Starting phenix.real_space_refine on Sat Jun 14 07:38:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bza_45061/06_2025/9bza_45061_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bza_45061/06_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_45061/06_2025/9bza_45061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bza_45061/06_2025/9bza_45061.map" model { file = "/net/cci-nas-00/data/ceres_data/9bza_45061/06_2025/9bza_45061_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bza_45061/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 9.78, per 1000 atoms: 0.61 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: 4.13 Conformation dependent library (CDL) restraints added in 1.9 seconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 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: 5.15 Time building geometry restraints manager: 4.84 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 37.290 Find NCS groups from input model: 0.830 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.860 ------------------------------------------------------------------------------- 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 : 1.702 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: 0.7889 (m-30) REVERT: A 127 LEU cc_start: 0.8792 (mt) cc_final: 0.8565 (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: 0.8664 (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: 0.8628 (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: 0.8664 (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: 0.8213 (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: 0.8201 (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: 0.8160 (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: 0.7777 (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: 0.7542 (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: 0.3202 time to fit residues: 465.8890 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 : 1.873 ------------------------------------------------------------------------------- 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 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** 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 C 24 GLN 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 = 0.3721 r_free = 0.3721 target = 0.138460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.094936 restraints weight = 34889.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.098628 restraints weight = 17028.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.100881 restraints weight = 10161.835| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 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 = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16386 Z= 0.242 Angle : 0.737 10.665 22134 Z= 0.385 Chirality : 0.046 0.312 2360 Planarity : 0.004 0.031 2818 Dihedral : 11.794 170.900 2256 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 5.07 % Allowed : 20.22 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.19), residues: 1932 helix: 1.28 (0.15), residues: 1133 sheet: 0.23 (0.43), residues: 130 loop : 0.58 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 9 HIS 0.007 0.001 HIS A 438 PHE 0.036 0.003 PHE D 168 TYR 0.025 0.002 TYR D 162 ARG 0.008 0.001 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.04797 ( 871) hydrogen bonds : angle 5.18540 ( 2571) covalent geometry : bond 0.00527 (16386) covalent geometry : angle 0.73699 (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: 87 poor density : 693 time to evaluate : 1.844 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 15 GLU cc_start: 0.8688 (tp30) cc_final: 0.8421 (tp30) REVERT: A 51 LEU cc_start: 0.9490 (tp) cc_final: 0.9272 (tp) REVERT: A 60 GLU cc_start: 0.9082 (mt-10) cc_final: 0.8808 (pt0) REVERT: A 64 TYR cc_start: 0.9207 (m-10) cc_final: 0.8476 (m-80) REVERT: A 65 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8473 (mm-30) REVERT: A 143 LEU cc_start: 0.9311 (tp) cc_final: 0.9106 (tp) REVERT: A 147 GLN cc_start: 0.9032 (mt0) cc_final: 0.8029 (mm-40) REVERT: A 172 LEU cc_start: 0.9576 (mp) cc_final: 0.8955 (mp) REVERT: A 202 ASN cc_start: 0.9612 (t0) cc_final: 0.9271 (t0) REVERT: A 251 LEU cc_start: 0.9535 (tp) cc_final: 0.9171 (tp) REVERT: A 259 ASN cc_start: 0.8819 (m-40) cc_final: 0.8598 (m-40) REVERT: A 263 ASP cc_start: 0.8724 (m-30) cc_final: 0.8424 (m-30) REVERT: A 270 ASP cc_start: 0.8827 (m-30) cc_final: 0.8594 (m-30) REVERT: A 286 ASP cc_start: 0.8691 (m-30) cc_final: 0.8162 (m-30) REVERT: A 321 GLU cc_start: 0.8972 (tp30) cc_final: 0.8684 (tp30) REVERT: A 348 MET cc_start: 0.8365 (OUTLIER) cc_final: 0.8019 (tmm) REVERT: A 362 ASP cc_start: 0.8585 (m-30) cc_final: 0.7687 (m-30) REVERT: A 394 TYR cc_start: 0.9186 (m-80) cc_final: 0.8684 (m-10) REVERT: A 400 GLU cc_start: 0.8270 (pp20) cc_final: 0.7416 (pp20) REVERT: A 402 GLU cc_start: 0.8480 (mm-30) cc_final: 0.7794 (mm-30) REVERT: A 406 ASP cc_start: 0.8389 (m-30) cc_final: 0.7979 (m-30) REVERT: A 407 ILE cc_start: 0.9291 (mt) cc_final: 0.8777 (mt) REVERT: A 493 MET cc_start: 0.9394 (tmm) cc_final: 0.9182 (tmm) REVERT: A 501 GLN cc_start: 0.9352 (OUTLIER) cc_final: 0.9046 (tt0) REVERT: A 505 GLU cc_start: 0.8919 (mt-10) cc_final: 0.8716 (mt-10) REVERT: A 515 ASP cc_start: 0.8960 (m-30) cc_final: 0.8445 (m-30) REVERT: A 550 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7308 (ptm) REVERT: A 595 MET cc_start: 0.9091 (mmp) cc_final: 0.8871 (mmp) REVERT: A 598 MET cc_start: 0.8886 (mtp) cc_final: 0.8647 (mtp) REVERT: A 615 MET cc_start: 0.9066 (mmp) cc_final: 0.8598 (mmp) REVERT: A 626 TYR cc_start: 0.9037 (m-80) cc_final: 0.8821 (m-80) REVERT: A 640 MET cc_start: 0.9372 (OUTLIER) cc_final: 0.9061 (tpp) REVERT: A 647 HIS cc_start: 0.9246 (m-70) cc_final: 0.8927 (m-70) REVERT: A 668 ASN cc_start: 0.9630 (m-40) cc_final: 0.9280 (m-40) REVERT: A 683 TYR cc_start: 0.8585 (t80) cc_final: 0.8099 (t80) REVERT: A 686 ARG cc_start: 0.8353 (mtp85) cc_final: 0.8083 (mtp-110) REVERT: B 12 LEU cc_start: 0.9499 (mt) cc_final: 0.9202 (mp) REVERT: B 15 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8832 (mt-10) REVERT: B 27 ASP cc_start: 0.9409 (OUTLIER) cc_final: 0.9087 (p0) REVERT: B 31 GLU cc_start: 0.8913 (mp0) cc_final: 0.8467 (mp0) REVERT: B 95 MET cc_start: 0.9376 (tpp) cc_final: 0.9142 (tpp) REVERT: B 147 GLN cc_start: 0.9245 (mt0) cc_final: 0.8036 (mt0) REVERT: B 149 TYR cc_start: 0.9210 (t80) cc_final: 0.8560 (t80) REVERT: B 157 LEU cc_start: 0.9345 (tp) cc_final: 0.9103 (tp) REVERT: B 161 ARG cc_start: 0.7973 (ttm110) cc_final: 0.6802 (ttm110) REVERT: B 202 ASN cc_start: 0.9483 (t0) cc_final: 0.9184 (t0) REVERT: B 204 SER cc_start: 0.9359 (m) cc_final: 0.9139 (t) REVERT: B 214 LYS cc_start: 0.8821 (ttmm) cc_final: 0.8318 (mmtt) REVERT: B 236 TYR cc_start: 0.9171 (t80) cc_final: 0.8872 (t80) REVERT: B 250 TYR cc_start: 0.9154 (m-80) cc_final: 0.8931 (m-80) REVERT: B 286 ASP cc_start: 0.8516 (OUTLIER) cc_final: 0.8267 (m-30) REVERT: B 296 LYS cc_start: 0.8749 (mttt) cc_final: 0.8502 (mmmt) REVERT: B 317 MET cc_start: 0.8765 (ptp) cc_final: 0.8473 (ptp) REVERT: B 322 MET cc_start: 0.9445 (mmm) cc_final: 0.9209 (tpp) REVERT: B 348 MET cc_start: 0.8979 (ptp) cc_final: 0.8443 (ptp) REVERT: B 361 GLN cc_start: 0.9051 (tt0) cc_final: 0.8727 (tp40) REVERT: B 362 ASP cc_start: 0.8914 (m-30) cc_final: 0.8191 (m-30) REVERT: B 376 VAL cc_start: 0.9625 (t) cc_final: 0.9240 (t) REVERT: B 389 SER cc_start: 0.9122 (p) cc_final: 0.8807 (p) REVERT: B 392 SER cc_start: 0.9530 (m) cc_final: 0.9174 (p) REVERT: B 396 ASP cc_start: 0.8886 (m-30) cc_final: 0.8646 (m-30) REVERT: B 415 ASN cc_start: 0.9586 (t0) cc_final: 0.9262 (t0) REVERT: B 459 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.8727 (mtmm) REVERT: B 467 ASN cc_start: 0.9492 (t0) cc_final: 0.9185 (m-40) REVERT: B 493 MET cc_start: 0.9687 (tmm) cc_final: 0.9228 (tmm) REVERT: B 494 MET cc_start: 0.9636 (mtp) cc_final: 0.9376 (ttm) REVERT: B 515 ASP cc_start: 0.9255 (m-30) cc_final: 0.8944 (m-30) REVERT: B 543 ILE cc_start: 0.9732 (mm) cc_final: 0.9399 (mm) REVERT: B 588 GLN cc_start: 0.9477 (mm-40) cc_final: 0.8826 (mm-40) REVERT: B 615 MET cc_start: 0.9288 (mmp) cc_final: 0.8810 (mmm) REVERT: B 634 MET cc_start: 0.9258 (mmm) cc_final: 0.8954 (mmt) REVERT: B 640 MET cc_start: 0.9457 (tpp) cc_final: 0.9177 (tpp) REVERT: B 665 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.8857 (ttt90) REVERT: B 667 LEU cc_start: 0.9110 (tp) cc_final: 0.8808 (tp) REVERT: C 96 MET cc_start: 0.6588 (mmm) cc_final: 0.6347 (mmm) REVERT: C 242 TYR cc_start: 0.2153 (t80) cc_final: 0.1658 (t80) REVERT: C 245 ASP cc_start: 0.8602 (t70) cc_final: 0.8240 (m-30) REVERT: C 246 LEU cc_start: 0.8292 (mp) cc_final: 0.7753 (mt) REVERT: D 72 THR cc_start: 0.8490 (p) cc_final: 0.8237 (p) REVERT: D 96 MET cc_start: 0.7594 (mmt) cc_final: 0.7174 (mmt) REVERT: D 109 PHE cc_start: 0.8624 (m-10) cc_final: 0.8412 (m-80) REVERT: D 127 GLN cc_start: 0.9133 (mm-40) cc_final: 0.8903 (mp10) REVERT: D 158 VAL cc_start: 0.9563 (t) cc_final: 0.9325 (t) REVERT: D 162 TYR cc_start: 0.9104 (m-10) cc_final: 0.8744 (m-80) REVERT: D 185 MET cc_start: 0.6632 (mmm) cc_final: 0.6384 (mmm) REVERT: D 224 LEU cc_start: 0.9158 (mt) cc_final: 0.8884 (mt) REVERT: D 227 PHE cc_start: 0.8334 (m-80) cc_final: 0.8005 (m-80) REVERT: D 268 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7741 (mm) REVERT: D 316 LYS cc_start: 0.9131 (tmmt) cc_final: 0.8738 (ttpp) outliers start: 87 outliers final: 48 residues processed: 743 average time/residue: 0.2636 time to fit residues: 292.6807 Evaluate side-chains 690 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 633 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL 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 424 SER 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 550 MET 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 49 HIS Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 193 SER 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 277 THR Chi-restraints excluded: chain B residue 286 ASP 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 461 ILE 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 B residue 665 ARG 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 154 PHE Chi-restraints excluded: chain D residue 223 GLU 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: 1.9990 chunk 168 optimal weight: 8.9990 chunk 175 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 57 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 171 optimal weight: 0.9980 chunk 189 optimal weight: 5.9990 chunk 141 optimal weight: 10.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 410 ASN B 668 ASN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.136777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.093726 restraints weight = 35482.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.097208 restraints weight = 17248.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.099410 restraints weight = 10490.861| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 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 = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16386 Z= 0.198 Angle : 0.668 8.521 22134 Z= 0.350 Chirality : 0.044 0.184 2360 Planarity : 0.004 0.038 2818 Dihedral : 11.333 170.907 2251 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.43 % Allowed : 23.89 % Favored : 71.68 % 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: 1.18 (0.19), residues: 1932 helix: 1.19 (0.15), residues: 1131 sheet: -0.23 (0.39), residues: 150 loop : 0.55 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP C 124 HIS 0.007 0.001 HIS D 101 PHE 0.032 0.002 PHE D 320 TYR 0.039 0.002 TYR D 142 ARG 0.006 0.001 ARG A 600 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 871) hydrogen bonds : angle 5.00508 ( 2571) covalent geometry : bond 0.00438 (16386) covalent geometry : angle 0.66773 (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 743 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 667 time to evaluate : 1.777 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 16 ILE cc_start: 0.9437 (mm) cc_final: 0.9184 (tp) REVERT: A 29 ASP cc_start: 0.9393 (t70) cc_final: 0.9088 (t70) REVERT: A 51 LEU cc_start: 0.9517 (tp) cc_final: 0.9314 (tp) REVERT: A 147 GLN cc_start: 0.9006 (mt0) cc_final: 0.7971 (mm-40) REVERT: A 157 LEU cc_start: 0.9513 (tp) cc_final: 0.9278 (tp) REVERT: A 161 ARG cc_start: 0.8622 (ttm110) cc_final: 0.8316 (ttm110) REVERT: A 172 LEU cc_start: 0.9557 (mp) cc_final: 0.9000 (mp) REVERT: A 202 ASN cc_start: 0.9622 (t0) cc_final: 0.9214 (t0) REVERT: A 214 LYS cc_start: 0.8981 (tppt) cc_final: 0.8625 (mmtt) REVERT: A 228 LYS cc_start: 0.9496 (mmmm) cc_final: 0.8882 (tppt) REVERT: A 231 ASP cc_start: 0.8952 (OUTLIER) cc_final: 0.8425 (t0) REVERT: A 243 ARG cc_start: 0.7425 (tmt-80) cc_final: 0.7189 (tmt-80) REVERT: A 251 LEU cc_start: 0.9543 (tp) cc_final: 0.9125 (tp) REVERT: A 263 ASP cc_start: 0.8596 (m-30) cc_final: 0.8359 (m-30) REVERT: A 270 ASP cc_start: 0.8876 (m-30) cc_final: 0.8634 (m-30) REVERT: A 301 PHE cc_start: 0.9454 (m-80) cc_final: 0.9211 (m-10) REVERT: A 321 GLU cc_start: 0.9107 (tp30) cc_final: 0.8741 (tp30) REVERT: A 341 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8884 (mmtm) REVERT: A 348 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.8107 (tmm) REVERT: A 361 GLN cc_start: 0.9192 (tt0) cc_final: 0.8705 (tp-100) REVERT: A 400 GLU cc_start: 0.8369 (pp20) cc_final: 0.7731 (pp20) REVERT: A 402 GLU cc_start: 0.8525 (mm-30) cc_final: 0.7727 (mm-30) REVERT: A 406 ASP cc_start: 0.8440 (m-30) cc_final: 0.8080 (m-30) REVERT: A 407 ILE cc_start: 0.9302 (mt) cc_final: 0.8811 (mt) REVERT: A 493 MET cc_start: 0.9426 (tmm) cc_final: 0.9116 (tmm) REVERT: A 505 GLU cc_start: 0.8899 (mt-10) cc_final: 0.8682 (mt-10) REVERT: A 515 ASP cc_start: 0.9026 (m-30) cc_final: 0.8525 (m-30) REVERT: A 590 SER cc_start: 0.9353 (t) cc_final: 0.9102 (m) REVERT: A 602 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.5226 (tt0) REVERT: A 604 ARG cc_start: 0.9029 (mmp80) cc_final: 0.8613 (mmt-90) REVERT: A 615 MET cc_start: 0.9158 (mmp) cc_final: 0.8810 (mmp) REVERT: A 640 MET cc_start: 0.9611 (OUTLIER) cc_final: 0.9094 (tpp) REVERT: A 646 GLN cc_start: 0.8916 (pt0) cc_final: 0.8595 (pt0) REVERT: A 647 HIS cc_start: 0.9169 (m-70) cc_final: 0.8896 (m-70) REVERT: A 668 ASN cc_start: 0.9634 (m-40) cc_final: 0.9293 (m-40) REVERT: A 686 ARG cc_start: 0.8478 (mtp85) cc_final: 0.8245 (mtp-110) REVERT: B 31 GLU cc_start: 0.8918 (mp0) cc_final: 0.8654 (mp0) REVERT: B 95 MET cc_start: 0.9374 (tpp) cc_final: 0.9079 (tpp) REVERT: B 119 GLU cc_start: 0.9016 (mp0) cc_final: 0.8379 (mp0) REVERT: B 147 GLN cc_start: 0.9353 (mt0) cc_final: 0.9009 (mt0) REVERT: B 149 TYR cc_start: 0.9259 (t80) cc_final: 0.8646 (t80) REVERT: B 164 ARG cc_start: 0.8644 (ptt-90) cc_final: 0.8241 (ttp80) REVERT: B 194 LYS cc_start: 0.9576 (OUTLIER) cc_final: 0.9347 (pttt) REVERT: B 202 ASN cc_start: 0.9458 (t0) cc_final: 0.9136 (t0) REVERT: B 204 SER cc_start: 0.9348 (m) cc_final: 0.9108 (t) REVERT: B 214 LYS cc_start: 0.8836 (ttmm) cc_final: 0.8254 (mmtm) REVERT: B 236 TYR cc_start: 0.9237 (t80) cc_final: 0.8836 (t80) REVERT: B 274 ARG cc_start: 0.8983 (tpp80) cc_final: 0.8771 (tpp80) REVERT: B 296 LYS cc_start: 0.9052 (mttt) cc_final: 0.8795 (mmmt) REVERT: B 312 GLN cc_start: 0.8794 (OUTLIER) cc_final: 0.8531 (pm20) REVERT: B 361 GLN cc_start: 0.9080 (tt0) cc_final: 0.8686 (tt0) REVERT: B 362 ASP cc_start: 0.8881 (m-30) cc_final: 0.8111 (m-30) REVERT: B 376 VAL cc_start: 0.9660 (t) cc_final: 0.9272 (t) REVERT: B 389 SER cc_start: 0.9124 (p) cc_final: 0.8863 (p) REVERT: B 396 ASP cc_start: 0.8919 (m-30) cc_final: 0.8600 (m-30) REVERT: B 415 ASN cc_start: 0.9528 (t0) cc_final: 0.9082 (t0) REVERT: B 447 ASN cc_start: 0.8792 (m-40) cc_final: 0.8551 (m-40) REVERT: B 459 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.8768 (mtmm) REVERT: B 467 ASN cc_start: 0.9430 (t0) cc_final: 0.9121 (m-40) REVERT: B 472 LEU cc_start: 0.9561 (mm) cc_final: 0.9309 (mm) REVERT: B 483 GLU cc_start: 0.9342 (mp0) cc_final: 0.8974 (mp0) REVERT: B 493 MET cc_start: 0.9692 (tmm) cc_final: 0.9111 (tmm) REVERT: B 515 ASP cc_start: 0.9290 (m-30) cc_final: 0.9025 (m-30) REVERT: B 586 TYR cc_start: 0.9084 (m-80) cc_final: 0.8403 (m-10) REVERT: B 615 MET cc_start: 0.9205 (mmp) cc_final: 0.8784 (mmm) REVERT: B 631 ASP cc_start: 0.9289 (m-30) cc_final: 0.9087 (m-30) REVERT: B 634 MET cc_start: 0.9280 (mmm) cc_final: 0.8965 (mmt) REVERT: B 640 MET cc_start: 0.9481 (tpp) cc_final: 0.9187 (tpp) REVERT: B 659 LYS cc_start: 0.7994 (tptt) cc_final: 0.7760 (tptt) REVERT: C 96 MET cc_start: 0.7004 (mmm) cc_final: 0.6203 (mmm) REVERT: C 100 VAL cc_start: 0.2612 (t) cc_final: 0.2112 (t) REVERT: C 197 ASP cc_start: 0.7166 (t0) cc_final: 0.6895 (t70) REVERT: C 245 ASP cc_start: 0.8611 (t70) cc_final: 0.8230 (m-30) REVERT: C 246 LEU cc_start: 0.8187 (mp) cc_final: 0.7912 (mt) REVERT: D 96 MET cc_start: 0.7750 (mmt) cc_final: 0.7446 (mmt) REVERT: D 157 MET cc_start: 0.9605 (ptp) cc_final: 0.9400 (ptp) REVERT: D 174 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.8280 (t80) REVERT: D 185 MET cc_start: 0.6836 (mmm) cc_final: 0.6491 (mmm) REVERT: D 223 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.8953 (pt0) outliers start: 76 outliers final: 45 residues processed: 704 average time/residue: 0.2643 time to fit residues: 279.3121 Evaluate side-chains 696 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 641 time to evaluate : 1.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL 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 216 VAL Chi-restraints excluded: chain A residue 223 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 439 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 602 GLU Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 155 THR 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 277 THR Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 314 MET 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 459 LYS Chi-restraints excluded: chain B residue 460 SER 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 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 100 VAL Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 211 GLU 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: 10.0000 chunk 99 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 71 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN D 28 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN D 136 GLN D 234 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.134441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.091962 restraints weight = 36379.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.095409 restraints weight = 17916.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.097503 restraints weight = 10868.853| |-----------------------------------------------------------------------------| r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3042 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3042 r_free = 0.3042 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3042 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.6114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16386 Z= 0.291 Angle : 0.717 8.621 22134 Z= 0.377 Chirality : 0.046 0.198 2360 Planarity : 0.004 0.043 2818 Dihedral : 11.284 174.186 2249 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 6.24 % Allowed : 23.02 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.19), residues: 1932 helix: 0.99 (0.15), residues: 1114 sheet: -0.68 (0.37), residues: 166 loop : 0.55 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 44 HIS 0.006 0.002 HIS A 438 PHE 0.035 0.002 PHE D 227 TYR 0.026 0.002 TYR D 142 ARG 0.005 0.001 ARG A 446 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 871) hydrogen bonds : angle 5.09179 ( 2571) covalent geometry : bond 0.00631 (16386) covalent geometry : angle 0.71723 (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 755 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 648 time to evaluate : 1.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.9226 (m-10) cc_final: 0.8827 (m-10) REVERT: A 103 ASP cc_start: 0.8846 (m-30) cc_final: 0.8602 (m-30) REVERT: A 107 LYS cc_start: 0.9207 (OUTLIER) cc_final: 0.8966 (mmmm) REVERT: A 147 GLN cc_start: 0.9054 (mt0) cc_final: 0.8031 (mm-40) REVERT: A 157 LEU cc_start: 0.9506 (tp) cc_final: 0.9280 (tp) REVERT: A 161 ARG cc_start: 0.8600 (ttm110) cc_final: 0.8249 (ttm110) REVERT: A 172 LEU cc_start: 0.9575 (mp) cc_final: 0.9067 (mp) REVERT: A 202 ASN cc_start: 0.9590 (t0) cc_final: 0.9172 (t0) REVERT: A 251 LEU cc_start: 0.9540 (tp) cc_final: 0.9104 (tp) REVERT: A 263 ASP cc_start: 0.8641 (m-30) cc_final: 0.8374 (m-30) REVERT: A 286 ASP cc_start: 0.8778 (m-30) cc_final: 0.8276 (m-30) REVERT: A 301 PHE cc_start: 0.9516 (m-80) cc_final: 0.9316 (m-10) REVERT: A 321 GLU cc_start: 0.9208 (tp30) cc_final: 0.8894 (tp30) REVERT: A 341 LYS cc_start: 0.9166 (OUTLIER) cc_final: 0.8886 (mmtm) REVERT: A 348 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8224 (tmm) REVERT: A 361 GLN cc_start: 0.9291 (tt0) cc_final: 0.8756 (tp-100) REVERT: A 362 ASP cc_start: 0.8565 (m-30) cc_final: 0.7931 (m-30) REVERT: A 384 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.7842 (pm20) REVERT: A 389 SER cc_start: 0.9528 (OUTLIER) cc_final: 0.9200 (p) REVERT: A 400 GLU cc_start: 0.8502 (pp20) cc_final: 0.7970 (pp20) REVERT: A 402 GLU cc_start: 0.8721 (mm-30) cc_final: 0.7850 (mm-30) REVERT: A 406 ASP cc_start: 0.8349 (m-30) cc_final: 0.8009 (m-30) REVERT: A 407 ILE cc_start: 0.9296 (mt) cc_final: 0.8765 (mt) REVERT: A 458 MET cc_start: 0.8931 (mmp) cc_final: 0.8144 (mmp) REVERT: A 479 TYR cc_start: 0.9175 (t80) cc_final: 0.8825 (t80) REVERT: A 493 MET cc_start: 0.9434 (tmm) cc_final: 0.8988 (tmm) REVERT: A 505 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8661 (mt-10) REVERT: A 515 ASP cc_start: 0.9028 (m-30) cc_final: 0.8630 (m-30) REVERT: A 526 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8502 (mm-30) REVERT: A 598 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8459 (mtp) REVERT: A 604 ARG cc_start: 0.9091 (mmp80) cc_final: 0.8625 (mmp80) REVERT: A 615 MET cc_start: 0.9266 (mmp) cc_final: 0.8668 (mmp) REVERT: A 640 MET cc_start: 0.9669 (OUTLIER) cc_final: 0.9004 (tpp) REVERT: A 647 HIS cc_start: 0.9269 (m-70) cc_final: 0.8860 (m170) REVERT: A 668 ASN cc_start: 0.9639 (m-40) cc_final: 0.9403 (m-40) REVERT: A 686 ARG cc_start: 0.8746 (mtp85) cc_final: 0.8336 (mtp-110) REVERT: B 30 LYS cc_start: 0.9481 (tptt) cc_final: 0.9234 (tptt) REVERT: B 31 GLU cc_start: 0.8879 (mp0) cc_final: 0.8606 (mp0) REVERT: B 112 LYS cc_start: 0.9655 (mmmt) cc_final: 0.9354 (mmmt) REVERT: B 119 GLU cc_start: 0.9083 (mp0) cc_final: 0.8453 (mp0) REVERT: B 129 PHE cc_start: 0.9629 (m-10) cc_final: 0.9382 (m-10) REVERT: B 147 GLN cc_start: 0.9495 (mt0) cc_final: 0.9279 (mt0) REVERT: B 149 TYR cc_start: 0.9407 (t80) cc_final: 0.8196 (t80) REVERT: B 161 ARG cc_start: 0.8434 (ttm170) cc_final: 0.7972 (ttm110) REVERT: B 172 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9074 (mt) REVERT: B 194 LYS cc_start: 0.9578 (OUTLIER) cc_final: 0.9312 (pttt) REVERT: B 202 ASN cc_start: 0.9337 (t0) cc_final: 0.9088 (t0) REVERT: B 204 SER cc_start: 0.9298 (m) cc_final: 0.9095 (t) REVERT: B 214 LYS cc_start: 0.8925 (ttmm) cc_final: 0.8455 (mmtp) REVERT: B 236 TYR cc_start: 0.9333 (t80) cc_final: 0.9041 (t80) REVERT: B 296 LYS cc_start: 0.9292 (mttt) cc_final: 0.9020 (mmmt) REVERT: B 315 ASP cc_start: 0.8723 (p0) cc_final: 0.8430 (p0) REVERT: B 316 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8434 (tm-30) REVERT: B 361 GLN cc_start: 0.9094 (tt0) cc_final: 0.8839 (tt0) REVERT: B 362 ASP cc_start: 0.8919 (OUTLIER) cc_final: 0.8363 (m-30) REVERT: B 376 VAL cc_start: 0.9659 (t) cc_final: 0.9433 (t) REVERT: B 394 TYR cc_start: 0.9433 (m-80) cc_final: 0.9207 (m-80) REVERT: B 415 ASN cc_start: 0.9382 (t0) cc_final: 0.9015 (t0) REVERT: B 467 ASN cc_start: 0.9483 (t0) cc_final: 0.9134 (m-40) REVERT: B 493 MET cc_start: 0.9693 (tmm) cc_final: 0.9117 (tmm) REVERT: B 548 GLU cc_start: 0.9037 (mm-30) cc_final: 0.8482 (mm-30) REVERT: B 560 LYS cc_start: 0.9503 (mmtm) cc_final: 0.9294 (mmtp) REVERT: B 615 MET cc_start: 0.9216 (mmp) cc_final: 0.8843 (mmp) REVERT: B 628 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8701 (mp0) REVERT: B 659 LYS cc_start: 0.8059 (tptt) cc_final: 0.7806 (tptt) REVERT: C 245 ASP cc_start: 0.8638 (t70) cc_final: 0.8246 (m-30) REVERT: C 256 VAL cc_start: 0.3542 (t) cc_final: 0.3071 (t) REVERT: D 96 MET cc_start: 0.7595 (mmt) cc_final: 0.7119 (mmt) REVERT: D 98 ASN cc_start: 0.8735 (m-40) cc_final: 0.8452 (m110) REVERT: D 110 MET cc_start: 0.8344 (ppp) cc_final: 0.7606 (ptt) REVERT: D 137 MET cc_start: 0.5815 (mmm) cc_final: 0.5576 (mtt) REVERT: D 162 TYR cc_start: 0.9040 (m-10) cc_final: 0.8765 (m-80) REVERT: D 169 TYR cc_start: 0.8585 (m-80) cc_final: 0.8303 (m-80) REVERT: D 174 TYR cc_start: 0.8644 (OUTLIER) cc_final: 0.8435 (t80) REVERT: D 185 MET cc_start: 0.6942 (mmm) cc_final: 0.6586 (mmm) outliers start: 107 outliers final: 67 residues processed: 692 average time/residue: 0.2666 time to fit residues: 275.8715 Evaluate side-chains 688 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 610 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 47 PHE Chi-restraints excluded: chain A residue 80 VAL 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 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 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 389 SER Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 437 THR Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 598 MET 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 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 352 GLU Chi-restraints excluded: chain B residue 358 ILE Chi-restraints excluded: chain B residue 362 ASP 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 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 460 SER Chi-restraints excluded: chain B residue 461 ILE 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 637 VAL 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 108 ILE Chi-restraints excluded: chain C residue 200 ILE 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 129 LYS Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 154 PHE Chi-restraints excluded: chain D residue 174 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 67 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 182 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 86 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 127 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.137251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.095630 restraints weight = 36676.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.099101 restraints weight = 18038.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.101346 restraints weight = 11237.654| |-----------------------------------------------------------------------------| r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3147 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3147 r_free = 0.3147 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 = 0.3147 r_free = 0.3147 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3147 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.6407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16386 Z= 0.149 Angle : 0.677 11.984 22134 Z= 0.352 Chirality : 0.045 0.239 2360 Planarity : 0.004 0.039 2818 Dihedral : 10.813 170.404 2246 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.37 % Allowed : 27.45 % Favored : 68.18 % 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: 0.85 (0.18), residues: 1932 helix: 0.93 (0.15), residues: 1122 sheet: -0.57 (0.38), residues: 158 loop : 0.48 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 124 HIS 0.005 0.001 HIS D 101 PHE 0.052 0.002 PHE D 109 TYR 0.051 0.002 TYR D 142 ARG 0.011 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.04158 ( 871) hydrogen bonds : angle 5.06293 ( 2571) covalent geometry : bond 0.00333 (16386) covalent geometry : angle 0.67688 (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 746 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 671 time to evaluate : 1.826 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 31 GLU cc_start: 0.9143 (pt0) cc_final: 0.8875 (pm20) REVERT: A 65 GLU cc_start: 0.8636 (mm-30) cc_final: 0.7930 (mp0) REVERT: A 103 ASP cc_start: 0.8869 (m-30) cc_final: 0.8636 (m-30) REVERT: A 107 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8912 (mmmm) REVERT: A 119 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8093 (mt-10) REVERT: A 144 MET cc_start: 0.8919 (mtm) cc_final: 0.8512 (mtt) REVERT: A 147 GLN cc_start: 0.8971 (mt0) cc_final: 0.7903 (mm-40) REVERT: A 161 ARG cc_start: 0.8445 (ttm110) cc_final: 0.8070 (ttm110) REVERT: A 172 LEU cc_start: 0.9484 (mp) cc_final: 0.8936 (mp) REVERT: A 228 LYS cc_start: 0.9446 (mmmm) cc_final: 0.8873 (tppt) REVERT: A 251 LEU cc_start: 0.9546 (tp) cc_final: 0.9193 (tp) REVERT: A 263 ASP cc_start: 0.8716 (m-30) cc_final: 0.8433 (m-30) REVERT: A 286 ASP cc_start: 0.8751 (m-30) cc_final: 0.8266 (m-30) REVERT: A 290 GLU cc_start: 0.8707 (tm-30) cc_final: 0.8442 (tm-30) REVERT: A 321 GLU cc_start: 0.9141 (tp30) cc_final: 0.8828 (tp30) REVERT: A 348 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8195 (tmm) REVERT: A 361 GLN cc_start: 0.9180 (tt0) cc_final: 0.8800 (tp-100) REVERT: A 362 ASP cc_start: 0.8479 (m-30) cc_final: 0.7705 (m-30) REVERT: A 377 LYS cc_start: 0.9269 (mttm) cc_final: 0.9061 (mtmm) REVERT: A 384 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7697 (pm20) REVERT: A 400 GLU cc_start: 0.8417 (pp20) cc_final: 0.8084 (pp20) REVERT: A 402 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8169 (mm-30) REVERT: A 406 ASP cc_start: 0.8151 (m-30) cc_final: 0.7926 (m-30) REVERT: A 407 ILE cc_start: 0.9201 (mt) cc_final: 0.8725 (mt) REVERT: A 493 MET cc_start: 0.9374 (tmm) cc_final: 0.9037 (tmm) REVERT: A 505 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8612 (mt-10) REVERT: A 515 ASP cc_start: 0.9008 (m-30) cc_final: 0.8572 (m-30) REVERT: A 570 MET cc_start: 0.9179 (mtp) cc_final: 0.8897 (mtp) REVERT: A 598 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8510 (mtp) REVERT: A 615 MET cc_start: 0.9314 (mmp) cc_final: 0.8705 (mmp) REVERT: A 640 MET cc_start: 0.9653 (OUTLIER) cc_final: 0.9029 (tpp) REVERT: A 647 HIS cc_start: 0.9150 (m-70) cc_final: 0.8888 (m90) REVERT: A 668 ASN cc_start: 0.9646 (m-40) cc_final: 0.9357 (m-40) REVERT: A 686 ARG cc_start: 0.8687 (mtp85) cc_final: 0.8247 (mtp-110) REVERT: B 30 LYS cc_start: 0.9455 (tptt) cc_final: 0.9191 (tptt) REVERT: B 31 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8583 (mp0) REVERT: B 65 GLU cc_start: 0.8610 (mm-30) cc_final: 0.8205 (mm-30) REVERT: B 95 MET cc_start: 0.9335 (tpp) cc_final: 0.8867 (tpp) REVERT: B 112 LYS cc_start: 0.9618 (mmmt) cc_final: 0.9287 (mmmt) REVERT: B 119 GLU cc_start: 0.9026 (mp0) cc_final: 0.8446 (mp0) REVERT: B 128 PHE cc_start: 0.9546 (t80) cc_final: 0.9279 (t80) REVERT: B 129 PHE cc_start: 0.9545 (m-10) cc_final: 0.9316 (m-10) REVERT: B 147 GLN cc_start: 0.9515 (mt0) cc_final: 0.9248 (mt0) REVERT: B 149 TYR cc_start: 0.9407 (t80) cc_final: 0.8320 (t80) REVERT: B 172 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.8353 (mt) REVERT: B 194 LYS cc_start: 0.9551 (OUTLIER) cc_final: 0.9282 (pttt) REVERT: B 202 ASN cc_start: 0.9363 (t0) cc_final: 0.8899 (t0) REVERT: B 204 SER cc_start: 0.9288 (m) cc_final: 0.9009 (t) REVERT: B 214 LYS cc_start: 0.8889 (ttmm) cc_final: 0.8312 (mmtp) REVERT: B 221 LYS cc_start: 0.9330 (mmtp) cc_final: 0.9032 (mttp) REVERT: B 235 ARG cc_start: 0.9133 (ttm-80) cc_final: 0.8932 (ttm110) REVERT: B 236 TYR cc_start: 0.9244 (t80) cc_final: 0.8945 (t80) REVERT: B 263 ASP cc_start: 0.9201 (m-30) cc_final: 0.8865 (m-30) REVERT: B 267 ILE cc_start: 0.9287 (OUTLIER) cc_final: 0.9073 (pp) REVERT: B 291 LEU cc_start: 0.9397 (mt) cc_final: 0.9191 (mt) REVERT: B 296 LYS cc_start: 0.9290 (mttt) cc_final: 0.9003 (mmmt) REVERT: B 361 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8581 (tp40) REVERT: B 376 VAL cc_start: 0.9604 (t) cc_final: 0.9030 (t) REVERT: B 377 LYS cc_start: 0.9283 (mttt) cc_final: 0.8934 (mtmm) REVERT: B 394 TYR cc_start: 0.9401 (m-80) cc_final: 0.9166 (m-80) REVERT: B 406 ASP cc_start: 0.8325 (m-30) cc_final: 0.7956 (t0) REVERT: B 415 ASN cc_start: 0.9322 (t0) cc_final: 0.8905 (t0) REVERT: B 466 MET cc_start: 0.9162 (ptp) cc_final: 0.8832 (ptp) REVERT: B 467 ASN cc_start: 0.9403 (t0) cc_final: 0.8742 (t0) REVERT: B 483 GLU cc_start: 0.9327 (mp0) cc_final: 0.8846 (pm20) REVERT: B 493 MET cc_start: 0.9644 (tmm) cc_final: 0.9086 (tmm) REVERT: B 494 MET cc_start: 0.9330 (ttm) cc_final: 0.9052 (mmt) REVERT: B 505 GLU cc_start: 0.8876 (mt-10) cc_final: 0.8364 (mt-10) REVERT: B 527 TYR cc_start: 0.9261 (t80) cc_final: 0.9001 (t80) REVERT: B 548 GLU cc_start: 0.8975 (mm-30) cc_final: 0.8360 (mm-30) REVERT: B 586 TYR cc_start: 0.9057 (m-80) cc_final: 0.8550 (m-10) REVERT: B 588 GLN cc_start: 0.9545 (mm-40) cc_final: 0.9246 (mm-40) REVERT: B 604 ARG cc_start: 0.8937 (tpp80) cc_final: 0.8490 (mmm-85) REVERT: B 615 MET cc_start: 0.9261 (mmp) cc_final: 0.8930 (mmp) REVERT: B 645 GLN cc_start: 0.9577 (tp40) cc_final: 0.9117 (tp-100) REVERT: B 659 LYS cc_start: 0.7841 (tptt) cc_final: 0.7523 (tptt) REVERT: C 74 MET cc_start: 0.4540 (mpp) cc_final: 0.4181 (mpp) REVERT: C 112 LEU cc_start: 0.6728 (pp) cc_final: 0.6296 (pp) REVERT: C 256 VAL cc_start: 0.3504 (t) cc_final: 0.3099 (t) REVERT: C 261 ARG cc_start: 0.8151 (mpp80) cc_final: 0.7899 (mpp80) REVERT: D 46 TYR cc_start: 0.9472 (m-10) cc_final: 0.8931 (m-10) REVERT: D 95 MET cc_start: 0.7674 (tmm) cc_final: 0.7135 (tmm) REVERT: D 110 MET cc_start: 0.8233 (ppp) cc_final: 0.7674 (ptt) REVERT: D 116 GLU cc_start: 0.9348 (pm20) cc_final: 0.9060 (pm20) REVERT: D 157 MET cc_start: 0.9668 (ptp) cc_final: 0.9387 (ptp) REVERT: D 185 MET cc_start: 0.6953 (mmm) cc_final: 0.6689 (mmm) outliers start: 75 outliers final: 56 residues processed: 703 average time/residue: 0.2679 time to fit residues: 281.5244 Evaluate side-chains 700 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 634 time to evaluate : 2.017 ------------------------------------------------------------------------------- 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 107 LYS Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 216 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 408 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 591 THR Chi-restraints excluded: chain A residue 598 MET 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 31 GLU Chi-restraints excluded: chain B residue 155 THR 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 246 SER Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 361 GLN 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 443 THR Chi-restraints excluded: chain B residue 460 SER Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 512 GLU 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 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 C residue 207 LEU 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 129 LYS Chi-restraints excluded: chain D residue 130 TYR Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 31 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 156 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 115 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 169 optimal weight: 7.9990 chunk 113 optimal weight: 8.9990 chunk 177 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS A 551 HIS ** 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 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 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** 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 = 0.134155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.092447 restraints weight = 36604.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.095914 restraints weight = 18038.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.098081 restraints weight = 10851.934| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3057 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3057 r_free = 0.3057 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 = 0.3057 r_free = 0.3057 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3057 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.6829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 16386 Z= 0.343 Angle : 0.797 15.514 22134 Z= 0.417 Chirality : 0.049 0.348 2360 Planarity : 0.004 0.044 2818 Dihedral : 11.163 172.502 2246 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 21.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 6.82 % Allowed : 26.57 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.18), residues: 1932 helix: 0.58 (0.15), residues: 1146 sheet: -0.74 (0.39), residues: 166 loop : 0.21 (0.24), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 124 HIS 0.008 0.002 HIS A 438 PHE 0.049 0.003 PHE D 227 TYR 0.049 0.002 TYR D 142 ARG 0.006 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.04511 ( 871) hydrogen bonds : angle 5.35716 ( 2571) covalent geometry : bond 0.00743 (16386) covalent geometry : angle 0.79660 (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 735 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 618 time to evaluate : 1.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9018 (tttt) cc_final: 0.8772 (ttpp) REVERT: A 31 GLU cc_start: 0.9069 (pt0) cc_final: 0.8723 (pm20) REVERT: A 64 TYR cc_start: 0.9392 (m-10) cc_final: 0.9115 (m-10) REVERT: A 65 GLU cc_start: 0.8790 (mm-30) cc_final: 0.7956 (mp0) REVERT: A 103 ASP cc_start: 0.8913 (m-30) cc_final: 0.8660 (m-30) REVERT: A 107 LYS cc_start: 0.9191 (OUTLIER) cc_final: 0.8934 (mmmm) REVERT: A 119 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8197 (mt-10) REVERT: A 121 ARG cc_start: 0.9341 (OUTLIER) cc_final: 0.9064 (tpt90) REVERT: A 147 GLN cc_start: 0.9142 (mt0) cc_final: 0.8098 (mm-40) REVERT: A 172 LEU cc_start: 0.9553 (mp) cc_final: 0.9045 (mp) REVERT: A 251 LEU cc_start: 0.9590 (tp) cc_final: 0.9241 (tp) REVERT: A 263 ASP cc_start: 0.8653 (m-30) cc_final: 0.8318 (m-30) REVERT: A 321 GLU cc_start: 0.9159 (tp30) cc_final: 0.8893 (tp30) REVERT: A 341 LYS cc_start: 0.9184 (OUTLIER) cc_final: 0.8747 (mmtm) REVERT: A 348 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8266 (tmm) REVERT: A 355 TYR cc_start: 0.8596 (m-10) cc_final: 0.8340 (m-10) REVERT: A 361 GLN cc_start: 0.9326 (tt0) cc_final: 0.9023 (tp-100) REVERT: A 384 GLU cc_start: 0.8706 (OUTLIER) cc_final: 0.8088 (pm20) REVERT: A 406 ASP cc_start: 0.8311 (m-30) cc_final: 0.7948 (m-30) REVERT: A 407 ILE cc_start: 0.9265 (mt) cc_final: 0.8779 (mt) REVERT: A 458 MET cc_start: 0.9017 (mmp) cc_final: 0.8130 (mmt) REVERT: A 479 TYR cc_start: 0.9229 (t80) cc_final: 0.8902 (t80) REVERT: A 493 MET cc_start: 0.9331 (tmm) cc_final: 0.8940 (tmm) REVERT: A 505 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8579 (mt-10) REVERT: A 515 ASP cc_start: 0.8980 (m-30) cc_final: 0.8638 (m-30) REVERT: A 570 MET cc_start: 0.9249 (mtp) cc_final: 0.8998 (mtp) REVERT: A 598 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8277 (mtp) REVERT: A 615 MET cc_start: 0.9275 (mmp) cc_final: 0.8624 (mmp) REVERT: A 640 MET cc_start: 0.9657 (OUTLIER) cc_final: 0.8942 (tpp) REVERT: A 647 HIS cc_start: 0.9262 (m-70) cc_final: 0.9020 (m90) REVERT: A 668 ASN cc_start: 0.9594 (m-40) cc_final: 0.9361 (m-40) REVERT: A 686 ARG cc_start: 0.8793 (mtp85) cc_final: 0.8316 (mtp85) REVERT: B 30 LYS cc_start: 0.9454 (tptt) cc_final: 0.9186 (tptt) REVERT: B 31 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8596 (mp0) REVERT: B 65 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8345 (mm-30) REVERT: B 95 MET cc_start: 0.9285 (tpp) cc_final: 0.8304 (tpp) REVERT: B 99 LYS cc_start: 0.9490 (mmtt) cc_final: 0.8623 (tppp) REVERT: B 119 GLU cc_start: 0.9057 (mp0) cc_final: 0.8385 (mp0) REVERT: B 120 ASP cc_start: 0.8823 (m-30) cc_final: 0.8579 (m-30) REVERT: B 129 PHE cc_start: 0.9631 (m-10) cc_final: 0.9391 (m-10) REVERT: B 147 GLN cc_start: 0.9587 (mt0) cc_final: 0.9285 (mt0) REVERT: B 149 TYR cc_start: 0.9473 (t80) cc_final: 0.8071 (t80) REVERT: B 161 ARG cc_start: 0.8325 (ttm110) cc_final: 0.7995 (ttm110) REVERT: B 172 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.8500 (mt) REVERT: B 194 LYS cc_start: 0.9592 (OUTLIER) cc_final: 0.9340 (pttt) REVERT: B 202 ASN cc_start: 0.9256 (t0) cc_final: 0.9006 (t0) REVERT: B 204 SER cc_start: 0.9310 (m) cc_final: 0.9017 (t) REVERT: B 214 LYS cc_start: 0.8908 (ttmm) cc_final: 0.8341 (mmtp) REVERT: B 267 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9143 (pp) REVERT: B 296 LYS cc_start: 0.9348 (mttt) cc_final: 0.9053 (mmmt) REVERT: B 394 TYR cc_start: 0.9481 (m-80) cc_final: 0.9242 (m-80) REVERT: B 406 ASP cc_start: 0.8147 (m-30) cc_final: 0.7781 (t0) REVERT: B 415 ASN cc_start: 0.9344 (t0) cc_final: 0.9044 (t0) REVERT: B 467 ASN cc_start: 0.9517 (t0) cc_final: 0.9166 (m-40) REVERT: B 493 MET cc_start: 0.9620 (tmm) cc_final: 0.9266 (tmm) REVERT: B 548 GLU cc_start: 0.9002 (mm-30) cc_final: 0.8468 (mm-30) REVERT: B 588 GLN cc_start: 0.9597 (mm-40) cc_final: 0.9388 (mm-40) REVERT: B 615 MET cc_start: 0.9259 (mmp) cc_final: 0.8824 (mmp) REVERT: B 628 GLU cc_start: 0.8912 (mt-10) cc_final: 0.8675 (mp0) REVERT: B 659 LYS cc_start: 0.7926 (tptt) cc_final: 0.7652 (tptt) REVERT: C 174 TYR cc_start: 0.4365 (OUTLIER) cc_final: 0.3897 (t80) REVERT: C 256 VAL cc_start: 0.4111 (t) cc_final: 0.3538 (t) REVERT: C 261 ARG cc_start: 0.8001 (mpp80) cc_final: 0.7759 (mpp80) REVERT: D 96 MET cc_start: 0.7281 (mmt) cc_final: 0.7011 (mmt) REVERT: D 98 ASN cc_start: 0.8918 (m-40) cc_final: 0.8607 (m-40) REVERT: D 110 MET cc_start: 0.8429 (ppp) cc_final: 0.7771 (ptt) REVERT: D 162 TYR cc_start: 0.9252 (m-10) cc_final: 0.8842 (m-80) REVERT: D 174 TYR cc_start: 0.8800 (OUTLIER) cc_final: 0.8598 (t80) REVERT: D 185 MET cc_start: 0.7003 (mmm) cc_final: 0.6620 (mmm) REVERT: D 236 TYR cc_start: 0.8545 (t80) cc_final: 0.8199 (t80) outliers start: 117 outliers final: 87 residues processed: 666 average time/residue: 0.2673 time to fit residues: 267.9842 Evaluate side-chains 694 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 594 time to evaluate : 2.037 ------------------------------------------------------------------------------- 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 107 LYS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 199 VAL 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 306 ILE 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 414 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 429 VAL Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 624 PHE 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 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 226 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 320 ASN Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 358 ILE 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 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 460 SER Chi-restraints excluded: chain B residue 499 SER 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 644 ILE 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 145 ILE Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 200 ILE Chi-restraints excluded: chain C residue 207 LEU 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 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 154 PHE Chi-restraints excluded: chain D residue 174 TYR Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 262 TYR Chi-restraints excluded: chain D residue 269 MET 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 39 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 161 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 146 optimal weight: 3.9990 chunk 184 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 chunk 175 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 270 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.134495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.093583 restraints weight = 36700.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.096974 restraints weight = 17827.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.099209 restraints weight = 10673.988| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3126 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3126 r_free = 0.3126 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3126 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.7027 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= 0.175 Angle : 0.740 11.497 22134 Z= 0.382 Chirality : 0.047 0.259 2360 Planarity : 0.004 0.044 2818 Dihedral : 10.743 176.060 2246 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 4.84 % Allowed : 30.36 % Favored : 64.80 % 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: 0.45 (0.18), residues: 1932 helix: 0.66 (0.15), residues: 1132 sheet: -0.68 (0.38), residues: 160 loop : 0.18 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 124 HIS 0.006 0.001 HIS A 469 PHE 0.036 0.002 PHE D 168 TYR 0.047 0.002 TYR D 142 ARG 0.007 0.001 ARG A 665 Details of bonding type rmsd hydrogen bonds : bond 0.04304 ( 871) hydrogen bonds : angle 5.20812 ( 2571) covalent geometry : bond 0.00403 (16386) covalent geometry : angle 0.74034 (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 731 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 648 time to evaluate : 1.730 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: 0.9045 (pt0) cc_final: 0.8691 (pm20) REVERT: A 51 LEU cc_start: 0.9206 (tp) cc_final: 0.8989 (mp) REVERT: A 64 TYR cc_start: 0.9315 (m-10) cc_final: 0.9064 (m-10) REVERT: A 65 GLU cc_start: 0.8778 (mm-30) cc_final: 0.7916 (mp0) REVERT: A 107 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8965 (mmmm) REVERT: A 119 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8201 (mt-10) REVERT: A 121 ARG cc_start: 0.9327 (OUTLIER) cc_final: 0.9090 (tpt90) REVERT: A 147 GLN cc_start: 0.9044 (mt0) cc_final: 0.7968 (mm-40) REVERT: A 172 LEU cc_start: 0.9516 (mp) cc_final: 0.9006 (mp) REVERT: A 232 ASN cc_start: 0.9460 (m-40) cc_final: 0.9233 (m-40) REVERT: A 243 ARG cc_start: 0.7031 (tmt-80) cc_final: 0.6797 (tmt-80) REVERT: A 251 LEU cc_start: 0.9560 (tp) cc_final: 0.9356 (tp) REVERT: A 252 ASN cc_start: 0.9216 (t0) cc_final: 0.8698 (t0) REVERT: A 263 ASP cc_start: 0.8686 (m-30) cc_final: 0.8355 (m-30) REVERT: A 277 THR cc_start: 0.9096 (m) cc_final: 0.8878 (p) REVERT: A 321 GLU cc_start: 0.9158 (tp30) cc_final: 0.8875 (tp30) REVERT: A 348 MET cc_start: 0.8633 (tmm) cc_final: 0.7727 (tmm) REVERT: A 352 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7711 (mt-10) REVERT: A 361 GLN cc_start: 0.9193 (tt0) cc_final: 0.8985 (tp40) REVERT: A 362 ASP cc_start: 0.8444 (m-30) cc_final: 0.8082 (m-30) REVERT: A 377 LYS cc_start: 0.9290 (mttm) cc_final: 0.9078 (mtmm) REVERT: A 384 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.7642 (pm20) REVERT: A 390 GLN cc_start: 0.8836 (mt0) cc_final: 0.8626 (mt0) REVERT: A 406 ASP cc_start: 0.8259 (m-30) cc_final: 0.7915 (m-30) REVERT: A 407 ILE cc_start: 0.9165 (mt) cc_final: 0.8764 (mt) REVERT: A 458 MET cc_start: 0.8804 (mmp) cc_final: 0.8069 (mmt) REVERT: A 479 TYR cc_start: 0.9185 (t80) cc_final: 0.8864 (t80) REVERT: A 493 MET cc_start: 0.9325 (tmm) cc_final: 0.8966 (tmm) REVERT: A 505 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8579 (mt-10) REVERT: A 515 ASP cc_start: 0.8978 (m-30) cc_final: 0.8574 (m-30) REVERT: A 570 MET cc_start: 0.9272 (mtp) cc_final: 0.9028 (mtp) REVERT: A 598 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8402 (mtp) REVERT: A 615 MET cc_start: 0.9295 (mmp) cc_final: 0.8644 (mmp) REVERT: A 632 MET cc_start: 0.8890 (mtp) cc_final: 0.8666 (mtp) REVERT: A 640 MET cc_start: 0.9656 (OUTLIER) cc_final: 0.8979 (tpp) REVERT: A 647 HIS cc_start: 0.9162 (m-70) cc_final: 0.8919 (m90) REVERT: A 668 ASN cc_start: 0.9644 (m-40) cc_final: 0.9350 (m-40) REVERT: A 686 ARG cc_start: 0.8777 (mtp85) cc_final: 0.8249 (mtp-110) REVERT: B 30 LYS cc_start: 0.9427 (tptt) cc_final: 0.9171 (tptt) REVERT: B 31 GLU cc_start: 0.8857 (OUTLIER) cc_final: 0.8561 (mt-10) REVERT: B 65 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8224 (mm-30) REVERT: B 99 LYS cc_start: 0.9444 (mmtt) cc_final: 0.8659 (tppp) REVERT: B 116 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8624 (mt-10) REVERT: B 119 GLU cc_start: 0.9015 (mp0) cc_final: 0.8524 (mp0) REVERT: B 120 ASP cc_start: 0.8860 (m-30) cc_final: 0.8650 (m-30) REVERT: B 128 PHE cc_start: 0.9568 (t80) cc_final: 0.9256 (t80) REVERT: B 149 TYR cc_start: 0.9465 (t80) cc_final: 0.8217 (t80) REVERT: B 161 ARG cc_start: 0.8304 (ttm110) cc_final: 0.7983 (ttm110) REVERT: B 172 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.8455 (mt) REVERT: B 194 LYS cc_start: 0.9558 (OUTLIER) cc_final: 0.9299 (pttt) REVERT: B 202 ASN cc_start: 0.9284 (t0) cc_final: 0.8832 (t0) REVERT: B 204 SER cc_start: 0.9307 (m) cc_final: 0.8986 (p) REVERT: B 211 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7751 (mm-30) REVERT: B 221 LYS cc_start: 0.9315 (mmtp) cc_final: 0.9014 (mmmm) REVERT: B 263 ASP cc_start: 0.9166 (m-30) cc_final: 0.8816 (m-30) REVERT: B 267 ILE cc_start: 0.9326 (OUTLIER) cc_final: 0.9086 (pp) REVERT: B 296 LYS cc_start: 0.9388 (mttt) cc_final: 0.9090 (mmmt) REVERT: B 361 GLN cc_start: 0.9061 (tt0) cc_final: 0.8646 (tp40) REVERT: B 394 TYR cc_start: 0.9454 (m-80) cc_final: 0.9183 (m-80) REVERT: B 406 ASP cc_start: 0.8223 (m-30) cc_final: 0.7997 (t0) REVERT: B 415 ASN cc_start: 0.9326 (t0) cc_final: 0.8862 (t0) REVERT: B 459 LYS cc_start: 0.9252 (mttp) cc_final: 0.8643 (mtmm) REVERT: B 466 MET cc_start: 0.9131 (ptp) cc_final: 0.8893 (ptp) REVERT: B 467 ASN cc_start: 0.9307 (t0) cc_final: 0.8466 (t0) REVERT: B 483 GLU cc_start: 0.9315 (mp0) cc_final: 0.8884 (pm20) REVERT: B 493 MET cc_start: 0.9612 (tmm) cc_final: 0.9054 (tmm) REVERT: B 494 MET cc_start: 0.9285 (ttm) cc_final: 0.9017 (mmt) REVERT: B 505 GLU cc_start: 0.8865 (mt-10) cc_final: 0.8302 (mt-10) REVERT: B 548 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8364 (mm-30) REVERT: B 586 TYR cc_start: 0.9123 (m-80) cc_final: 0.8381 (m-10) REVERT: B 588 GLN cc_start: 0.9546 (mm-40) cc_final: 0.9269 (mm110) REVERT: B 604 ARG cc_start: 0.8936 (tpp80) cc_final: 0.8472 (mmm-85) REVERT: B 615 MET cc_start: 0.9250 (mmp) cc_final: 0.8883 (mmp) REVERT: B 640 MET cc_start: 0.9481 (tpp) cc_final: 0.9233 (tpp) REVERT: B 645 GLN cc_start: 0.9605 (tp40) cc_final: 0.9103 (tp-100) REVERT: B 659 LYS cc_start: 0.7852 (tptt) cc_final: 0.7541 (tptt) REVERT: B 684 TYR cc_start: 0.8484 (OUTLIER) cc_final: 0.8046 (m-10) REVERT: C 174 TYR cc_start: 0.4358 (OUTLIER) cc_final: 0.4117 (t80) REVERT: C 256 VAL cc_start: 0.3828 (t) cc_final: 0.3222 (t) REVERT: C 261 ARG cc_start: 0.7966 (mpp80) cc_final: 0.7738 (mpp80) REVERT: D 46 TYR cc_start: 0.9434 (m-10) cc_final: 0.8869 (m-10) REVERT: D 80 HIS cc_start: 0.8024 (m90) cc_final: 0.7151 (t-90) REVERT: D 100 VAL cc_start: 0.7877 (OUTLIER) cc_final: 0.7583 (p) REVERT: D 110 MET cc_start: 0.8412 (ppp) cc_final: 0.7727 (ptt) REVERT: D 162 TYR cc_start: 0.9208 (m-10) cc_final: 0.8825 (m-80) REVERT: D 185 MET cc_start: 0.6995 (mmm) cc_final: 0.6707 (mmm) REVERT: D 281 ASP cc_start: 0.7852 (OUTLIER) cc_final: 0.7419 (t70) outliers start: 83 outliers final: 60 residues processed: 680 average time/residue: 0.2892 time to fit residues: 294.4060 Evaluate side-chains 692 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 619 time to evaluate : 2.116 ------------------------------------------------------------------------------- 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 107 LYS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 155 THR 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 317 MET Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE 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 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 224 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 321 GLU Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 512 GLU 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 684 TYR 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 207 LEU Chi-restraints excluded: chain C residue 250 VAL 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 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 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: 1.9990 chunk 159 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 180 optimal weight: 0.0040 chunk 108 optimal weight: 1.9990 overall best weight: 0.9796 ------------------------------------------------------------------------------- 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 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** 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 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 127 GLN ** C 201 HIS ** 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** D 127 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.136451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.095559 restraints weight = 36313.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.099026 restraints weight = 17620.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.101283 restraints weight = 10597.690| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- 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: 2 | |-----------------------------------------------------------------------------| |-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: 2 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.7259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16386 Z= 0.160 Angle : 0.756 16.011 22134 Z= 0.385 Chirality : 0.048 0.266 2360 Planarity : 0.004 0.045 2818 Dihedral : 10.509 175.167 2246 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.55 % Allowed : 31.99 % Favored : 63.46 % 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: 0.50 (0.18), residues: 1932 helix: 0.70 (0.15), residues: 1125 sheet: 0.20 (0.44), residues: 124 loop : -0.06 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP C 124 HIS 0.017 0.001 HIS A 469 PHE 0.057 0.002 PHE D 227 TYR 0.048 0.002 TYR D 142 ARG 0.007 0.001 ARG A 446 Details of bonding type rmsd hydrogen bonds : bond 0.04270 ( 871) hydrogen bonds : angle 5.23630 ( 2571) covalent geometry : bond 0.00373 (16386) covalent geometry : angle 0.75592 (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 725 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 647 time to evaluate : 2.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8800 (mm-30) cc_final: 0.8042 (mp0) REVERT: A 107 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8923 (mmmm) REVERT: A 119 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8183 (mt-10) REVERT: A 144 MET cc_start: 0.8886 (mtm) cc_final: 0.8466 (mtt) REVERT: A 161 ARG cc_start: 0.8643 (ttm110) cc_final: 0.8309 (ttm110) REVERT: A 172 LEU cc_start: 0.9505 (mp) cc_final: 0.9012 (mp) REVERT: A 232 ASN cc_start: 0.9500 (m-40) cc_final: 0.9234 (m-40) REVERT: A 243 ARG cc_start: 0.7133 (tmt-80) cc_final: 0.6877 (tmt-80) REVERT: A 252 ASN cc_start: 0.9213 (t0) cc_final: 0.8756 (t0) REVERT: A 263 ASP cc_start: 0.8689 (m-30) cc_final: 0.8342 (m-30) REVERT: A 319 MET cc_start: 0.9323 (tpp) cc_final: 0.9054 (tpp) REVERT: A 321 GLU cc_start: 0.9134 (tp30) cc_final: 0.8866 (tp30) REVERT: A 348 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.7601 (tmm) REVERT: A 352 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7352 (mt-10) REVERT: A 362 ASP cc_start: 0.8442 (m-30) cc_final: 0.8108 (m-30) REVERT: A 384 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7910 (pm20) REVERT: A 390 GLN cc_start: 0.8902 (mt0) cc_final: 0.8672 (mt0) REVERT: A 406 ASP cc_start: 0.8381 (m-30) cc_final: 0.8105 (m-30) REVERT: A 407 ILE cc_start: 0.9107 (mt) cc_final: 0.8765 (mt) REVERT: A 446 ARG cc_start: 0.8463 (mtm110) cc_final: 0.8202 (mtm110) REVERT: A 459 LYS cc_start: 0.8831 (mtmm) cc_final: 0.8373 (ttmm) REVERT: A 479 TYR cc_start: 0.9123 (t80) cc_final: 0.8884 (t80) REVERT: A 493 MET cc_start: 0.9343 (tmm) cc_final: 0.9015 (tmm) REVERT: A 505 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8546 (mt-10) REVERT: A 515 ASP cc_start: 0.8975 (m-30) cc_final: 0.8574 (m-30) REVERT: A 570 MET cc_start: 0.9176 (mtp) cc_final: 0.8959 (mtp) REVERT: A 588 GLN cc_start: 0.9218 (mm-40) cc_final: 0.8989 (tp40) REVERT: A 615 MET cc_start: 0.9317 (mmp) cc_final: 0.8625 (mmp) REVERT: A 632 MET cc_start: 0.8894 (mtp) cc_final: 0.8681 (mtp) REVERT: A 640 MET cc_start: 0.9636 (OUTLIER) cc_final: 0.8917 (tpp) REVERT: A 647 HIS cc_start: 0.9122 (m-70) cc_final: 0.8768 (m170) REVERT: A 668 ASN cc_start: 0.9651 (m-40) cc_final: 0.9321 (m-40) REVERT: B 30 LYS cc_start: 0.9421 (tptt) cc_final: 0.9145 (tptt) REVERT: B 31 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8522 (mp0) REVERT: B 65 GLU cc_start: 0.8595 (mm-30) cc_final: 0.8221 (mm-30) REVERT: B 95 MET cc_start: 0.9214 (tpp) cc_final: 0.8198 (tpp) REVERT: B 99 LYS cc_start: 0.9404 (mmtt) cc_final: 0.8560 (tppp) REVERT: B 112 LYS cc_start: 0.9547 (mmmt) cc_final: 0.9227 (mmmt) REVERT: B 119 GLU cc_start: 0.8998 (mp0) cc_final: 0.8349 (mp0) REVERT: B 128 PHE cc_start: 0.9512 (t80) cc_final: 0.9222 (t80) REVERT: B 149 TYR cc_start: 0.9444 (t80) cc_final: 0.8257 (t80) REVERT: B 161 ARG cc_start: 0.8390 (ttm110) cc_final: 0.7289 (ttm110) REVERT: B 164 ARG cc_start: 0.8773 (ptt90) cc_final: 0.8360 (ptt90) REVERT: B 172 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.8459 (mt) REVERT: B 194 LYS cc_start: 0.9531 (OUTLIER) cc_final: 0.9253 (pttt) REVERT: B 202 ASN cc_start: 0.9315 (t0) cc_final: 0.9017 (t0) REVERT: B 204 SER cc_start: 0.9279 (m) cc_final: 0.9035 (t) REVERT: B 221 LYS cc_start: 0.9287 (mmtp) cc_final: 0.8910 (mmmm) REVERT: B 263 ASP cc_start: 0.9118 (m-30) cc_final: 0.8756 (m-30) REVERT: B 267 ILE cc_start: 0.9313 (OUTLIER) cc_final: 0.9064 (pp) REVERT: B 296 LYS cc_start: 0.9376 (mttt) cc_final: 0.9079 (mmmt) REVERT: B 357 TYR cc_start: 0.8653 (m-10) cc_final: 0.7869 (m-10) REVERT: B 386 LEU cc_start: 0.9459 (mt) cc_final: 0.9207 (mt) REVERT: B 394 TYR cc_start: 0.9426 (m-80) cc_final: 0.9167 (m-80) REVERT: B 406 ASP cc_start: 0.8185 (m-30) cc_final: 0.7972 (t0) REVERT: B 415 ASN cc_start: 0.9292 (t0) cc_final: 0.9008 (t0) REVERT: B 447 ASN cc_start: 0.8689 (m-40) cc_final: 0.8039 (m-40) REVERT: B 459 LYS cc_start: 0.9240 (mttp) cc_final: 0.8693 (mtmm) REVERT: B 467 ASN cc_start: 0.9148 (t0) cc_final: 0.8874 (m-40) REVERT: B 483 GLU cc_start: 0.9314 (mp0) cc_final: 0.8866 (pm20) REVERT: B 493 MET cc_start: 0.9609 (tmm) cc_final: 0.9052 (tmm) REVERT: B 494 MET cc_start: 0.9231 (ttm) cc_final: 0.8973 (mmt) REVERT: B 548 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8356 (mm-30) REVERT: B 586 TYR cc_start: 0.9130 (m-80) cc_final: 0.8551 (m-10) REVERT: B 610 LYS cc_start: 0.9039 (ptpt) cc_final: 0.8516 (ptmt) REVERT: B 613 TYR cc_start: 0.9056 (t80) cc_final: 0.8785 (t80) REVERT: B 615 MET cc_start: 0.9278 (mmp) cc_final: 0.9061 (mmp) REVERT: B 618 LEU cc_start: 0.9533 (tp) cc_final: 0.9162 (mp) REVERT: B 628 GLU cc_start: 0.8887 (mt-10) cc_final: 0.8676 (mm-30) REVERT: B 632 MET cc_start: 0.8464 (ttp) cc_final: 0.8068 (mtp) REVERT: B 645 GLN cc_start: 0.9585 (tp40) cc_final: 0.9090 (tp-100) REVERT: B 659 LYS cc_start: 0.7696 (tptt) cc_final: 0.7415 (tptt) REVERT: C 174 TYR cc_start: 0.4415 (OUTLIER) cc_final: 0.4027 (t80) REVERT: C 245 ASP cc_start: 0.8587 (t70) cc_final: 0.8203 (m-30) REVERT: C 256 VAL cc_start: 0.3710 (t) cc_final: 0.3410 (t) REVERT: D 46 TYR cc_start: 0.9424 (m-10) cc_final: 0.8831 (m-10) REVERT: D 80 HIS cc_start: 0.7943 (m90) cc_final: 0.7015 (t-90) REVERT: D 95 MET cc_start: 0.8111 (tmm) cc_final: 0.7752 (tmm) REVERT: D 98 ASN cc_start: 0.8490 (m-40) cc_final: 0.8182 (m-40) REVERT: D 110 MET cc_start: 0.8369 (ppp) cc_final: 0.7690 (ptt) REVERT: D 155 LYS cc_start: 0.9254 (mttt) cc_final: 0.8703 (mmmm) REVERT: D 162 TYR cc_start: 0.9141 (m-10) cc_final: 0.8726 (m-80) REVERT: D 185 MET cc_start: 0.7114 (mmm) cc_final: 0.6854 (mmm) REVERT: D 281 ASP cc_start: 0.7822 (OUTLIER) cc_final: 0.7384 (t70) REVERT: D 316 LYS cc_start: 0.9064 (tmmt) cc_final: 0.8838 (tmmt) REVERT: D 317 ASP cc_start: 0.8625 (t0) cc_final: 0.8353 (t0) outliers start: 78 outliers final: 56 residues processed: 676 average time/residue: 0.2718 time to fit residues: 276.5439 Evaluate side-chains 696 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 630 time to evaluate : 1.927 ------------------------------------------------------------------------------- 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 107 LYS 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 317 MET 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 408 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 451 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 644 ILE 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 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 246 SER Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 286 ASP 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 435 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 499 SER 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 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 142 TYR Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 207 LEU 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 281 ASP Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 315 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 111 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 182 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 127 optimal weight: 0.9980 chunk 188 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 387 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.135674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.094574 restraints weight = 36360.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.098029 restraints weight = 17924.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.100312 restraints weight = 10811.634| |-----------------------------------------------------------------------------| r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 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 = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.7447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16386 Z= 0.189 Angle : 0.790 11.499 22134 Z= 0.405 Chirality : 0.050 0.286 2360 Planarity : 0.004 0.065 2818 Dihedral : 10.591 174.267 2246 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 4.20 % Allowed : 33.33 % Favored : 62.47 % 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: 0.34 (0.18), residues: 1932 helix: 0.58 (0.15), residues: 1135 sheet: 0.22 (0.45), residues: 124 loop : -0.16 (0.22), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 124 HIS 0.017 0.001 HIS A 469 PHE 0.033 0.002 PHE D 168 TYR 0.050 0.002 TYR D 142 ARG 0.007 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04318 ( 871) hydrogen bonds : angle 5.34008 ( 2571) covalent geometry : bond 0.00438 (16386) covalent geometry : angle 0.79004 (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 704 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 632 time to evaluate : 1.930 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.9027 (pt0) cc_final: 0.8511 (pm20) REVERT: A 52 LYS cc_start: 0.9532 (tmtt) cc_final: 0.9122 (tptt) REVERT: A 64 TYR cc_start: 0.9375 (m-10) cc_final: 0.9028 (m-80) REVERT: A 65 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8178 (mp0) REVERT: A 107 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8962 (mmmm) REVERT: A 119 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8162 (mt-10) REVERT: A 121 ARG cc_start: 0.9318 (OUTLIER) cc_final: 0.9017 (tpt90) REVERT: A 147 GLN cc_start: 0.9090 (mt0) cc_final: 0.8005 (mm-40) REVERT: A 172 LEU cc_start: 0.9535 (mp) cc_final: 0.9048 (mp) REVERT: A 232 ASN cc_start: 0.9496 (m-40) cc_final: 0.9163 (m-40) REVERT: A 243 ARG cc_start: 0.7173 (tmt-80) cc_final: 0.6910 (tmt-80) REVERT: A 252 ASN cc_start: 0.9213 (t0) cc_final: 0.8993 (t0) REVERT: A 263 ASP cc_start: 0.8703 (m-30) cc_final: 0.8359 (m-30) REVERT: A 319 MET cc_start: 0.9327 (tpp) cc_final: 0.9073 (tpp) REVERT: A 321 GLU cc_start: 0.9139 (tp30) cc_final: 0.8878 (tp30) REVERT: A 348 MET cc_start: 0.8558 (tmm) cc_final: 0.7641 (tmm) REVERT: A 352 GLU cc_start: 0.8264 (mt-10) cc_final: 0.7535 (mt-10) REVERT: A 362 ASP cc_start: 0.8430 (m-30) cc_final: 0.8104 (m-30) REVERT: A 384 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.7700 (pm20) REVERT: A 390 GLN cc_start: 0.8914 (mt0) cc_final: 0.8703 (mt0) REVERT: A 402 GLU cc_start: 0.8728 (mm-30) cc_final: 0.8481 (mm-30) REVERT: A 406 ASP cc_start: 0.8445 (m-30) cc_final: 0.8176 (m-30) REVERT: A 407 ILE cc_start: 0.9149 (mt) cc_final: 0.8813 (mt) REVERT: A 458 MET cc_start: 0.8625 (mmp) cc_final: 0.8041 (mmp) REVERT: A 459 LYS cc_start: 0.8830 (mtmm) cc_final: 0.8364 (ttmm) REVERT: A 479 TYR cc_start: 0.9138 (t80) cc_final: 0.8919 (t80) REVERT: A 493 MET cc_start: 0.9372 (tmm) cc_final: 0.8974 (tmm) REVERT: A 505 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8518 (mt-10) REVERT: A 515 ASP cc_start: 0.8976 (m-30) cc_final: 0.8541 (m-30) REVERT: A 570 MET cc_start: 0.9165 (mtp) cc_final: 0.8910 (mtp) REVERT: A 590 SER cc_start: 0.9376 (t) cc_final: 0.9140 (m) REVERT: A 615 MET cc_start: 0.9282 (mmp) cc_final: 0.8614 (mmp) REVERT: A 632 MET cc_start: 0.8870 (mtp) cc_final: 0.8667 (mtp) REVERT: A 640 MET cc_start: 0.9671 (OUTLIER) cc_final: 0.8935 (tpp) REVERT: A 668 ASN cc_start: 0.9639 (m-40) cc_final: 0.9325 (m-40) REVERT: B 30 LYS cc_start: 0.9431 (tptt) cc_final: 0.9152 (tptt) REVERT: B 31 GLU cc_start: 0.8882 (OUTLIER) cc_final: 0.8522 (mp0) REVERT: B 65 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8216 (mm-30) REVERT: B 95 MET cc_start: 0.9233 (tpp) cc_final: 0.8166 (tpp) REVERT: B 99 LYS cc_start: 0.9415 (mmtt) cc_final: 0.8569 (tppp) REVERT: B 112 LYS cc_start: 0.9554 (mmmt) cc_final: 0.9232 (mmmt) REVERT: B 119 GLU cc_start: 0.9018 (mp0) cc_final: 0.8355 (mp0) REVERT: B 128 PHE cc_start: 0.9529 (t80) cc_final: 0.9230 (t80) REVERT: B 149 TYR cc_start: 0.9442 (t80) cc_final: 0.8245 (t80) REVERT: B 161 ARG cc_start: 0.8365 (ttm110) cc_final: 0.7372 (ttm110) REVERT: B 164 ARG cc_start: 0.8781 (ptt90) cc_final: 0.8383 (ptt90) REVERT: B 172 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.8476 (mt) REVERT: B 194 LYS cc_start: 0.9545 (OUTLIER) cc_final: 0.9258 (pttt) REVERT: B 202 ASN cc_start: 0.9302 (t0) cc_final: 0.9062 (t0) REVERT: B 204 SER cc_start: 0.9311 (m) cc_final: 0.9102 (t) REVERT: B 211 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7762 (mm-30) REVERT: B 221 LYS cc_start: 0.9284 (mmtp) cc_final: 0.9007 (mmmm) REVERT: B 263 ASP cc_start: 0.9118 (m-30) cc_final: 0.8753 (m-30) REVERT: B 267 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.9082 (pp) REVERT: B 296 LYS cc_start: 0.9351 (mttt) cc_final: 0.9026 (mmmt) REVERT: B 357 TYR cc_start: 0.8760 (m-10) cc_final: 0.8287 (m-10) REVERT: B 361 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8547 (tt0) REVERT: B 394 TYR cc_start: 0.9423 (m-80) cc_final: 0.9146 (m-80) REVERT: B 415 ASN cc_start: 0.9340 (t0) cc_final: 0.9042 (t0) REVERT: B 447 ASN cc_start: 0.8724 (m-40) cc_final: 0.8104 (m-40) REVERT: B 459 LYS cc_start: 0.9270 (mttp) cc_final: 0.8740 (mtmm) REVERT: B 467 ASN cc_start: 0.9068 (t0) cc_final: 0.8862 (m-40) REVERT: B 483 GLU cc_start: 0.9322 (mp0) cc_final: 0.8902 (pm20) REVERT: B 493 MET cc_start: 0.9607 (tmm) cc_final: 0.9040 (tmm) REVERT: B 494 MET cc_start: 0.9265 (ttm) cc_final: 0.8970 (mmt) REVERT: B 548 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8376 (mm-30) REVERT: B 585 SER cc_start: 0.9358 (p) cc_final: 0.8798 (t) REVERT: B 586 TYR cc_start: 0.9120 (m-80) cc_final: 0.8397 (m-10) REVERT: B 613 TYR cc_start: 0.9068 (t80) cc_final: 0.8746 (t80) REVERT: B 618 LEU cc_start: 0.9570 (tp) cc_final: 0.9229 (mp) REVERT: B 628 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8662 (mm-30) REVERT: B 632 MET cc_start: 0.8421 (ttp) cc_final: 0.8040 (mtp) REVERT: B 645 GLN cc_start: 0.9624 (tp40) cc_final: 0.9188 (tp-100) REVERT: C 44 TRP cc_start: 0.7348 (t-100) cc_final: 0.6516 (t-100) REVERT: C 174 TYR cc_start: 0.4432 (OUTLIER) cc_final: 0.4073 (t80) REVERT: C 245 ASP cc_start: 0.8539 (t70) cc_final: 0.8185 (m-30) REVERT: C 256 VAL cc_start: 0.3904 (t) cc_final: 0.3589 (t) REVERT: D 46 TYR cc_start: 0.9406 (m-10) cc_final: 0.8845 (m-10) REVERT: D 80 HIS cc_start: 0.8088 (m90) cc_final: 0.7136 (t-90) REVERT: D 95 MET cc_start: 0.7953 (tmm) cc_final: 0.7434 (tmm) REVERT: D 98 ASN cc_start: 0.8296 (m-40) cc_final: 0.7990 (m-40) REVERT: D 110 MET cc_start: 0.8367 (ppp) cc_final: 0.7671 (ptt) REVERT: D 155 LYS cc_start: 0.9265 (mttt) cc_final: 0.8864 (mmtt) REVERT: D 162 TYR cc_start: 0.9109 (m-10) cc_final: 0.8684 (m-80) REVERT: D 174 TYR cc_start: 0.8820 (OUTLIER) cc_final: 0.8494 (t80) REVERT: D 185 MET cc_start: 0.7076 (mmm) cc_final: 0.6807 (mmm) REVERT: D 242 TYR cc_start: 0.8724 (OUTLIER) cc_final: 0.8498 (m-80) REVERT: D 281 ASP cc_start: 0.7690 (OUTLIER) cc_final: 0.7278 (t70) REVERT: D 316 LYS cc_start: 0.9031 (tmmt) cc_final: 0.8817 (tmmt) outliers start: 72 outliers final: 53 residues processed: 662 average time/residue: 0.2883 time to fit residues: 287.2562 Evaluate side-chains 684 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 618 time to evaluate : 2.272 ------------------------------------------------------------------------------- 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 107 LYS Chi-restraints excluded: chain A residue 121 ARG Chi-restraints excluded: chain A residue 139 GLU 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 317 MET Chi-restraints excluded: chain A residue 320 ASN Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 646 GLN 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 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 246 SER Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 321 GLU 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 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 602 GLU Chi-restraints excluded: chain B residue 611 THR Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 687 THR 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 207 LEU 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 174 TYR Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 242 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 137 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 160 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 120 optimal weight: 0.5980 chunk 135 optimal weight: 0.9990 chunk 148 optimal weight: 20.0000 chunk 127 optimal weight: 0.3980 chunk 68 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- 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 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 GLN ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN C 214 ASN ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.138547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.097229 restraints weight = 36553.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.100830 restraints weight = 17629.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.103053 restraints weight = 10730.409| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3202 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3202 r_free = 0.3202 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3202 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.7673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16386 Z= 0.160 Angle : 0.819 16.513 22134 Z= 0.413 Chirality : 0.050 0.308 2360 Planarity : 0.004 0.067 2818 Dihedral : 10.407 167.622 2245 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.79 % Allowed : 34.27 % Favored : 61.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.18), residues: 1932 helix: 0.60 (0.15), residues: 1130 sheet: -0.27 (0.42), residues: 142 loop : -0.19 (0.23), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 124 HIS 0.017 0.001 HIS A 469 PHE 0.033 0.002 PHE D 168 TYR 0.053 0.002 TYR D 142 ARG 0.014 0.001 ARG A 446 Details of bonding type rmsd hydrogen bonds : bond 0.04294 ( 871) hydrogen bonds : angle 5.34979 ( 2571) covalent geometry : bond 0.00370 (16386) covalent geometry : angle 0.81938 (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 692 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 627 time to evaluate : 1.781 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: 0.9014 (pt0) cc_final: 0.8493 (pm20) REVERT: A 52 LYS cc_start: 0.9572 (tmtt) cc_final: 0.9151 (tptt) REVERT: A 107 LYS cc_start: 0.9274 (OUTLIER) cc_final: 0.8937 (mmmm) REVERT: A 119 GLU cc_start: 0.8499 (mt-10) cc_final: 0.8131 (mt-10) REVERT: A 121 ARG cc_start: 0.9255 (OUTLIER) cc_final: 0.8928 (tpt90) REVERT: A 161 ARG cc_start: 0.8562 (ttm110) cc_final: 0.8184 (ttm-80) REVERT: A 172 LEU cc_start: 0.9538 (mp) cc_final: 0.9058 (mp) REVERT: A 184 ARG cc_start: 0.9278 (mmm-85) cc_final: 0.8819 (tpt90) REVERT: A 221 LYS cc_start: 0.9399 (mmtp) cc_final: 0.8569 (mttt) REVERT: A 232 ASN cc_start: 0.9420 (m-40) cc_final: 0.9146 (m-40) REVERT: A 243 ARG cc_start: 0.7325 (tmt-80) cc_final: 0.7063 (tmt-80) REVERT: A 252 ASN cc_start: 0.9147 (t0) cc_final: 0.8936 (t0) REVERT: A 263 ASP cc_start: 0.8674 (m-30) cc_final: 0.8323 (m-30) REVERT: A 319 MET cc_start: 0.9321 (tpp) cc_final: 0.9024 (tpp) REVERT: A 321 GLU cc_start: 0.9112 (tp30) cc_final: 0.8861 (tp30) REVERT: A 348 MET cc_start: 0.8504 (tmm) cc_final: 0.8035 (tmm) REVERT: A 362 ASP cc_start: 0.8376 (m-30) cc_final: 0.7958 (m-30) REVERT: A 384 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7874 (pm20) REVERT: A 390 GLN cc_start: 0.8932 (mt0) cc_final: 0.8705 (mt0) REVERT: A 402 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8452 (mm-30) REVERT: A 406 ASP cc_start: 0.8365 (m-30) cc_final: 0.8113 (m-30) REVERT: A 407 ILE cc_start: 0.9117 (mt) cc_final: 0.8808 (mt) REVERT: A 458 MET cc_start: 0.8451 (mmp) cc_final: 0.7871 (mmp) REVERT: A 459 LYS cc_start: 0.8787 (mtmm) cc_final: 0.8309 (ttmm) REVERT: A 493 MET cc_start: 0.9307 (tmm) cc_final: 0.8928 (tmm) REVERT: A 505 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8550 (mt-10) REVERT: A 515 ASP cc_start: 0.8985 (m-30) cc_final: 0.8629 (m-30) REVERT: A 615 MET cc_start: 0.9324 (mmp) cc_final: 0.8627 (mmp) REVERT: A 640 MET cc_start: 0.9663 (OUTLIER) cc_final: 0.9030 (tpp) REVERT: A 646 GLN cc_start: 0.9337 (OUTLIER) cc_final: 0.8745 (pm20) REVERT: A 668 ASN cc_start: 0.9635 (m-40) cc_final: 0.9276 (m-40) REVERT: B 30 LYS cc_start: 0.9441 (tptt) cc_final: 0.9161 (tptt) REVERT: B 31 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8503 (mp0) REVERT: B 65 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8218 (mm-30) REVERT: B 95 MET cc_start: 0.9210 (tpp) cc_final: 0.8063 (tpp) REVERT: B 98 PHE cc_start: 0.9635 (t80) cc_final: 0.9368 (t80) REVERT: B 99 LYS cc_start: 0.9390 (mmtt) cc_final: 0.8530 (tppp) REVERT: B 112 LYS cc_start: 0.9489 (mmmt) cc_final: 0.9147 (mmmt) REVERT: B 116 GLU cc_start: 0.8983 (mt-10) cc_final: 0.8664 (mp0) REVERT: B 117 ARG cc_start: 0.8978 (mtp85) cc_final: 0.8618 (mtp85) REVERT: B 119 GLU cc_start: 0.8903 (mp0) cc_final: 0.8186 (mp0) REVERT: B 128 PHE cc_start: 0.9522 (t80) cc_final: 0.9237 (t80) REVERT: B 147 GLN cc_start: 0.9471 (mt0) cc_final: 0.9098 (mm-40) REVERT: B 149 TYR cc_start: 0.9377 (t80) cc_final: 0.8250 (t80) REVERT: B 161 ARG cc_start: 0.8423 (ttm110) cc_final: 0.7519 (ttm110) REVERT: B 194 LYS cc_start: 0.9528 (OUTLIER) cc_final: 0.9251 (pttt) REVERT: B 202 ASN cc_start: 0.9307 (t0) cc_final: 0.9101 (t0) REVERT: B 211 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7763 (mm-30) REVERT: B 257 ASP cc_start: 0.9181 (m-30) cc_final: 0.8669 (m-30) REVERT: B 263 ASP cc_start: 0.9084 (m-30) cc_final: 0.8711 (m-30) REVERT: B 267 ILE cc_start: 0.9289 (OUTLIER) cc_final: 0.9021 (pp) REVERT: B 296 LYS cc_start: 0.9355 (mttt) cc_final: 0.9008 (mmmt) REVERT: B 357 TYR cc_start: 0.8580 (m-10) cc_final: 0.8297 (m-10) REVERT: B 361 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8530 (tp40) REVERT: B 366 LYS cc_start: 0.9526 (ptpt) cc_final: 0.9284 (ptmm) REVERT: B 394 TYR cc_start: 0.9361 (m-80) cc_final: 0.9077 (m-80) REVERT: B 415 ASN cc_start: 0.9315 (t0) cc_final: 0.9084 (t0) REVERT: B 447 ASN cc_start: 0.8723 (m-40) cc_final: 0.7561 (m-40) REVERT: B 459 LYS cc_start: 0.9275 (mttp) cc_final: 0.8625 (mtmm) REVERT: B 467 ASN cc_start: 0.9029 (t0) cc_final: 0.8811 (m-40) REVERT: B 493 MET cc_start: 0.9568 (tmm) cc_final: 0.9030 (tmm) REVERT: B 494 MET cc_start: 0.9238 (ttm) cc_final: 0.8909 (mmt) REVERT: B 546 LEU cc_start: 0.9549 (mm) cc_final: 0.9270 (tt) REVERT: B 548 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8386 (mm-30) REVERT: B 585 SER cc_start: 0.9319 (p) cc_final: 0.8677 (t) REVERT: B 586 TYR cc_start: 0.9104 (m-80) cc_final: 0.8452 (m-10) REVERT: B 588 GLN cc_start: 0.9539 (mm-40) cc_final: 0.9145 (mm-40) REVERT: B 613 TYR cc_start: 0.8999 (t80) cc_final: 0.8687 (t80) REVERT: B 618 LEU cc_start: 0.9535 (tp) cc_final: 0.9195 (mp) REVERT: B 632 MET cc_start: 0.8338 (ttp) cc_final: 0.8045 (mtp) REVERT: C 44 TRP cc_start: 0.7275 (t-100) cc_final: 0.6820 (t-100) REVERT: C 174 TYR cc_start: 0.4494 (OUTLIER) cc_final: 0.4110 (t80) REVERT: C 245 ASP cc_start: 0.8538 (t70) cc_final: 0.8153 (m-30) REVERT: C 256 VAL cc_start: 0.3598 (t) cc_final: 0.3274 (t) REVERT: D 46 TYR cc_start: 0.9378 (m-10) cc_final: 0.8829 (m-10) REVERT: D 80 HIS cc_start: 0.8056 (m90) cc_final: 0.7419 (t-90) REVERT: D 95 MET cc_start: 0.7935 (tmm) cc_final: 0.7485 (tmm) REVERT: D 98 ASN cc_start: 0.8176 (m-40) cc_final: 0.7882 (m-40) REVERT: D 110 MET cc_start: 0.8253 (ppp) cc_final: 0.7788 (ppp) REVERT: D 127 GLN cc_start: 0.9276 (OUTLIER) cc_final: 0.8729 (mp10) REVERT: D 155 LYS cc_start: 0.9259 (mttt) cc_final: 0.8816 (mmmm) REVERT: D 157 MET cc_start: 0.9559 (ptp) cc_final: 0.9301 (ppp) REVERT: D 162 TYR cc_start: 0.9060 (m-10) cc_final: 0.8628 (m-80) REVERT: D 174 TYR cc_start: 0.8833 (OUTLIER) cc_final: 0.8426 (t80) REVERT: D 242 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.8445 (m-80) REVERT: D 281 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.6801 (t70) REVERT: D 316 LYS cc_start: 0.8945 (tmmt) cc_final: 0.8707 (tmmt) outliers start: 65 outliers final: 45 residues processed: 653 average time/residue: 0.2893 time to fit residues: 283.2459 Evaluate side-chains 677 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 618 time to evaluate : 1.760 ------------------------------------------------------------------------------- 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 107 LYS Chi-restraints excluded: chain A residue 121 ARG 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 317 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 424 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 451 VAL Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 640 MET Chi-restraints excluded: chain A residue 646 GLN 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 267 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 443 THR Chi-restraints excluded: chain B residue 570 MET 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 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 207 LEU Chi-restraints excluded: chain C residue 250 VAL Chi-restraints excluded: chain C residue 312 VAL 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 174 TYR 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 312 VAL 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: 4.9990 chunk 2 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 179 optimal weight: 9.9990 chunk 190 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 180 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** 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 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN 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 = 0.3752 r_free = 0.3752 target = 0.137416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.096215 restraints weight = 36538.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.099656 restraints weight = 18122.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.101811 restraints weight = 10924.253| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 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 = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.7787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 16386 Z= 0.178 Angle : 0.825 16.235 22134 Z= 0.418 Chirality : 0.050 0.272 2360 Planarity : 0.004 0.062 2818 Dihedral : 10.276 163.635 2245 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.08 % Allowed : 34.27 % Favored : 61.66 % 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: 0.28 (0.18), residues: 1932 helix: 0.60 (0.15), residues: 1122 sheet: -0.35 (0.42), residues: 142 loop : -0.17 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 124 HIS 0.017 0.001 HIS A 469 PHE 0.032 0.002 PHE D 168 TYR 0.052 0.002 TYR D 142 ARG 0.013 0.001 ARG A 446 Details of bonding type rmsd hydrogen bonds : bond 0.04282 ( 871) hydrogen bonds : angle 5.35017 ( 2571) covalent geometry : bond 0.00416 (16386) covalent geometry : angle 0.82486 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7141.60 seconds wall clock time: 124 minutes 52.60 seconds (7492.60 seconds total)