9198 (p) REVERT: A 400 GLU cc_start: 0.8450 (pp20) cc_final: 0.8121 (pp20) REVERT: A 402 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8249 (mm-30) REVERT: A 405 LEU cc_start: 0.9309 (mt) cc_final: 0.9083 (mp) REVERT: A 406 ASP cc_start: 0.8391 (m-30) cc_final: 0.8000 (t0) REVERT: A 407 ILE cc_start: 0.9195 (mt) cc_final: 0.8783 (mt) REVERT: A 447 ASN cc_start: 0.8317 (m110) cc_final: 0.7826 (m-40) REVERT: A 458 MET cc_start: 0.9006 (mmp) cc_final: 0.8252 (mmt) REVERT: A 479 TYR cc_start: 0.9107 (t80) cc_final: 0.8723 (t80) REVERT: A 493 MET cc_start: 0.9398 (tmm) cc_final: 0.8966 (tmm) REVERT: A 515 ASP cc_start: 0.9021 (m-30) cc_final: 0.8588 (m-30) REVERT: A 570 MET cc_start: 0.9206 (mtp) cc_final: 0.9000 (mtp) REVERT: A 588 GLN cc_start: 0.9261 (mm-40) cc_final: 0.8917 (mm-40) REVERT: A 590 SER cc_start: 0.9363 (t) cc_final: 0.8762 (p) REVERT: A 598 MET cc_start: 0.8433 (mmm) cc_final: 0.8229 (mmm) REVERT: A 615 MET cc_start: 0.9258 (mmp) cc_final: 0.8591 (mmp) REVERT: A 640 MET cc_start: 0.9663 (OUTLIER) cc_final: 0.8995 (tpp) REVERT: A 668 ASN cc_start: 0.9684 (m-40) cc_final: 0.9413 (m-40) REVERT: B 30 LYS cc_start: 0.9457 (tptt) cc_final: 0.9215 (tptt) REVERT: B 31 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8550 (mt-10) REVERT: B 54 LYS cc_start: 0.9613 (ttmt) cc_final: 0.9386 (ttmm) REVERT: B 65 GLU cc_start: 0.8613 (mm-30) cc_final: 0.8261 (mm-30) REVERT: B 112 LYS cc_start: 0.9614 (mmmt) cc_final: 0.9299 (mmmt) REVERT: B 119 GLU cc_start: 0.9034 (mp0) cc_final: 0.8480 (mp0) REVERT: B 129 PHE cc_start: 0.9608 (m-10) cc_final: 0.9318 (m-10) REVERT: B 149 TYR cc_start: 0.9429 (t80) cc_final: 0.8261 (t80) REVERT: B 157 LEU cc_start: 0.9370 (tp) cc_final: 0.9111 (tp) REVERT: B 161 ARG cc_start: 0.8242 (ttm110) cc_final: 0.7186 (ttm110) REVERT: B 172 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.8446 (mt) REVERT: B 194 LYS cc_start: 0.9588 (OUTLIER) cc_final: 0.9312 (pttt) REVERT: B 202 ASN cc_start: 0.9397 (t0) cc_final: 0.9104 (t0) REVERT: B 214 LYS cc_start: 0.8815 (ttmm) cc_final: 0.8284 (mmtp) REVERT: B 263 ASP cc_start: 0.9210 (m-30) cc_final: 0.8925 (m-30) REVERT: B 296 LYS cc_start: 0.9278 (mttt) cc_final: 0.8971 (mmmt) REVERT: B 361 GLN cc_start: 0.9023 (OUTLIER) cc_final: 0.8763 (tt0) REVERT: B 389 SER cc_start: 0.8933 (p) cc_final: 0.8679 (p) REVERT: B 394 TYR cc_start: 0.9429 (m-80) cc_final: 0.9195 (m-80) REVERT: B 406 ASP cc_start: 0.8298 (m-30) cc_final: 0.8057 (t0) REVERT: B 447 ASN cc_start: 0.8356 (m110) cc_final: 0.8120 (m-40) REVERT: B 467 ASN cc_start: 0.9351 (m-40) cc_final: 0.9002 (m-40) REVERT: B 471 TYR cc_start: 0.9344 (t80) cc_final: 0.8695 (t80) REVERT: B 493 MET cc_start: 0.9650 (tmm) cc_final: 0.9029 (tmm) REVERT: B 505 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8362 (mt-10) REVERT: B 548 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8438 (mm-30) REVERT: B 586 TYR cc_start: 0.9149 (m-80) cc_final: 0.8596 (m-10) REVERT: B 615 MET cc_start: 0.9229 (mmp) cc_final: 0.8856 (mmp) REVERT: B 628 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8716 (mp0) REVERT: B 640 MET cc_start: 0.9408 (tpp) cc_final: 0.9177 (tpp) REVERT: B 659 LYS cc_start: 0.7883 (tptt) cc_final: 0.7512 (tptt) REVERT: C 74 MET cc_start: 0.4769 (mpp) cc_final: 0.4564 (mpp) REVERT: C 96 MET cc_start: 0.7199 (mmm) cc_final: 0.6633 (mmm) REVERT: C 174 TYR cc_start: 0.4324 (OUTLIER) cc_final: 0.3841 (t80) REVERT: C 256 VAL cc_start: 0.3205 (t) cc_final: 0.2904 (t) REVERT: D 56 MET cc_start: 0.8305 (mpp) cc_final: 0.8042 (mpp) REVERT: D 80 HIS cc_start: 0.8032 (m90) cc_final: 0.7105 (t-90) REVERT: D 96 MET cc_start: 0.7226 (mmt) cc_final: 0.6820 (mmt) REVERT: D 110 MET cc_start: 0.8336 (ppp) cc_final: 0.7726 (ptt) REVERT: D 162 TYR cc_start: 0.9139 (m-10) cc_final: 0.8779 (m-80) REVERT: D 185 MET cc_start: 0.6990 (mmm) cc_final: 0.6641 (mmm) REVERT: D 271 LEU cc_start: 0.8562 (mt) cc_final: 0.8280 (mt) outliers start: 93 outliers final: 64 residues processed: 666 average time/residue: 0.2567 time to fit residues: 259.4097 Evaluate side-chains 684 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 609 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 346 LEU Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 443 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 379 SER Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 250 VAL 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 100 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 312 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 39 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 chunk 23 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 146 optimal weight: 5.9990 chunk 184 optimal weight: 6.9990 chunk 119 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 24 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 588 GLN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN C 214 ASN D 25 ASN ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.133905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.092642 restraints weight = 36844.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.095856 restraints weight = 18074.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.098104 restraints weight = 11013.262| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3112 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3112 r_free = 0.3112 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3112 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.6838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16386 Z= 0.203 Angle : 0.728 11.839 22134 Z= 0.376 Chirality : 0.048 0.268 2360 Planarity : 0.004 0.052 2818 Dihedral : 10.634 169.101 2246 Min Nonbonded Distance : 1.818 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 5.07 % Allowed : 29.90 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.18), residues: 1932 helix: 0.83 (0.15), residues: 1134 sheet: -0.59 (0.40), residues: 162 loop : 0.21 (0.24), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 124 HIS 0.008 0.001 HIS A 469 PHE 0.031 0.002 PHE D 109 TYR 0.046 0.002 TYR D 142 ARG 0.009 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 871) hydrogen bonds : angle 5.18434 ( 2571) covalent geometry : bond 0.00457 (16386) covalent geometry : angle 0.72763 (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 724 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 637 time to evaluate : 1.803 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 119 GLU cc_start: 0.8565 (mt-10) cc_final: 0.8171 (mt-10) REVERT: A 150 GLN cc_start: 0.9109 (tm-30) cc_final: 0.8843 (tm-30) REVERT: A 172 LEU cc_start: 0.9503 (mp) cc_final: 0.8697 (mp) REVERT: A 191 GLN cc_start: 0.8391 (mm-40) cc_final: 0.7878 (mt0) REVERT: A 214 LYS cc_start: 0.8925 (tppt) cc_final: 0.8643 (mmtt) REVERT: A 228 LYS cc_start: 0.9439 (mmmm) cc_final: 0.8930 (mmtm) REVERT: A 232 ASN cc_start: 0.9351 (m-40) cc_final: 0.9100 (m110) REVERT: A 251 LEU cc_start: 0.9574 (tp) cc_final: 0.9208 (tp) REVERT: A 263 ASP cc_start: 0.8673 (m-30) cc_final: 0.8363 (m-30) REVERT: A 286 ASP cc_start: 0.8723 (m-30) cc_final: 0.8231 (m-30) REVERT: A 290 GLU cc_start: 0.8728 (tm-30) cc_final: 0.8489 (tm-30) REVERT: A 321 GLU cc_start: 0.9178 (tp30) cc_final: 0.8895 (tp30) REVERT: A 341 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8749 (mmtm) REVERT: A 348 MET cc_start: 0.8654 (tmm) cc_final: 0.7827 (tmm) REVERT: A 352 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7756 (mt-10) REVERT: A 361 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.8899 (tp-100) REVERT: A 362 ASP cc_start: 0.8458 (m-30) cc_final: 0.7550 (m-30) REVERT: A 384 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.7827 (pm20) REVERT: A 389 SER cc_start: 0.9495 (OUTLIER) cc_final: 0.9193 (p) REVERT: A 400 GLU cc_start: 0.8450 (pp20) cc_final: 0.8201 (pp20) REVERT: A 402 GLU cc_start: 0.8700 (mm-30) cc_final: 0.8298 (mm-30) REVERT: A 406 ASP cc_start: 0.8383 (m-30) cc_final: 0.8062 (t0) REVERT: A 407 ILE cc_start: 0.9137 (mt) cc_final: 0.8708 (mt) REVERT: A 447 ASN cc_start: 0.7933 (m110) cc_final: 0.6976 (m110) REVERT: A 458 MET cc_start: 0.8925 (mmp) cc_final: 0.8222 (mmt) REVERT: A 479 TYR cc_start: 0.9105 (t80) cc_final: 0.8770 (t80) REVERT: A 493 MET cc_start: 0.9385 (tmm) cc_final: 0.8957 (tmm) REVERT: A 515 ASP cc_start: 0.9032 (m-30) cc_final: 0.8581 (m-30) REVERT: A 526 GLU cc_start: 0.8583 (mp0) cc_final: 0.8269 (mp0) REVERT: A 590 SER cc_start: 0.9172 (t) cc_final: 0.8763 (p) REVERT: A 602 GLU cc_start: 0.8174 (tt0) cc_final: 0.7654 (tp30) REVERT: A 604 ARG cc_start: 0.8792 (mmp80) cc_final: 0.8529 (mmt90) REVERT: A 615 MET cc_start: 0.9290 (mmp) cc_final: 0.8596 (mmp) REVERT: A 640 MET cc_start: 0.9653 (OUTLIER) cc_final: 0.8945 (tpp) REVERT: A 668 ASN cc_start: 0.9694 (m-40) cc_final: 0.9400 (m-40) REVERT: B 30 LYS cc_start: 0.9423 (tptt) cc_final: 0.9174 (tptt) REVERT: B 31 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8561 (mt-10) REVERT: B 65 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8184 (mm-30) REVERT: B 95 MET cc_start: 0.9314 (tpp) cc_final: 0.8868 (tpp) REVERT: B 98 PHE cc_start: 0.9707 (t80) cc_final: 0.9452 (t80) REVERT: B 112 LYS cc_start: 0.9592 (mmmt) cc_final: 0.9260 (mmmt) REVERT: B 119 GLU cc_start: 0.9027 (mp0) cc_final: 0.8391 (mp0) REVERT: B 129 PHE cc_start: 0.9597 (m-10) cc_final: 0.9358 (m-10) REVERT: B 149 TYR cc_start: 0.9457 (t80) cc_final: 0.8222 (t80) REVERT: B 157 LEU cc_start: 0.9395 (tp) cc_final: 0.9151 (tp) REVERT: B 161 ARG cc_start: 0.8264 (ttm110) cc_final: 0.7336 (ttm110) REVERT: B 172 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.8445 (mt) REVERT: B 194 LYS cc_start: 0.9571 (OUTLIER) cc_final: 0.9296 (pttt) REVERT: B 202 ASN cc_start: 0.9372 (t0) cc_final: 0.9071 (t0) REVERT: B 214 LYS cc_start: 0.8786 (ttmm) cc_final: 0.8419 (tppt) REVERT: B 263 ASP cc_start: 0.9194 (m-30) cc_final: 0.8893 (m-30) REVERT: B 296 LYS cc_start: 0.9332 (mttt) cc_final: 0.9019 (mmmt) REVERT: B 361 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8558 (tt0) REVERT: B 386 LEU cc_start: 0.9491 (mt) cc_final: 0.9192 (mt) REVERT: B 389 SER cc_start: 0.8843 (p) cc_final: 0.8584 (p) REVERT: B 394 TYR cc_start: 0.9377 (m-80) cc_final: 0.9128 (m-80) REVERT: B 406 ASP cc_start: 0.8245 (m-30) cc_final: 0.8044 (t0) REVERT: B 447 ASN cc_start: 0.8246 (m110) cc_final: 0.7949 (m-40) REVERT: B 471 TYR cc_start: 0.9323 (t80) cc_final: 0.8696 (t80) REVERT: B 493 MET cc_start: 0.9635 (tmm) cc_final: 0.9028 (tmm) REVERT: B 505 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8341 (mt-10) REVERT: B 548 GLU cc_start: 0.9016 (mm-30) cc_final: 0.8418 (mm-30) REVERT: B 586 TYR cc_start: 0.9137 (m-80) cc_final: 0.8603 (m-10) REVERT: B 615 MET cc_start: 0.9220 (mmp) cc_final: 0.8880 (mmp) REVERT: B 628 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8537 (mp0) REVERT: B 631 ASP cc_start: 0.9309 (m-30) cc_final: 0.8892 (p0) REVERT: B 640 MET cc_start: 0.9425 (tpp) cc_final: 0.9207 (tpp) REVERT: B 659 LYS cc_start: 0.7756 (tptt) cc_final: 0.7439 (tptt) REVERT: C 174 TYR cc_start: 0.4332 (OUTLIER) cc_final: 0.3877 (t80) REVERT: C 249 GLN cc_start: 0.6153 (pm20) cc_final: 0.5940 (pm20) REVERT: C 256 VAL cc_start: 0.3201 (t) cc_final: 0.2885 (t) REVERT: D 46 TYR cc_start: 0.9460 (m-10) cc_final: 0.8835 (m-10) REVERT: D 80 HIS cc_start: 0.8090 (m90) cc_final: 0.6920 (t-90) REVERT: D 93 MET cc_start: 0.7188 (ppp) cc_final: 0.6133 (pmm) REVERT: D 95 MET cc_start: 0.8101 (tmm) cc_final: 0.7472 (tmm) REVERT: D 110 MET cc_start: 0.8377 (ppp) cc_final: 0.7816 (ptt) REVERT: D 162 TYR cc_start: 0.9139 (m-10) cc_final: 0.8708 (m-80) REVERT: D 185 MET cc_start: 0.6984 (mmm) cc_final: 0.6649 (mmm) REVERT: D 231 LEU cc_start: 0.9024 (mt) cc_final: 0.8518 (pp) REVERT: D 271 LEU cc_start: 0.8517 (mt) cc_final: 0.8241 (mt) outliers start: 87 outliers final: 66 residues processed: 670 average time/residue: 0.2583 time to fit residues: 261.5443 Evaluate side-chains 687 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 611 time to evaluate : 1.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 31 GLU Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 357 TYR Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 653 SER Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 352 GLU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 233 ASN Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 100 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 159 optimal weight: 20.0000 chunk 72 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 183 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 180 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 127 GLN C 214 ASN ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.136958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.095648 restraints weight = 36325.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.099083 restraints weight = 17771.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.101362 restraints weight = 10656.125| |-----------------------------------------------------------------------------| r_work (final): 0.3166 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.7054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16386 Z= 0.159 Angle : 0.746 16.828 22134 Z= 0.381 Chirality : 0.048 0.455 2360 Planarity : 0.004 0.047 2818 Dihedral : 10.310 166.915 2246 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 16.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.37 % Allowed : 31.64 % Favored : 63.99 % 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 (0.18), residues: 1932 helix: 0.81 (0.15), residues: 1125 sheet: -0.59 (0.40), residues: 158 loop : 0.29 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 124 HIS 0.007 0.001 HIS A 469 PHE 0.059 0.002 PHE D 227 TYR 0.049 0.002 TYR D 142 ARG 0.008 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04209 ( 871) hydrogen bonds : angle 5.19228 ( 2571) covalent geometry : bond 0.00364 (16386) covalent geometry : angle 0.74560 (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 718 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 643 time to evaluate : 1.809 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 27 ASP cc_start: 0.9115 (p0) cc_final: 0.8770 (p0) REVERT: A 51 LEU cc_start: 0.9202 (tp) cc_final: 0.8958 (mp) REVERT: A 106 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.8923 (mt) REVERT: A 119 GLU cc_start: 0.8532 (mt-10) cc_final: 0.8144 (mt-10) REVERT: A 150 GLN cc_start: 0.9093 (tm-30) cc_final: 0.8801 (tm-30) REVERT: A 172 LEU cc_start: 0.9527 (mp) cc_final: 0.8707 (mp) REVERT: A 190 MET cc_start: 0.9362 (tpp) cc_final: 0.9011 (mmp) REVERT: A 228 LYS cc_start: 0.9365 (mmmm) cc_final: 0.8654 (tppt) REVERT: A 232 ASN cc_start: 0.9349 (m-40) cc_final: 0.9118 (m110) REVERT: A 263 ASP cc_start: 0.8651 (m-30) cc_final: 0.8326 (m-30) REVERT: A 266 LYS cc_start: 0.8525 (tptp) cc_final: 0.8314 (tptt) REVERT: A 286 ASP cc_start: 0.8673 (m-30) cc_final: 0.8194 (m-30) REVERT: A 290 GLU cc_start: 0.8694 (tm-30) cc_final: 0.8389 (tm-30) REVERT: A 321 GLU cc_start: 0.9135 (tp30) cc_final: 0.8846 (tp30) REVERT: A 348 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.7748 (tmm) REVERT: A 352 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7464 (mt-10) REVERT: A 361 GLN cc_start: 0.9191 (tt0) cc_final: 0.8952 (tp40) REVERT: A 362 ASP cc_start: 0.8353 (m-30) cc_final: 0.7271 (m-30) REVERT: A 384 GLU cc_start: 0.8546 (OUTLIER) cc_final: 0.7783 (pm20) REVERT: A 389 SER cc_start: 0.9560 (OUTLIER) cc_final: 0.9241 (p) REVERT: A 400 GLU cc_start: 0.8451 (pp20) cc_final: 0.8154 (pp20) REVERT: A 402 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8244 (mm-30) REVERT: A 406 ASP cc_start: 0.8400 (m-30) cc_final: 0.8028 (t0) REVERT: A 407 ILE cc_start: 0.9109 (mt) cc_final: 0.8712 (mt) REVERT: A 458 MET cc_start: 0.8720 (mmp) cc_final: 0.7979 (mmt) REVERT: A 479 TYR cc_start: 0.9058 (t80) cc_final: 0.8742 (t80) REVERT: A 493 MET cc_start: 0.9374 (tmm) cc_final: 0.9001 (tmm) REVERT: A 515 ASP cc_start: 0.9014 (m-30) cc_final: 0.8562 (m-30) REVERT: A 604 ARG cc_start: 0.8724 (mmp80) cc_final: 0.8440 (mmt-90) REVERT: A 615 MET cc_start: 0.9281 (mmp) cc_final: 0.8791 (mmp) REVERT: A 634 MET cc_start: 0.8658 (mmt) cc_final: 0.8006 (mmt) REVERT: A 640 MET cc_start: 0.9626 (OUTLIER) cc_final: 0.8891 (tpp) REVERT: A 668 ASN cc_start: 0.9680 (m-40) cc_final: 0.9409 (m110) REVERT: B 30 LYS cc_start: 0.9408 (tptt) cc_final: 0.9153 (tptt) REVERT: B 31 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8507 (mt-10) REVERT: B 40 TYR cc_start: 0.9374 (t80) cc_final: 0.8911 (t80) REVERT: B 95 MET cc_start: 0.9308 (tpp) cc_final: 0.8786 (tpp) REVERT: B 98 PHE cc_start: 0.9695 (t80) cc_final: 0.9367 (t80) REVERT: B 112 LYS cc_start: 0.9557 (mmmt) cc_final: 0.9231 (mmmt) REVERT: B 119 GLU cc_start: 0.8978 (mp0) cc_final: 0.8361 (mp0) REVERT: B 149 TYR cc_start: 0.9392 (t80) cc_final: 0.8275 (t80) REVERT: B 161 ARG cc_start: 0.8252 (ttm110) cc_final: 0.7836 (mmm-85) REVERT: B 172 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8432 (mt) REVERT: B 194 LYS cc_start: 0.9537 (OUTLIER) cc_final: 0.9233 (pttt) REVERT: B 202 ASN cc_start: 0.9316 (t0) cc_final: 0.9014 (t0) REVERT: B 263 ASP cc_start: 0.9153 (m-30) cc_final: 0.8728 (m-30) REVERT: B 266 LYS cc_start: 0.9295 (mtpp) cc_final: 0.9069 (mttp) REVERT: B 296 LYS cc_start: 0.9338 (mttt) cc_final: 0.9023 (mmmt) REVERT: B 357 TYR cc_start: 0.8583 (m-10) cc_final: 0.8098 (m-10) REVERT: B 361 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8524 (tp40) REVERT: B 386 LEU cc_start: 0.9414 (mt) cc_final: 0.9137 (mt) REVERT: B 389 SER cc_start: 0.8813 (p) cc_final: 0.8525 (p) REVERT: B 394 TYR cc_start: 0.9341 (m-80) cc_final: 0.9093 (m-80) REVERT: B 447 ASN cc_start: 0.8272 (m110) cc_final: 0.7591 (m-40) REVERT: B 471 TYR cc_start: 0.9183 (t80) cc_final: 0.8649 (t80) REVERT: B 483 GLU cc_start: 0.9318 (mp0) cc_final: 0.8598 (mm-30) REVERT: B 493 MET cc_start: 0.9624 (tmm) cc_final: 0.9024 (tmm) REVERT: B 548 GLU cc_start: 0.9010 (mm-30) cc_final: 0.8422 (mm-30) REVERT: B 585 SER cc_start: 0.9317 (p) cc_final: 0.8696 (t) REVERT: B 586 TYR cc_start: 0.9033 (m-80) cc_final: 0.8393 (m-10) REVERT: B 602 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.6544 (pt0) REVERT: B 613 TYR cc_start: 0.9019 (t80) cc_final: 0.8792 (t80) REVERT: B 615 MET cc_start: 0.9182 (mmp) cc_final: 0.8921 (mmp) REVERT: B 628 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8506 (mp0) REVERT: B 631 ASP cc_start: 0.9294 (m-30) cc_final: 0.8945 (p0) REVERT: B 645 GLN cc_start: 0.9554 (tp40) cc_final: 0.9049 (tp-100) REVERT: B 659 LYS cc_start: 0.7573 (tptt) cc_final: 0.7297 (tptt) REVERT: C 96 MET cc_start: 0.7035 (mmm) cc_final: 0.6269 (mmm) REVERT: C 149 ASP cc_start: 0.8588 (t0) cc_final: 0.8300 (t0) REVERT: C 150 GLU cc_start: 0.9431 (pm20) cc_final: 0.9226 (tp30) REVERT: C 174 TYR cc_start: 0.4329 (OUTLIER) cc_final: 0.3920 (t80) REVERT: C 245 ASP cc_start: 0.8568 (t70) cc_final: 0.8234 (m-30) REVERT: C 256 VAL cc_start: 0.3052 (t) cc_final: 0.2746 (t) REVERT: C 269 MET cc_start: 0.7067 (tpt) cc_final: 0.6462 (tmm) REVERT: D 46 TYR cc_start: 0.9427 (m-10) cc_final: 0.8802 (m-10) REVERT: D 80 HIS cc_start: 0.7949 (m90) cc_final: 0.6959 (t-90) REVERT: D 110 MET cc_start: 0.8433 (ppp) cc_final: 0.7838 (ptt) REVERT: D 162 TYR cc_start: 0.9147 (m-10) cc_final: 0.8669 (m-80) REVERT: D 185 MET cc_start: 0.7048 (mmm) cc_final: 0.6760 (mmm) REVERT: D 231 LEU cc_start: 0.9075 (mt) cc_final: 0.8667 (pp) REVERT: D 271 LEU cc_start: 0.8542 (mt) cc_final: 0.8252 (mt) outliers start: 75 outliers final: 57 residues processed: 672 average time/residue: 0.2653 time to fit residues: 272.2683 Evaluate side-chains 699 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 631 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 31 GLU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 213 ILE Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 127 GLN Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 129 LYS Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 111 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 182 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 115 optimal weight: 0.0570 chunk 127 optimal weight: 2.9990 chunk 188 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 overall best weight: 0.9700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN A 501 GLN A 646 GLN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN D 25 ASN ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.137178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.095534 restraints weight = 36480.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.098937 restraints weight = 17847.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.101183 restraints weight = 10734.089| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.7289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16386 Z= 0.160 Angle : 0.779 15.891 22134 Z= 0.397 Chirality : 0.050 0.479 2360 Planarity : 0.004 0.076 2818 Dihedral : 10.176 165.806 2246 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.96 % Allowed : 32.40 % Favored : 63.64 % 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: 0.44 (0.18), residues: 1932 helix: 0.69 (0.15), residues: 1146 sheet: -0.61 (0.40), residues: 158 loop : 0.05 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 124 HIS 0.016 0.001 HIS A 469 PHE 0.036 0.002 PHE D 168 TYR 0.054 0.002 TYR D 142 ARG 0.008 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04254 ( 871) hydrogen bonds : angle 5.28536 ( 2571) covalent geometry : bond 0.00369 (16386) covalent geometry : angle 0.77937 (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 701 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 633 time to evaluate : 1.695 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 31 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8175 (pm20) REVERT: A 51 LEU cc_start: 0.9201 (tp) cc_final: 0.8956 (mp) REVERT: A 119 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8123 (mt-10) REVERT: A 147 GLN cc_start: 0.9106 (mt0) cc_final: 0.8101 (mt0) REVERT: A 150 GLN cc_start: 0.9085 (tm-30) cc_final: 0.8640 (tm-30) REVERT: A 172 LEU cc_start: 0.9525 (mp) cc_final: 0.8695 (mp) REVERT: A 184 ARG cc_start: 0.9169 (mmm-85) cc_final: 0.8807 (mmm-85) REVERT: A 190 MET cc_start: 0.9345 (tpp) cc_final: 0.8957 (mmp) REVERT: A 191 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8360 (mt0) REVERT: A 221 LYS cc_start: 0.9427 (mmtp) cc_final: 0.8719 (mptt) REVERT: A 228 LYS cc_start: 0.9342 (mmmm) cc_final: 0.8981 (mmtm) REVERT: A 252 ASN cc_start: 0.9059 (t0) cc_final: 0.8755 (t0) REVERT: A 263 ASP cc_start: 0.8690 (m-30) cc_final: 0.8357 (m-30) REVERT: A 286 ASP cc_start: 0.8681 (m-30) cc_final: 0.8191 (m-30) REVERT: A 290 GLU cc_start: 0.8688 (tm-30) cc_final: 0.8382 (tm-30) REVERT: A 321 GLU cc_start: 0.9132 (tp30) cc_final: 0.8856 (tp30) REVERT: A 341 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8734 (mmtm) REVERT: A 348 MET cc_start: 0.8553 (tmm) cc_final: 0.7740 (tmm) REVERT: A 352 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7521 (mt-10) REVERT: A 361 GLN cc_start: 0.9175 (tt0) cc_final: 0.8812 (tp-100) REVERT: A 362 ASP cc_start: 0.8358 (m-30) cc_final: 0.7278 (m-30) REVERT: A 384 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.7889 (pm20) REVERT: A 400 GLU cc_start: 0.8420 (pp20) cc_final: 0.8124 (pp20) REVERT: A 402 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8235 (mm-30) REVERT: A 406 ASP cc_start: 0.8382 (m-30) cc_final: 0.8029 (t0) REVERT: A 407 ILE cc_start: 0.9111 (mt) cc_final: 0.8776 (mt) REVERT: A 458 MET cc_start: 0.8579 (mmp) cc_final: 0.7966 (mmp) REVERT: A 479 TYR cc_start: 0.9089 (t80) cc_final: 0.8790 (t80) REVERT: A 493 MET cc_start: 0.9388 (tmm) cc_final: 0.9016 (tmm) REVERT: A 494 MET cc_start: 0.9368 (OUTLIER) cc_final: 0.9156 (ttm) REVERT: A 515 ASP cc_start: 0.8988 (m-30) cc_final: 0.8488 (m-30) REVERT: A 588 GLN cc_start: 0.9280 (mm-40) cc_final: 0.8762 (mm-40) REVERT: A 615 MET cc_start: 0.9293 (mmp) cc_final: 0.8782 (mmp) REVERT: A 640 MET cc_start: 0.9608 (OUTLIER) cc_final: 0.8906 (tpp) REVERT: A 668 ASN cc_start: 0.9673 (m-40) cc_final: 0.9401 (m110) REVERT: B 30 LYS cc_start: 0.9413 (tptt) cc_final: 0.9122 (tptt) REVERT: B 31 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8528 (mp0) REVERT: B 95 MET cc_start: 0.9310 (tpp) cc_final: 0.8786 (tpp) REVERT: B 98 PHE cc_start: 0.9693 (t80) cc_final: 0.9309 (t80) REVERT: B 106 LEU cc_start: 0.9251 (tt) cc_final: 0.8613 (tt) REVERT: B 112 LYS cc_start: 0.9529 (mmmt) cc_final: 0.9191 (mmmt) REVERT: B 119 GLU cc_start: 0.8971 (mp0) cc_final: 0.8361 (mp0) REVERT: B 147 GLN cc_start: 0.9551 (mt0) cc_final: 0.9073 (mm-40) REVERT: B 149 TYR cc_start: 0.9358 (t80) cc_final: 0.8306 (t80) REVERT: B 161 ARG cc_start: 0.8396 (ttm110) cc_final: 0.7366 (ttm110) REVERT: B 194 LYS cc_start: 0.9529 (OUTLIER) cc_final: 0.9241 (pttt) REVERT: B 202 ASN cc_start: 0.9341 (t0) cc_final: 0.9030 (t0) REVERT: B 211 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7793 (mm-30) REVERT: B 214 LYS cc_start: 0.9055 (mtpp) cc_final: 0.8661 (mmtt) REVERT: B 232 ASN cc_start: 0.9342 (m-40) cc_final: 0.8864 (m110) REVERT: B 263 ASP cc_start: 0.9156 (m-30) cc_final: 0.8720 (m-30) REVERT: B 266 LYS cc_start: 0.9309 (mtpp) cc_final: 0.9072 (mttp) REVERT: B 296 LYS cc_start: 0.9324 (mttt) cc_final: 0.9018 (mmmt) REVERT: B 357 TYR cc_start: 0.8616 (m-10) cc_final: 0.7857 (m-10) REVERT: B 361 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8611 (tt0) REVERT: B 389 SER cc_start: 0.8831 (p) cc_final: 0.8590 (p) REVERT: B 394 TYR cc_start: 0.9386 (m-80) cc_final: 0.9113 (m-80) REVERT: B 447 ASN cc_start: 0.8260 (m110) cc_final: 0.7463 (m-40) REVERT: B 471 TYR cc_start: 0.9110 (t80) cc_final: 0.8653 (t80) REVERT: B 483 GLU cc_start: 0.9332 (mp0) cc_final: 0.8562 (mm-30) REVERT: B 493 MET cc_start: 0.9610 (tmm) cc_final: 0.9092 (tmm) REVERT: B 505 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8292 (mt-10) REVERT: B 548 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8538 (mm-30) REVERT: B 585 SER cc_start: 0.9257 (p) cc_final: 0.8534 (t) REVERT: B 586 TYR cc_start: 0.8967 (m-80) cc_final: 0.8443 (m-10) REVERT: B 590 SER cc_start: 0.8921 (OUTLIER) cc_final: 0.7954 (p) REVERT: B 602 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.6680 (pt0) REVERT: B 610 LYS cc_start: 0.9214 (ptpt) cc_final: 0.8778 (ptmt) REVERT: B 628 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8543 (mp0) REVERT: B 631 ASP cc_start: 0.9302 (m-30) cc_final: 0.8911 (p0) REVERT: B 659 LYS cc_start: 0.7524 (tptt) cc_final: 0.7257 (tptt) REVERT: C 44 TRP cc_start: 0.7382 (t-100) cc_final: 0.6433 (t-100) REVERT: C 96 MET cc_start: 0.7207 (mmm) cc_final: 0.6729 (mmm) REVERT: C 245 ASP cc_start: 0.8512 (t70) cc_final: 0.8169 (m-30) REVERT: C 256 VAL cc_start: 0.2920 (t) cc_final: 0.2603 (t) REVERT: C 269 MET cc_start: 0.7071 (tpt) cc_final: 0.6493 (tmm) REVERT: D 46 TYR cc_start: 0.9406 (m-10) cc_final: 0.8785 (m-10) REVERT: D 80 HIS cc_start: 0.7967 (m90) cc_final: 0.7262 (t-90) REVERT: D 95 MET cc_start: 0.7827 (tmm) cc_final: 0.7129 (tmm) REVERT: D 110 MET cc_start: 0.8447 (ppp) cc_final: 0.7862 (ptt) REVERT: D 127 GLN cc_start: 0.9335 (OUTLIER) cc_final: 0.8842 (mm110) REVERT: D 155 LYS cc_start: 0.9222 (mttt) cc_final: 0.8757 (mmmm) REVERT: D 162 TYR cc_start: 0.9115 (m-10) cc_final: 0.8642 (m-80) REVERT: D 185 MET cc_start: 0.7216 (mmm) cc_final: 0.6943 (mmm) REVERT: D 242 TYR cc_start: 0.8720 (m-80) cc_final: 0.8447 (m-80) REVERT: D 271 LEU cc_start: 0.8498 (mt) cc_final: 0.8213 (mt) outliers start: 68 outliers final: 50 residues processed: 657 average time/residue: 0.2506 time to fit residues: 249.0511 Evaluate side-chains 677 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 617 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 605 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 31 GLU Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 204 TYR Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 137 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 160 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 120 optimal weight: 0.0970 chunk 135 optimal weight: 0.9980 chunk 148 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN A 588 GLN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 214 ASN D 25 ASN ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.135595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.094763 restraints weight = 36645.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.098070 restraints weight = 18061.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.100157 restraints weight = 11081.981| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.7461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 16386 Z= 0.200 Angle : 0.813 15.061 22134 Z= 0.416 Chirality : 0.051 0.455 2360 Planarity : 0.004 0.055 2818 Dihedral : 10.339 166.535 2244 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.20 % Allowed : 32.40 % Favored : 63.40 % 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: 0.42 (0.18), residues: 1932 helix: 0.68 (0.15), residues: 1137 sheet: -0.32 (0.42), residues: 142 loop : -0.06 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 124 HIS 0.020 0.002 HIS A 469 PHE 0.034 0.002 PHE D 168 TYR 0.052 0.002 TYR D 142 ARG 0.010 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04314 ( 871) hydrogen bonds : angle 5.32703 ( 2571) covalent geometry : bond 0.00459 (16386) covalent geometry : angle 0.81320 (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 682 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 610 time to evaluate : 1.751 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 31 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8190 (pm20) REVERT: A 51 LEU cc_start: 0.9208 (tp) cc_final: 0.8957 (mp) REVERT: A 119 GLU cc_start: 0.8528 (mt-10) cc_final: 0.8195 (mt-10) REVERT: A 147 GLN cc_start: 0.9125 (mt0) cc_final: 0.8128 (mt0) REVERT: A 172 LEU cc_start: 0.9521 (mp) cc_final: 0.8694 (mp) REVERT: A 184 ARG cc_start: 0.9165 (mmm-85) cc_final: 0.8771 (mmm-85) REVERT: A 190 MET cc_start: 0.9349 (tpp) cc_final: 0.8993 (mmp) REVERT: A 221 LYS cc_start: 0.9418 (mmtp) cc_final: 0.8698 (mptt) REVERT: A 228 LYS cc_start: 0.9397 (mmmm) cc_final: 0.8957 (tppt) REVERT: A 252 ASN cc_start: 0.9087 (t0) cc_final: 0.8822 (t0) REVERT: A 263 ASP cc_start: 0.8636 (m-30) cc_final: 0.8319 (m-30) REVERT: A 267 ILE cc_start: 0.9576 (mp) cc_final: 0.9197 (pt) REVERT: A 290 GLU cc_start: 0.8685 (tm-30) cc_final: 0.8385 (tm-30) REVERT: A 321 GLU cc_start: 0.9140 (tp30) cc_final: 0.8887 (tp30) REVERT: A 341 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8737 (mmtm) REVERT: A 361 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.8918 (tp40) REVERT: A 384 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.7837 (pm20) REVERT: A 400 GLU cc_start: 0.8466 (pp20) cc_final: 0.8183 (pp20) REVERT: A 402 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8276 (mm-30) REVERT: A 406 ASP cc_start: 0.8311 (m-30) cc_final: 0.8015 (t0) REVERT: A 407 ILE cc_start: 0.9132 (mt) cc_final: 0.8779 (mt) REVERT: A 479 TYR cc_start: 0.9139 (t80) cc_final: 0.8871 (t80) REVERT: A 493 MET cc_start: 0.9421 (tmm) cc_final: 0.8972 (tmm) REVERT: A 515 ASP cc_start: 0.8991 (m-30) cc_final: 0.8583 (m-30) REVERT: A 588 GLN cc_start: 0.9239 (OUTLIER) cc_final: 0.8759 (mm110) REVERT: A 615 MET cc_start: 0.9258 (mmp) cc_final: 0.8735 (mmp) REVERT: A 640 MET cc_start: 0.9626 (OUTLIER) cc_final: 0.8889 (tpp) REVERT: A 668 ASN cc_start: 0.9679 (m-40) cc_final: 0.9397 (m110) REVERT: B 30 LYS cc_start: 0.9419 (tptt) cc_final: 0.9158 (tptt) REVERT: B 31 GLU cc_start: 0.8851 (OUTLIER) cc_final: 0.8526 (mt-10) REVERT: B 65 GLU cc_start: 0.8439 (mp0) cc_final: 0.7841 (mp0) REVERT: B 95 MET cc_start: 0.9335 (tpp) cc_final: 0.8288 (tpp) REVERT: B 98 PHE cc_start: 0.9696 (t80) cc_final: 0.9342 (t80) REVERT: B 99 LYS cc_start: 0.9365 (mmtt) cc_final: 0.8556 (tppp) REVERT: B 112 LYS cc_start: 0.9529 (mmmt) cc_final: 0.9187 (mmmt) REVERT: B 116 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8549 (mt-10) REVERT: B 119 GLU cc_start: 0.8998 (mp0) cc_final: 0.8380 (mp0) REVERT: B 149 TYR cc_start: 0.9393 (t80) cc_final: 0.8228 (t80) REVERT: B 161 ARG cc_start: 0.8497 (ttm110) cc_final: 0.7587 (ttm110) REVERT: B 164 ARG cc_start: 0.8923 (tmm-80) cc_final: 0.8348 (ttp80) REVERT: B 194 LYS cc_start: 0.9533 (OUTLIER) cc_final: 0.9232 (pttt) REVERT: B 211 GLU cc_start: 0.8138 (mm-30) cc_final: 0.7823 (mm-30) REVERT: B 232 ASN cc_start: 0.9331 (m-40) cc_final: 0.8854 (m110) REVERT: B 263 ASP cc_start: 0.9145 (m-30) cc_final: 0.8766 (m-30) REVERT: B 266 LYS cc_start: 0.9316 (mtpp) cc_final: 0.9053 (mttm) REVERT: B 296 LYS cc_start: 0.9340 (mttt) cc_final: 0.9038 (mmmt) REVERT: B 357 TYR cc_start: 0.8799 (m-10) cc_final: 0.8262 (m-10) REVERT: B 361 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8797 (tt0) REVERT: B 389 SER cc_start: 0.8734 (p) cc_final: 0.8498 (p) REVERT: B 394 TYR cc_start: 0.9392 (m-80) cc_final: 0.9113 (m-80) REVERT: B 447 ASN cc_start: 0.8317 (m110) cc_final: 0.7672 (m-40) REVERT: B 471 TYR cc_start: 0.9135 (t80) cc_final: 0.8688 (t80) REVERT: B 483 GLU cc_start: 0.9379 (mp0) cc_final: 0.8615 (mm-30) REVERT: B 493 MET cc_start: 0.9616 (tmm) cc_final: 0.9332 (tmm) REVERT: B 585 SER cc_start: 0.9263 (p) cc_final: 0.8554 (t) REVERT: B 586 TYR cc_start: 0.9004 (m-80) cc_final: 0.8213 (m-10) REVERT: B 590 SER cc_start: 0.9051 (OUTLIER) cc_final: 0.8113 (p) REVERT: B 602 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.6614 (pt0) REVERT: B 628 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8555 (mp0) REVERT: B 631 ASP cc_start: 0.9316 (m-30) cc_final: 0.9017 (p0) REVERT: B 659 LYS cc_start: 0.7478 (tptt) cc_final: 0.7114 (tptt) REVERT: C 44 TRP cc_start: 0.7359 (t-100) cc_final: 0.6801 (t-100) REVERT: C 96 MET cc_start: 0.6983 (mmm) cc_final: 0.6558 (mmm) REVERT: C 245 ASP cc_start: 0.8540 (t70) cc_final: 0.8180 (m-30) REVERT: C 256 VAL cc_start: 0.3117 (t) cc_final: 0.2851 (t) REVERT: C 269 MET cc_start: 0.7037 (tpt) cc_final: 0.6435 (tmm) REVERT: D 80 HIS cc_start: 0.8052 (m90) cc_final: 0.7448 (t-90) REVERT: D 95 MET cc_start: 0.7839 (tmm) cc_final: 0.7031 (tmm) REVERT: D 110 MET cc_start: 0.8443 (ppp) cc_final: 0.7812 (ptt) REVERT: D 127 GLN cc_start: 0.9349 (OUTLIER) cc_final: 0.8909 (mm110) REVERT: D 146 GLN cc_start: 0.9086 (mm110) cc_final: 0.8796 (mp10) REVERT: D 155 LYS cc_start: 0.9131 (mttt) cc_final: 0.8780 (mmmm) REVERT: D 157 MET cc_start: 0.9609 (ptm) cc_final: 0.9343 (ppp) REVERT: D 162 TYR cc_start: 0.9170 (m-10) cc_final: 0.8749 (m-80) REVERT: D 185 MET cc_start: 0.7192 (mmm) cc_final: 0.6938 (mmm) REVERT: D 242 TYR cc_start: 0.8791 (OUTLIER) cc_final: 0.8523 (m-80) outliers start: 72 outliers final: 56 residues processed: 638 average time/residue: 0.2583 time to fit residues: 248.7033 Evaluate side-chains 672 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 604 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 341 LYS Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 361 GLN Chi-restraints excluded: chain A residue 381 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 436 LEU Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 588 GLN Chi-restraints excluded: chain A residue 605 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 31 GLU Chi-restraints excluded: chain B residue 193 SER Chi-restraints excluded: chain B residue 194 LYS Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 361 GLN Chi-restraints excluded: chain B residue 408 SER Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 602 GLU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 29 PHE Chi-restraints excluded: chain C residue 84 HIS Chi-restraints excluded: chain C residue 107 ASN Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 142 TYR Chi-restraints excluded: chain C residue 231 LEU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain D residue 25 ASN Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 127 GLN Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 242 TYR Chi-restraints excluded: chain D residue 259 PHE Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 81 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 179 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 chunk 58 optimal weight: 0.7980 chunk 180 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.135513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.094090 restraints weight = 36591.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.097418 restraints weight = 18142.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.099556 restraints weight = 11079.488| |-----------------------------------------------------------------------------| r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.7496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.283 16386 Z= 0.279 Angle : 1.083 59.200 22134 Z= 0.602 Chirality : 0.056 0.648 2360 Planarity : 0.006 0.176 2818 Dihedral : 10.308 166.585 2243 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 22.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.78 % Allowed : 32.17 % Favored : 63.05 % Cbeta Deviations : 0.11 % 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: 0.41 (0.18), residues: 1932 helix: 0.67 (0.15), residues: 1137 sheet: -0.33 (0.42), residues: 142 loop : -0.07 (0.23), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 124 HIS 0.017 0.001 HIS A 469 PHE 0.035 0.002 PHE C 172 TYR 0.050 0.002 TYR D 142 ARG 0.012 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 871) hydrogen bonds : angle 5.33307 ( 2571) covalent geometry : bond 0.00664 (16386) covalent geometry : angle 1.08252 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6657.81 seconds wall clock time: 117 minutes 6.58 seconds (7026.58 seconds total)