Starting phenix.real_space_refine on Thu Aug 6 15:06:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzf_45066/08_2026/9bzf_45066_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzf_45066/08_2026/9bzf_45066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bzf_45066/08_2026/9bzf_45066_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzf_45066/08_2026/9bzf_45066_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bzf_45066/08_2026/9bzf_45066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzf_45066/08_2026/9bzf_45066.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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: 3.59, per 1000 atoms: 0.22 Number of scatterers: 16038 At special positions: 0 Unit cell: (100.386, 126.75, 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: 1.35 Conformation dependent library (CDL) restraints added in 706.6 milliseconds 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: 0.47 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: 4.093A 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: 3.664A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A 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: 3.695A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.393A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.628A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.676A 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: 3.873A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.646A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.027A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.118A 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: 4.067A 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: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.934A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.669A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.876A 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: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.901A 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: 8.394A 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: 7.799A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.478A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.185A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.049A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.751A 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: 2.84 Time building geometry restraints manager: 1.77 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: 4889 1.34 - 1.46: 3089 1.46 - 1.58: 8227 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" O3B TTP A 803 " pdb=" PG TTP A 803 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.610 0.138 2.00e-02 2.50e+03 4.79e+01 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=" O3A TTP A 803 " pdb=" PB TTP A 803 " ideal model delta sigma weight residual 1.675 1.606 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 21521 2.10 - 4.19: 532 4.19 - 6.29: 64 6.29 - 8.39: 8 8.39 - 10.49: 9 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 110.54 116.61 -6.07 1.36e+00 5.41e-01 1.99e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.09 -4.38 1.15e+00 7.56e-01 1.45e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.83 -4.33 1.23e+00 6.61e-01 1.24e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.67 -3.96 1.15e+00 7.56e-01 1.18e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.55 3.64 1.06e+00 8.90e-01 1.18e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.06: 9089 25.06 - 50.13: 656 50.13 - 75.19: 125 75.19 - 100.26: 26 100.26 - 125.32: 2 Dihedral angle restraints: 9898 sinusoidal: 4140 harmonic: 5758 Sorted by residual: dihedral pdb=" O4' GDP A 802 " pdb=" C1' GDP A 802 " pdb=" N9 GDP A 802 " pdb=" C8 GDP A 802 " ideal model delta sinusoidal sigma weight residual 27.02 -98.30 125.32 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" O4' GDP B 804 " pdb=" C1' GDP B 804 " pdb=" N9 GDP B 804 " pdb=" C8 GDP B 804 " ideal model delta sinusoidal sigma weight residual 27.02 -95.58 122.60 1 2.00e+01 2.50e-03 3.69e+01 dihedral pdb=" C VAL C 125 " pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual -122.00 -134.36 12.36 0 2.50e+00 1.60e-01 2.44e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2136 0.093 - 0.187: 192 0.187 - 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 5.44e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+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 " -0.018 2.00e-02 2.50e+03 1.13e-02 2.22e+00 pdb=" CG PHE D 92 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 177 " -0.017 2.00e-02 2.50e+03 9.84e-03 1.94e+00 pdb=" CG TYR C 177 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR C 177 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 177 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 177 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 177 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 177 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 177 " -0.010 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 132 2.51 - 3.11: 11553 3.11 - 3.70: 27046 3.70 - 4.30: 41515 4.30 - 4.90: 65404 Nonbonded interactions: 145650 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.012 3.040 ... (remaining 145645 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: 1.110 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.810 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 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: 0.020 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5783 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 0.139 16386 Z= 0.334 Angle : 0.788 10.486 22134 Z= 0.471 Chirality : 0.058 0.466 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.681 125.324 6202 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.34 % Allowed : 15.33 % Favored : 83.33 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.18), residues: 1932 helix: 0.59 (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 ARG 0.003 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.33 (16386) covalent geometry : angle 0.78778 / 0.47 (22134) hydrogen bonds : bond 0.15420 / 9.51 ( 871) hydrogen bonds : angle 6.51691 / 4.65 ( 2571) *********************** 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 901 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 878 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8173 (t0) cc_final: 0.7969 (t70) REVERT: A 37 PHE cc_start: 0.6566 (m-80) cc_final: 0.6213 (m-10) REVERT: A 41 ILE cc_start: 0.8350 (mm) cc_final: 0.8058 (mm) REVERT: A 101 TYR cc_start: 0.7570 (m-80) cc_final: 0.7216 (m-10) REVERT: A 119 GLU cc_start: 0.7561 (mp0) cc_final: 0.6800 (mp0) REVERT: A 143 LEU cc_start: 0.8763 (tp) cc_final: 0.8409 (tp) REVERT: A 168 VAL cc_start: 0.8904 (t) cc_final: 0.8646 (t) REVERT: A 181 ASP cc_start: 0.8597 (m-30) cc_final: 0.8145 (m-30) REVERT: A 191 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7520 (mm110) REVERT: A 258 ILE cc_start: 0.8700 (tp) cc_final: 0.8402 (tp) REVERT: A 264 THR cc_start: 0.8999 (p) cc_final: 0.8787 (m) REVERT: A 278 LEU cc_start: 0.8386 (tp) cc_final: 0.8154 (tp) REVERT: A 322 MET cc_start: 0.7510 (mmp) cc_final: 0.6584 (mmm) REVERT: A 362 ASP cc_start: 0.5877 (m-30) cc_final: 0.4814 (m-30) REVERT: A 425 ILE cc_start: 0.9125 (mt) cc_final: 0.8814 (mt) REVERT: A 431 LEU cc_start: 0.9210 (mt) cc_final: 0.8870 (mm) REVERT: A 436 LEU cc_start: 0.9165 (mt) cc_final: 0.8809 (mt) REVERT: A 447 ASN cc_start: 0.7619 (m-40) cc_final: 0.6723 (m110) REVERT: A 493 MET cc_start: 0.7568 (tmm) cc_final: 0.7062 (tmm) REVERT: A 494 MET cc_start: 0.7764 (mtp) cc_final: 0.7300 (mtp) REVERT: A 500 ILE cc_start: 0.9352 (mt) cc_final: 0.9024 (mt) REVERT: A 522 TYR cc_start: 0.7435 (m-80) cc_final: 0.6453 (m-10) REVERT: A 531 TYR cc_start: 0.6454 (m-80) cc_final: 0.6064 (m-80) REVERT: A 558 TRP cc_start: 0.8229 (m100) cc_final: 0.6925 (m100) REVERT: A 561 LEU cc_start: 0.8853 (tp) cc_final: 0.8601 (tp) REVERT: A 571 TYR cc_start: 0.6916 (t80) cc_final: 0.6597 (t80) REVERT: A 575 ARG cc_start: 0.8503 (mtm110) cc_final: 0.7973 (ptp90) REVERT: A 655 THR cc_start: 0.8855 (m) cc_final: 0.8483 (t) REVERT: A 684 TYR cc_start: 0.5726 (m-80) cc_final: 0.4259 (m-80) REVERT: B 41 ILE cc_start: 0.8888 (mm) cc_final: 0.8443 (mm) REVERT: B 51 LEU cc_start: 0.8225 (tp) cc_final: 0.7877 (tp) REVERT: B 78 LYS cc_start: 0.8360 (tttp) cc_final: 0.8114 (tttt) REVERT: B 95 MET cc_start: 0.6967 (tpp) cc_final: 0.6615 (tpp) REVERT: B 99 LYS cc_start: 0.8995 (mmtt) cc_final: 0.8748 (mmtt) REVERT: B 121 ARG cc_start: 0.8271 (tpm170) cc_final: 0.7561 (tpp-160) REVERT: B 122 ILE cc_start: 0.9011 (mt) cc_final: 0.8360 (mt) REVERT: B 147 GLN cc_start: 0.8114 (mt0) cc_final: 0.6125 (mt0) REVERT: B 157 LEU cc_start: 0.8161 (tp) cc_final: 0.7915 (tp) REVERT: B 172 LEU cc_start: 0.9041 (mp) cc_final: 0.8741 (mp) REVERT: B 181 ASP cc_start: 0.8259 (m-30) cc_final: 0.7809 (m-30) REVERT: B 191 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7852 (mm-40) REVERT: B 204 SER cc_start: 0.8945 (m) cc_final: 0.8457 (p) REVERT: B 258 ILE cc_start: 0.8950 (tp) cc_final: 0.8705 (tp) REVERT: B 291 LEU cc_start: 0.9105 (mt) cc_final: 0.8877 (mt) REVERT: B 319 MET cc_start: 0.7375 (tpp) cc_final: 0.7014 (mmp) REVERT: B 322 MET cc_start: 0.7547 (mmm) cc_final: 0.7007 (mmm) REVERT: B 467 ASN cc_start: 0.8417 (t0) cc_final: 0.8183 (m-40) REVERT: B 469 HIS cc_start: 0.8278 (t-170) cc_final: 0.7981 (t70) REVERT: B 515 ASP cc_start: 0.8433 (m-30) cc_final: 0.8185 (m-30) REVERT: B 522 TYR cc_start: 0.7414 (m-80) cc_final: 0.6996 (m-10) REVERT: B 570 MET cc_start: 0.6616 (mtm) cc_final: 0.5996 (mtm) REVERT: B 587 VAL cc_start: 0.8980 (t) cc_final: 0.8642 (t) REVERT: B 588 GLN cc_start: 0.7762 (mm-40) cc_final: 0.6652 (mm-40) REVERT: B 589 SER cc_start: 0.8503 (m) cc_final: 0.8043 (p) REVERT: B 627 LYS cc_start: 0.8225 (tttt) cc_final: 0.7889 (tttp) REVERT: B 631 ASP cc_start: 0.7629 (m-30) cc_final: 0.7177 (t0) REVERT: B 644 ILE cc_start: 0.8499 (mt) cc_final: 0.8200 (mt) REVERT: B 655 THR cc_start: 0.9341 (m) cc_final: 0.8555 (t) REVERT: C 56 MET cc_start: -0.0067 (mmm) cc_final: -0.0508 (ttp) REVERT: C 90 LEU cc_start: 0.5964 (mt) cc_final: 0.5475 (mt) REVERT: C 95 MET cc_start: 0.5795 (tmm) cc_final: 0.5485 (tmm) REVERT: D 185 MET cc_start: 0.2872 (mmm) cc_final: 0.0368 (mpp) outliers start: 23 outliers final: 6 residues processed: 887 average time/residue: 0.1473 time to fit residues: 189.0545 Evaluate side-chains 612 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 606 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 242 GLN A 304 HIS A 320 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN A 645 GLN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 218 ASN B 313 HIS B 645 GLN C 24 GLN C 28 GLN C 186 GLN C 238 ASN D 80 HIS ** 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.146509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.098573 restraints weight = 43214.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.102133 restraints weight = 26080.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.104443 restraints weight = 17683.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.105970 restraints weight = 13241.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.107173 restraints weight = 10591.599| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 11 (17 function evaluations) r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16386 Z= 0.166 Angle : 0.621 9.391 22134 Z= 0.332 Chirality : 0.042 0.208 2360 Planarity : 0.004 0.058 2818 Dihedral : 9.598 126.597 2290 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.23 % Allowed : 2.80 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.19), residues: 1932 helix: 1.51 (0.15), residues: 1121 sheet: -0.32 (0.39), residues: 148 loop : 0.58 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 446 TYR 0.029 0.002 TYR A 498 PHE 0.036 0.002 PHE D 320 TRP 0.010 0.001 TRP C 30 HIS 0.008 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (16386) covalent geometry : angle 0.62087 / 0.33 (22134) hydrogen bonds : bond 0.04543 / 2.90 ( 871) hydrogen bonds : angle 5.03433 / 3.58 ( 2571) *********************** 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 740 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 736 time to evaluate : 0.629 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: A 29 ASP cc_start: 0.9316 (t0) cc_final: 0.9010 (t70) REVERT: A 40 TYR cc_start: 0.9127 (t80) cc_final: 0.8798 (t80) REVERT: A 51 LEU cc_start: 0.9375 (tp) cc_final: 0.9024 (tp) REVERT: A 89 PHE cc_start: 0.8842 (t80) cc_final: 0.8155 (t80) REVERT: A 119 GLU cc_start: 0.9174 (mp0) cc_final: 0.8473 (tm-30) REVERT: A 143 LEU cc_start: 0.9375 (tp) cc_final: 0.8923 (tp) REVERT: A 148 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8458 (mt-10) REVERT: A 181 ASP cc_start: 0.9114 (m-30) cc_final: 0.8910 (m-30) REVERT: A 191 GLN cc_start: 0.9438 (mm-40) cc_final: 0.9069 (mm-40) REVERT: A 195 LEU cc_start: 0.9557 (mt) cc_final: 0.9308 (mt) REVERT: A 227 MET cc_start: 0.9227 (mtm) cc_final: 0.9026 (mtm) REVERT: A 235 ARG cc_start: 0.8757 (mtm110) cc_final: 0.8529 (mtm110) REVERT: A 252 ASN cc_start: 0.9356 (t0) cc_final: 0.8879 (t0) REVERT: A 307 TYR cc_start: 0.9521 (t80) cc_final: 0.9296 (t80) REVERT: A 322 MET cc_start: 0.9097 (mmp) cc_final: 0.8669 (mmm) REVERT: A 335 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7718 (mm-30) REVERT: A 342 LEU cc_start: 0.9608 (tp) cc_final: 0.9292 (tp) REVERT: A 350 ARG cc_start: 0.8565 (mmm-85) cc_final: 0.8115 (mmm-85) REVERT: A 370 ASN cc_start: 0.9352 (m-40) cc_final: 0.8980 (m110) REVERT: A 402 GLU cc_start: 0.8528 (mp0) cc_final: 0.8249 (mp0) REVERT: A 447 ASN cc_start: 0.8895 (m-40) cc_final: 0.8140 (m-40) REVERT: A 459 LYS cc_start: 0.9120 (mttp) cc_final: 0.8623 (mtmt) REVERT: A 468 LEU cc_start: 0.9779 (tp) cc_final: 0.9483 (tp) REVERT: A 472 LEU cc_start: 0.9732 (mt) cc_final: 0.9446 (mt) REVERT: A 500 ILE cc_start: 0.9654 (mt) cc_final: 0.9271 (mt) REVERT: A 515 ASP cc_start: 0.9227 (m-30) cc_final: 0.8889 (m-30) REVERT: A 522 TYR cc_start: 0.9222 (m-80) cc_final: 0.8747 (m-10) REVERT: A 570 MET cc_start: 0.9005 (mtp) cc_final: 0.7606 (mtp) REVERT: A 575 ARG cc_start: 0.9135 (mtm110) cc_final: 0.8296 (ptp90) REVERT: A 598 MET cc_start: 0.9264 (mtp) cc_final: 0.8638 (mmt) REVERT: A 615 MET cc_start: 0.8710 (mmp) cc_final: 0.8231 (mmp) REVERT: A 632 MET cc_start: 0.8917 (mtp) cc_final: 0.8492 (mtm) REVERT: A 645 GLN cc_start: 0.8761 (tp40) cc_final: 0.8522 (tp-100) REVERT: A 650 GLN cc_start: 0.8773 (mt0) cc_final: 0.8176 (mt0) REVERT: A 657 PHE cc_start: 0.8454 (m-80) cc_final: 0.7694 (m-80) REVERT: B 15 GLU cc_start: 0.9179 (tp30) cc_final: 0.8630 (tp30) REVERT: B 51 LEU cc_start: 0.9222 (tp) cc_final: 0.8791 (tp) REVERT: B 62 GLN cc_start: 0.9619 (mp-120) cc_final: 0.8962 (mp10) REVERT: B 65 GLU cc_start: 0.8992 (mm-30) cc_final: 0.8764 (mm-30) REVERT: B 95 MET cc_start: 0.9143 (tpp) cc_final: 0.8521 (tpp) REVERT: B 99 LYS cc_start: 0.9532 (mmmt) cc_final: 0.9035 (mmmt) REVERT: B 115 LEU cc_start: 0.9437 (mt) cc_final: 0.9234 (mt) REVERT: B 117 ARG cc_start: 0.9071 (ttm110) cc_final: 0.8771 (ttm110) REVERT: B 119 GLU cc_start: 0.9263 (mp0) cc_final: 0.8829 (mp0) REVERT: B 122 ILE cc_start: 0.9718 (mt) cc_final: 0.9478 (mt) REVERT: B 140 TYR cc_start: 0.9194 (m-80) cc_final: 0.8908 (m-10) REVERT: B 144 MET cc_start: 0.9238 (mtm) cc_final: 0.8826 (mtm) REVERT: B 147 GLN cc_start: 0.9255 (mt0) cc_final: 0.8856 (mt0) REVERT: B 205 LYS cc_start: 0.9406 (mmmt) cc_final: 0.8973 (mmmm) REVERT: B 211 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8295 (mm-30) REVERT: B 227 MET cc_start: 0.9414 (mtp) cc_final: 0.9160 (mtp) REVERT: B 236 TYR cc_start: 0.8988 (t80) cc_final: 0.8587 (t80) REVERT: B 251 LEU cc_start: 0.9496 (tp) cc_final: 0.9168 (tp) REVERT: B 283 VAL cc_start: 0.9478 (t) cc_final: 0.9268 (t) REVERT: B 286 ASP cc_start: 0.8709 (m-30) cc_final: 0.8231 (m-30) REVERT: B 288 PHE cc_start: 0.9395 (t80) cc_final: 0.9154 (t80) REVERT: B 291 LEU cc_start: 0.9603 (mt) cc_final: 0.9313 (mt) REVERT: B 308 LYS cc_start: 0.9388 (mtmt) cc_final: 0.9140 (ptpp) REVERT: B 322 MET cc_start: 0.9305 (mmm) cc_final: 0.8738 (mmm) REVERT: B 342 LEU cc_start: 0.9677 (tp) cc_final: 0.9316 (tp) REVERT: B 345 LYS cc_start: 0.9475 (tttt) cc_final: 0.9201 (tttt) REVERT: B 348 MET cc_start: 0.9287 (tpp) cc_final: 0.8341 (tpp) REVERT: B 362 ASP cc_start: 0.8986 (m-30) cc_final: 0.8110 (m-30) REVERT: B 373 ILE cc_start: 0.9663 (mt) cc_final: 0.9441 (tp) REVERT: B 375 LYS cc_start: 0.9219 (mmtm) cc_final: 0.8785 (mmtm) REVERT: B 393 SER cc_start: 0.9687 (t) cc_final: 0.9070 (p) REVERT: B 398 ASP cc_start: 0.8770 (t70) cc_final: 0.8390 (t70) REVERT: B 403 ILE cc_start: 0.9367 (mp) cc_final: 0.9041 (tp) REVERT: B 427 LYS cc_start: 0.9588 (ptpp) cc_final: 0.9229 (ptpp) REVERT: B 430 LYS cc_start: 0.9149 (ptpp) cc_final: 0.8901 (mtmm) REVERT: B 458 MET cc_start: 0.9411 (mmm) cc_final: 0.8882 (mmm) REVERT: B 494 MET cc_start: 0.9463 (mtt) cc_final: 0.9144 (mtt) REVERT: B 500 ILE cc_start: 0.9747 (mt) cc_final: 0.9419 (mt) REVERT: B 522 TYR cc_start: 0.9082 (m-80) cc_final: 0.8877 (m-10) REVERT: B 531 TYR cc_start: 0.8516 (m-80) cc_final: 0.6530 (m-80) REVERT: B 558 TRP cc_start: 0.9230 (m100) cc_final: 0.8367 (m100) REVERT: B 570 MET cc_start: 0.9449 (mtp) cc_final: 0.8700 (mtp) REVERT: B 586 TYR cc_start: 0.9346 (m-80) cc_final: 0.9063 (m-80) REVERT: B 603 GLU cc_start: 0.8809 (tm-30) cc_final: 0.8096 (tm-30) REVERT: B 615 MET cc_start: 0.8749 (mmp) cc_final: 0.8387 (mmp) REVERT: B 631 ASP cc_start: 0.9401 (m-30) cc_final: 0.9097 (t0) REVERT: B 648 ILE cc_start: 0.9624 (mm) cc_final: 0.9370 (mm) REVERT: B 667 LEU cc_start: 0.9052 (tp) cc_final: 0.8627 (tp) REVERT: B 668 ASN cc_start: 0.9364 (m-40) cc_final: 0.8866 (m-40) REVERT: B 677 ARG cc_start: 0.9650 (mmm160) cc_final: 0.9288 (mmm-85) REVERT: C 95 MET cc_start: 0.8467 (tmm) cc_final: 0.8099 (tmm) REVERT: C 100 VAL cc_start: 0.8939 (t) cc_final: 0.8361 (t) REVERT: C 101 HIS cc_start: 0.8101 (m90) cc_final: 0.7825 (m90) REVERT: C 136 GLN cc_start: 0.0140 (mt0) cc_final: -0.0205 (tp40) REVERT: C 185 MET cc_start: 0.2117 (tmm) cc_final: 0.1539 (mmm) REVERT: D 69 GLN cc_start: 0.8454 (tp40) cc_final: 0.7796 (tm-30) REVERT: D 169 TYR cc_start: 0.8509 (m-80) cc_final: 0.8170 (m-80) REVERT: D 179 TYR cc_start: 0.6611 (t80) cc_final: 0.6146 (t80) REVERT: D 185 MET cc_start: 0.1343 (mmm) cc_final: 0.0772 (mpp) REVERT: D 212 ILE cc_start: 0.8836 (pt) cc_final: 0.8612 (pt) outliers start: 4 outliers final: 0 residues processed: 737 average time/residue: 0.1376 time to fit residues: 149.5458 Evaluate side-chains 591 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 591 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 0.1980 chunk 131 optimal weight: 6.9990 chunk 164 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 182 optimal weight: 0.8980 chunk 159 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 150 optimal weight: 6.9990 chunk 63 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 158 optimal weight: 7.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 147 GLN A 180 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN A 304 HIS ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 GLN B 475 ASN C 127 GLN ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.131857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.087376 restraints weight = 46251.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.090519 restraints weight = 27889.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.092645 restraints weight = 18693.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.094058 restraints weight = 13838.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.095028 restraints weight = 11017.861| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16386 Z= 0.215 Angle : 0.650 8.484 22134 Z= 0.346 Chirality : 0.042 0.171 2360 Planarity : 0.004 0.111 2818 Dihedral : 9.263 130.154 2290 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.12 % Allowed : 3.15 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.19), residues: 1932 helix: 1.39 (0.15), residues: 1117 sheet: -0.48 (0.39), residues: 152 loop : 0.47 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 665 TYR 0.039 0.002 TYR B 612 PHE 0.020 0.002 PHE A 129 TRP 0.025 0.002 TRP C 124 HIS 0.006 0.001 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.22 (16386) covalent geometry : angle 0.64978 / 0.35 (22134) hydrogen bonds : bond 0.04259 / 2.71 ( 871) hydrogen bonds : angle 5.04815 / 3.62 ( 2571) *********************** 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 666 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 664 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9462 (t0) cc_final: 0.9220 (t70) REVERT: A 40 TYR cc_start: 0.9159 (t80) cc_final: 0.8940 (t80) REVERT: A 89 PHE cc_start: 0.9169 (t80) cc_final: 0.8814 (t80) REVERT: A 119 GLU cc_start: 0.9254 (mp0) cc_final: 0.8191 (tm-30) REVERT: A 143 LEU cc_start: 0.9386 (tp) cc_final: 0.8957 (tp) REVERT: A 148 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8299 (mt-10) REVERT: A 150 GLN cc_start: 0.9184 (tp40) cc_final: 0.8942 (tp-100) REVERT: A 172 LEU cc_start: 0.9284 (mp) cc_final: 0.8830 (mp) REVERT: A 181 ASP cc_start: 0.9160 (m-30) cc_final: 0.8848 (m-30) REVERT: A 195 LEU cc_start: 0.9592 (mt) cc_final: 0.9373 (mt) REVERT: A 204 SER cc_start: 0.9370 (m) cc_final: 0.9136 (m) REVERT: A 227 MET cc_start: 0.9342 (mtm) cc_final: 0.9128 (mtm) REVERT: A 250 TYR cc_start: 0.8733 (m-80) cc_final: 0.8317 (m-80) REVERT: A 252 ASN cc_start: 0.9483 (t0) cc_final: 0.9005 (t0) REVERT: A 307 TYR cc_start: 0.9543 (t80) cc_final: 0.9152 (t80) REVERT: A 348 MET cc_start: 0.9334 (ptp) cc_final: 0.9124 (ptp) REVERT: A 350 ARG cc_start: 0.8684 (mmm-85) cc_final: 0.8182 (mmm-85) REVERT: A 370 ASN cc_start: 0.9546 (m-40) cc_final: 0.9254 (m110) REVERT: A 394 TYR cc_start: 0.9261 (m-80) cc_final: 0.9016 (m-80) REVERT: A 406 ASP cc_start: 0.8829 (m-30) cc_final: 0.8499 (m-30) REVERT: A 407 ILE cc_start: 0.9096 (mt) cc_final: 0.8857 (mt) REVERT: A 415 ASN cc_start: 0.9592 (t0) cc_final: 0.8387 (t0) REVERT: A 417 LEU cc_start: 0.9785 (tt) cc_final: 0.9543 (tt) REVERT: A 418 ASN cc_start: 0.9612 (m-40) cc_final: 0.8957 (m-40) REVERT: A 446 ARG cc_start: 0.8312 (mtp85) cc_final: 0.8064 (mtp85) REVERT: A 459 LYS cc_start: 0.9280 (mttp) cc_final: 0.8415 (mtmm) REVERT: A 468 LEU cc_start: 0.9810 (tp) cc_final: 0.9528 (tp) REVERT: A 472 LEU cc_start: 0.9736 (mt) cc_final: 0.9441 (mt) REVERT: A 494 MET cc_start: 0.9528 (mtp) cc_final: 0.9100 (mtp) REVERT: A 499 SER cc_start: 0.9947 (t) cc_final: 0.9706 (p) REVERT: A 500 ILE cc_start: 0.9697 (mt) cc_final: 0.9479 (mt) REVERT: A 515 ASP cc_start: 0.9308 (m-30) cc_final: 0.9062 (m-30) REVERT: A 522 TYR cc_start: 0.9320 (m-80) cc_final: 0.8553 (m-10) REVERT: A 570 MET cc_start: 0.9319 (mtp) cc_final: 0.7798 (mtp) REVERT: A 575 ARG cc_start: 0.9315 (mtm110) cc_final: 0.8607 (ptp90) REVERT: A 586 TYR cc_start: 0.8925 (m-10) cc_final: 0.8722 (m-10) REVERT: A 598 MET cc_start: 0.9233 (mtp) cc_final: 0.8654 (mmm) REVERT: A 602 GLU cc_start: 0.8226 (pt0) cc_final: 0.7399 (pt0) REVERT: A 603 GLU cc_start: 0.8531 (tp30) cc_final: 0.7767 (tp30) REVERT: A 612 TYR cc_start: 0.8822 (m-10) cc_final: 0.8308 (m-80) REVERT: A 615 MET cc_start: 0.8755 (mmp) cc_final: 0.8478 (mmp) REVERT: A 645 GLN cc_start: 0.9001 (tp40) cc_final: 0.8798 (tp-100) REVERT: A 650 GLN cc_start: 0.8820 (mt0) cc_final: 0.8060 (mt0) REVERT: B 15 GLU cc_start: 0.9173 (tp30) cc_final: 0.8666 (tp30) REVERT: B 95 MET cc_start: 0.9193 (tpp) cc_final: 0.8630 (mmm) REVERT: B 99 LYS cc_start: 0.9580 (mmmt) cc_final: 0.9024 (mmmt) REVERT: B 115 LEU cc_start: 0.9561 (mt) cc_final: 0.9281 (mt) REVERT: B 136 LYS cc_start: 0.9588 (mmtp) cc_final: 0.9379 (mmmm) REVERT: B 139 GLU cc_start: 0.9484 (mp0) cc_final: 0.9182 (mp0) REVERT: B 144 MET cc_start: 0.9213 (mtm) cc_final: 0.8821 (mtm) REVERT: B 147 GLN cc_start: 0.9305 (mt0) cc_final: 0.8861 (mt0) REVERT: B 157 LEU cc_start: 0.9591 (tp) cc_final: 0.9360 (tp) REVERT: B 158 ASN cc_start: 0.9606 (m110) cc_final: 0.9112 (p0) REVERT: B 161 ARG cc_start: 0.8850 (ttm110) cc_final: 0.8076 (mtp85) REVERT: B 164 ARG cc_start: 0.9028 (ttp80) cc_final: 0.8678 (ttp80) REVERT: B 191 GLN cc_start: 0.9366 (mm-40) cc_final: 0.9147 (mm-40) REVERT: B 200 SER cc_start: 0.9115 (t) cc_final: 0.8813 (t) REVERT: B 211 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8221 (mm-30) REVERT: B 227 MET cc_start: 0.9451 (mtp) cc_final: 0.9137 (mtp) REVERT: B 251 LEU cc_start: 0.9454 (tp) cc_final: 0.9163 (tp) REVERT: B 286 ASP cc_start: 0.8782 (m-30) cc_final: 0.8286 (m-30) REVERT: B 290 GLU cc_start: 0.9315 (pp20) cc_final: 0.9098 (pp20) REVERT: B 308 LYS cc_start: 0.9390 (mtmt) cc_final: 0.9086 (ptpp) REVERT: B 312 GLN cc_start: 0.9113 (pm20) cc_final: 0.8886 (pm20) REVERT: B 314 MET cc_start: 0.8889 (ttt) cc_final: 0.8688 (ttt) REVERT: B 322 MET cc_start: 0.8769 (mmm) cc_final: 0.8440 (mmm) REVERT: B 342 LEU cc_start: 0.9759 (tp) cc_final: 0.9476 (tp) REVERT: B 345 LYS cc_start: 0.9572 (tttt) cc_final: 0.9206 (tttt) REVERT: B 350 ARG cc_start: 0.8686 (mtp85) cc_final: 0.8298 (mtp85) REVERT: B 362 ASP cc_start: 0.9063 (m-30) cc_final: 0.8073 (m-30) REVERT: B 370 ASN cc_start: 0.9540 (m-40) cc_final: 0.9100 (m110) REVERT: B 373 ILE cc_start: 0.9703 (mt) cc_final: 0.9358 (mt) REVERT: B 393 SER cc_start: 0.9597 (t) cc_final: 0.9064 (t) REVERT: B 398 ASP cc_start: 0.8791 (t70) cc_final: 0.8546 (t70) REVERT: B 402 GLU cc_start: 0.8668 (mp0) cc_final: 0.8325 (mp0) REVERT: B 403 ILE cc_start: 0.9425 (mp) cc_final: 0.8982 (tp) REVERT: B 427 LYS cc_start: 0.9549 (ptpp) cc_final: 0.9343 (ptpp) REVERT: B 494 MET cc_start: 0.9576 (mtt) cc_final: 0.9228 (mtt) REVERT: B 570 MET cc_start: 0.9318 (mtp) cc_final: 0.8598 (mtp) REVERT: B 585 SER cc_start: 0.9059 (p) cc_final: 0.8577 (t) REVERT: B 591 THR cc_start: 0.9058 (p) cc_final: 0.8762 (p) REVERT: B 606 TYR cc_start: 0.8496 (m-80) cc_final: 0.8269 (m-80) REVERT: B 615 MET cc_start: 0.8823 (mmp) cc_final: 0.8413 (mmp) REVERT: B 631 ASP cc_start: 0.9558 (m-30) cc_final: 0.9292 (m-30) REVERT: B 634 MET cc_start: 0.9400 (mmm) cc_final: 0.9089 (mmt) REVERT: B 648 ILE cc_start: 0.9594 (mm) cc_final: 0.9348 (mm) REVERT: B 668 ASN cc_start: 0.9429 (m-40) cc_final: 0.9000 (m-40) REVERT: B 677 ARG cc_start: 0.9657 (mmm160) cc_final: 0.9316 (mmm-85) REVERT: C 56 MET cc_start: -0.1311 (ttp) cc_final: -0.1599 (ttp) REVERT: C 95 MET cc_start: 0.8657 (tmm) cc_final: 0.8330 (tmm) REVERT: C 101 HIS cc_start: 0.7996 (m90) cc_final: 0.7739 (m90) REVERT: C 124 TRP cc_start: 0.7770 (t60) cc_final: 0.7191 (t60) REVERT: D 22 TYR cc_start: 0.5262 (t80) cc_final: 0.4961 (t80) REVERT: D 69 GLN cc_start: 0.8901 (tp40) cc_final: 0.8585 (tm-30) REVERT: D 97 GLU cc_start: 0.1006 (mm-30) cc_final: 0.0397 (mm-30) REVERT: D 146 GLN cc_start: 0.9205 (mt0) cc_final: 0.8978 (tm-30) REVERT: D 179 TYR cc_start: 0.6863 (t80) cc_final: 0.6614 (t80) REVERT: D 185 MET cc_start: 0.1969 (mmm) cc_final: 0.1438 (mpp) REVERT: D 201 HIS cc_start: 0.5860 (m170) cc_final: 0.5243 (m90) outliers start: 2 outliers final: 1 residues processed: 665 average time/residue: 0.1330 time to fit residues: 133.1568 Evaluate side-chains 572 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 571 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 9.9990 chunk 157 optimal weight: 20.0000 chunk 168 optimal weight: 5.9990 chunk 89 optimal weight: 0.0270 chunk 127 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 185 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 159 optimal weight: 9.9990 chunk 182 optimal weight: 9.9990 chunk 93 optimal weight: 4.9990 overall best weight: 2.5642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN A 14 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 HIS ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN D 91 ASN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.129383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.085865 restraints weight = 46184.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.088828 restraints weight = 27723.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.090643 restraints weight = 18613.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.092142 restraints weight = 14053.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.093080 restraints weight = 11210.996| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (19 function evaluations) r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.5899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16386 Z= 0.191 Angle : 0.603 6.338 22134 Z= 0.326 Chirality : 0.041 0.171 2360 Planarity : 0.004 0.070 2818 Dihedral : 9.031 133.307 2290 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.19), residues: 1932 helix: 1.35 (0.15), residues: 1121 sheet: -0.52 (0.38), residues: 154 loop : 0.44 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 117 TYR 0.035 0.002 TYR B 612 PHE 0.024 0.002 PHE A 129 TRP 0.015 0.002 TRP C 124 HIS 0.006 0.001 HIS B 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.19 (16386) covalent geometry : angle 0.60271 / 0.33 (22134) hydrogen bonds : bond 0.03932 / 2.48 ( 871) hydrogen bonds : angle 4.99231 / 3.57 ( 2571) *********************** 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 660 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 660 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9516 (t0) cc_final: 0.9131 (t70) REVERT: A 89 PHE cc_start: 0.9201 (t80) cc_final: 0.8796 (t80) REVERT: A 95 MET cc_start: 0.9084 (tpp) cc_final: 0.8274 (tpt) REVERT: A 116 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8364 (tt0) REVERT: A 117 ARG cc_start: 0.9239 (mtp180) cc_final: 0.8986 (mtt180) REVERT: A 119 GLU cc_start: 0.9228 (mp0) cc_final: 0.8236 (tm-30) REVERT: A 164 ARG cc_start: 0.8271 (ptm-80) cc_final: 0.7490 (ptm-80) REVERT: A 172 LEU cc_start: 0.9329 (mp) cc_final: 0.8951 (mp) REVERT: A 176 ASN cc_start: 0.8995 (t0) cc_final: 0.8504 (m-40) REVERT: A 195 LEU cc_start: 0.9591 (mt) cc_final: 0.9349 (mt) REVERT: A 204 SER cc_start: 0.9395 (m) cc_final: 0.9172 (m) REVERT: A 227 MET cc_start: 0.9333 (mtm) cc_final: 0.9020 (mtm) REVERT: A 251 LEU cc_start: 0.9613 (tp) cc_final: 0.9345 (tp) REVERT: A 252 ASN cc_start: 0.9467 (t0) cc_final: 0.8990 (t0) REVERT: A 307 TYR cc_start: 0.9637 (t80) cc_final: 0.9228 (t80) REVERT: A 320 ASN cc_start: 0.9407 (m-40) cc_final: 0.9079 (m-40) REVERT: A 322 MET cc_start: 0.9057 (tpt) cc_final: 0.8844 (mmm) REVERT: A 348 MET cc_start: 0.9330 (ptp) cc_final: 0.9087 (ptp) REVERT: A 350 ARG cc_start: 0.8754 (mmm-85) cc_final: 0.8219 (mmm-85) REVERT: A 370 ASN cc_start: 0.9621 (m-40) cc_final: 0.9375 (m-40) REVERT: A 394 TYR cc_start: 0.9284 (m-80) cc_final: 0.8660 (m-80) REVERT: A 406 ASP cc_start: 0.8893 (m-30) cc_final: 0.8607 (m-30) REVERT: A 407 ILE cc_start: 0.9165 (mt) cc_final: 0.8635 (mt) REVERT: A 415 ASN cc_start: 0.9281 (t0) cc_final: 0.8593 (t0) REVERT: A 418 ASN cc_start: 0.9501 (m110) cc_final: 0.8875 (m-40) REVERT: A 425 ILE cc_start: 0.9506 (mp) cc_final: 0.9276 (mp) REVERT: A 447 ASN cc_start: 0.9197 (m-40) cc_final: 0.8941 (m-40) REVERT: A 459 LYS cc_start: 0.9399 (mttp) cc_final: 0.8979 (mtmm) REVERT: A 468 LEU cc_start: 0.9791 (tp) cc_final: 0.9495 (tp) REVERT: A 472 LEU cc_start: 0.9761 (mt) cc_final: 0.9506 (mt) REVERT: A 493 MET cc_start: 0.9251 (tmm) cc_final: 0.8986 (tmm) REVERT: A 494 MET cc_start: 0.9440 (mtp) cc_final: 0.8932 (mtp) REVERT: A 499 SER cc_start: 0.9944 (t) cc_final: 0.9706 (p) REVERT: A 515 ASP cc_start: 0.9320 (m-30) cc_final: 0.9051 (m-30) REVERT: A 522 TYR cc_start: 0.9365 (m-80) cc_final: 0.8666 (m-10) REVERT: A 570 MET cc_start: 0.9430 (mtp) cc_final: 0.7876 (mtp) REVERT: A 575 ARG cc_start: 0.9349 (mtm110) cc_final: 0.8762 (ptp90) REVERT: A 586 TYR cc_start: 0.8913 (m-10) cc_final: 0.8659 (m-10) REVERT: A 599 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8870 (mt-10) REVERT: A 612 TYR cc_start: 0.8961 (m-10) cc_final: 0.8240 (m-80) REVERT: A 615 MET cc_start: 0.8813 (mmp) cc_final: 0.8524 (mmp) REVERT: A 645 GLN cc_start: 0.8968 (tp40) cc_final: 0.8754 (tp-100) REVERT: A 650 GLN cc_start: 0.8731 (mt0) cc_final: 0.7923 (mt0) REVERT: A 657 PHE cc_start: 0.8704 (m-80) cc_final: 0.8170 (m-80) REVERT: B 15 GLU cc_start: 0.9251 (tp30) cc_final: 0.8640 (tp30) REVERT: B 37 PHE cc_start: 0.9325 (m-10) cc_final: 0.9041 (m-10) REVERT: B 95 MET cc_start: 0.9222 (tpp) cc_final: 0.8683 (tpp) REVERT: B 99 LYS cc_start: 0.9564 (mmmt) cc_final: 0.9141 (mmmt) REVERT: B 107 LYS cc_start: 0.9628 (mptt) cc_final: 0.9303 (mmtt) REVERT: B 136 LYS cc_start: 0.9648 (mmtp) cc_final: 0.9388 (mmmm) REVERT: B 139 GLU cc_start: 0.9476 (mp0) cc_final: 0.9223 (mp0) REVERT: B 144 MET cc_start: 0.9203 (mtm) cc_final: 0.8856 (mtm) REVERT: B 147 GLN cc_start: 0.9286 (mt0) cc_final: 0.7880 (mt0) REVERT: B 150 GLN cc_start: 0.9519 (tp40) cc_final: 0.9280 (tp-100) REVERT: B 157 LEU cc_start: 0.9606 (tp) cc_final: 0.9344 (tp) REVERT: B 158 ASN cc_start: 0.9618 (m110) cc_final: 0.9206 (p0) REVERT: B 161 ARG cc_start: 0.8841 (ttm110) cc_final: 0.8173 (mtp85) REVERT: B 168 VAL cc_start: 0.9242 (t) cc_final: 0.9007 (t) REVERT: B 176 ASN cc_start: 0.8959 (t0) cc_final: 0.8756 (t0) REVERT: B 200 SER cc_start: 0.8967 (t) cc_final: 0.8745 (t) REVERT: B 211 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8272 (mm-30) REVERT: B 217 GLU cc_start: 0.9162 (pp20) cc_final: 0.8918 (tm-30) REVERT: B 218 ASN cc_start: 0.9625 (t0) cc_final: 0.9340 (t0) REVERT: B 227 MET cc_start: 0.9403 (mtp) cc_final: 0.9178 (mtp) REVERT: B 251 LEU cc_start: 0.9458 (tp) cc_final: 0.9142 (tp) REVERT: B 286 ASP cc_start: 0.8801 (m-30) cc_final: 0.8165 (m-30) REVERT: B 296 LYS cc_start: 0.8957 (mmpt) cc_final: 0.8583 (mtmm) REVERT: B 312 GLN cc_start: 0.9246 (pm20) cc_final: 0.8680 (pm20) REVERT: B 322 MET cc_start: 0.8734 (mmm) cc_final: 0.8532 (mmm) REVERT: B 333 LYS cc_start: 0.9592 (ttmm) cc_final: 0.9277 (ttmm) REVERT: B 345 LYS cc_start: 0.9641 (tttt) cc_final: 0.9313 (tttt) REVERT: B 350 ARG cc_start: 0.8743 (mtp85) cc_final: 0.8237 (mtp85) REVERT: B 362 ASP cc_start: 0.9170 (m-30) cc_final: 0.8110 (m-30) REVERT: B 370 ASN cc_start: 0.9580 (m-40) cc_final: 0.9186 (m110) REVERT: B 373 ILE cc_start: 0.9693 (mt) cc_final: 0.9359 (mt) REVERT: B 375 LYS cc_start: 0.9226 (mmtm) cc_final: 0.9017 (mmtm) REVERT: B 393 SER cc_start: 0.9568 (t) cc_final: 0.9034 (t) REVERT: B 398 ASP cc_start: 0.8823 (t70) cc_final: 0.8564 (t70) REVERT: B 399 GLU cc_start: 0.8804 (mp0) cc_final: 0.8435 (mp0) REVERT: B 402 GLU cc_start: 0.8632 (mp0) cc_final: 0.8265 (mp0) REVERT: B 403 ILE cc_start: 0.9384 (mp) cc_final: 0.8932 (tp) REVERT: B 494 MET cc_start: 0.9586 (mtt) cc_final: 0.9073 (mtt) REVERT: B 501 GLN cc_start: 0.9731 (tt0) cc_final: 0.9048 (tp-100) REVERT: B 570 MET cc_start: 0.9238 (mtp) cc_final: 0.8904 (mtp) REVERT: B 585 SER cc_start: 0.9079 (p) cc_final: 0.8641 (t) REVERT: B 588 GLN cc_start: 0.9467 (mm-40) cc_final: 0.8664 (mm110) REVERT: B 591 THR cc_start: 0.9237 (p) cc_final: 0.8939 (p) REVERT: B 606 TYR cc_start: 0.8499 (m-80) cc_final: 0.8143 (m-10) REVERT: B 615 MET cc_start: 0.9039 (mmp) cc_final: 0.8673 (mmp) REVERT: B 631 ASP cc_start: 0.9283 (m-30) cc_final: 0.9022 (m-30) REVERT: B 657 PHE cc_start: 0.8648 (m-80) cc_final: 0.8425 (m-80) REVERT: B 667 LEU cc_start: 0.9327 (tp) cc_final: 0.8992 (tp) REVERT: B 668 ASN cc_start: 0.9428 (m-40) cc_final: 0.8996 (m110) REVERT: B 677 ARG cc_start: 0.9653 (mmm160) cc_final: 0.9297 (mmm-85) REVERT: B 683 TYR cc_start: 0.9180 (t80) cc_final: 0.8744 (t80) REVERT: C 95 MET cc_start: 0.8918 (tmm) cc_final: 0.8701 (tmm) REVERT: C 136 GLN cc_start: -0.0687 (mt0) cc_final: -0.1249 (tp-100) REVERT: D 69 GLN cc_start: 0.8920 (tp40) cc_final: 0.8533 (tm-30) REVERT: D 100 VAL cc_start: 0.4579 (t) cc_final: 0.3918 (p) REVERT: D 146 GLN cc_start: 0.9255 (mt0) cc_final: 0.9046 (tm-30) REVERT: D 185 MET cc_start: 0.2287 (mmm) cc_final: 0.1753 (mpp) REVERT: D 197 ASP cc_start: 0.9507 (t70) cc_final: 0.9210 (t70) REVERT: D 201 HIS cc_start: 0.6260 (m170) cc_final: 0.5359 (m90) outliers start: 0 outliers final: 0 residues processed: 660 average time/residue: 0.1323 time to fit residues: 130.7295 Evaluate side-chains 570 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 570 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 120 optimal weight: 7.9990 chunk 37 optimal weight: 0.0670 chunk 126 optimal weight: 8.9990 chunk 129 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 115 optimal weight: 0.2980 chunk 168 optimal weight: 7.9990 chunk 157 optimal weight: 30.0000 overall best weight: 2.4724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 ASN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN C 127 GLN C 201 HIS D 181 GLN D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.130755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.087096 restraints weight = 46806.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.090200 restraints weight = 27278.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.092231 restraints weight = 18219.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.093649 restraints weight = 13486.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.094643 restraints weight = 10627.112| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.6400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16386 Z= 0.184 Angle : 0.602 10.384 22134 Z= 0.322 Chirality : 0.042 0.158 2360 Planarity : 0.004 0.056 2818 Dihedral : 8.874 134.782 2290 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 16.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.12 % Allowed : 1.75 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.19), residues: 1932 helix: 1.19 (0.15), residues: 1131 sheet: -0.58 (0.39), residues: 142 loop : 0.34 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 161 TYR 0.042 0.002 TYR A 683 PHE 0.029 0.002 PHE B 81 TRP 0.028 0.002 TRP C 124 HIS 0.006 0.001 HIS A 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.18 (16386) covalent geometry : angle 0.60206 / 0.32 (22134) hydrogen bonds : bond 0.03848 / 2.45 ( 871) hydrogen bonds : angle 4.98865 / 3.56 ( 2571) *********************** 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 655 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 653 time to evaluate : 0.730 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9514 (t0) cc_final: 0.9081 (t70) REVERT: A 89 PHE cc_start: 0.9187 (t80) cc_final: 0.8934 (t80) REVERT: A 95 MET cc_start: 0.8937 (tpp) cc_final: 0.8196 (tpt) REVERT: A 116 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8483 (tt0) REVERT: A 117 ARG cc_start: 0.9251 (mtp180) cc_final: 0.9043 (mtt180) REVERT: A 129 PHE cc_start: 0.9192 (m-80) cc_final: 0.8751 (m-80) REVERT: A 143 LEU cc_start: 0.9605 (tp) cc_final: 0.9229 (tp) REVERT: A 147 GLN cc_start: 0.9311 (mm-40) cc_final: 0.8941 (mm110) REVERT: A 172 LEU cc_start: 0.9199 (mp) cc_final: 0.8924 (mp) REVERT: A 190 MET cc_start: 0.9550 (mmm) cc_final: 0.9261 (mmm) REVERT: A 195 LEU cc_start: 0.9617 (mt) cc_final: 0.9394 (mt) REVERT: A 227 MET cc_start: 0.9385 (mtm) cc_final: 0.9081 (mtm) REVERT: A 235 ARG cc_start: 0.8775 (mtm110) cc_final: 0.8480 (mtm110) REVERT: A 252 ASN cc_start: 0.9399 (t0) cc_final: 0.8851 (t0) REVERT: A 266 LYS cc_start: 0.9389 (mttp) cc_final: 0.8958 (mttp) REVERT: A 307 TYR cc_start: 0.9639 (t80) cc_final: 0.9155 (t80) REVERT: A 322 MET cc_start: 0.9100 (tpt) cc_final: 0.8862 (mmm) REVERT: A 348 MET cc_start: 0.9322 (ptp) cc_final: 0.9087 (ptp) REVERT: A 350 ARG cc_start: 0.8893 (mmm-85) cc_final: 0.8359 (mmm-85) REVERT: A 370 ASN cc_start: 0.9657 (m-40) cc_final: 0.9399 (m-40) REVERT: A 394 TYR cc_start: 0.9213 (m-80) cc_final: 0.8930 (m-80) REVERT: A 406 ASP cc_start: 0.8909 (m-30) cc_final: 0.8615 (m-30) REVERT: A 407 ILE cc_start: 0.9113 (mt) cc_final: 0.8601 (mt) REVERT: A 421 GLU cc_start: 0.9241 (tm-30) cc_final: 0.8985 (tm-30) REVERT: A 446 ARG cc_start: 0.8508 (mtp85) cc_final: 0.7831 (mtp85) REVERT: A 447 ASN cc_start: 0.9159 (m-40) cc_final: 0.8837 (m-40) REVERT: A 459 LYS cc_start: 0.9313 (mttp) cc_final: 0.8658 (mtmt) REVERT: A 468 LEU cc_start: 0.9613 (tp) cc_final: 0.9307 (tp) REVERT: A 472 LEU cc_start: 0.9747 (mt) cc_final: 0.9459 (mt) REVERT: A 479 TYR cc_start: 0.9162 (t80) cc_final: 0.8794 (t80) REVERT: A 493 MET cc_start: 0.9179 (tmm) cc_final: 0.8823 (tmm) REVERT: A 494 MET cc_start: 0.9423 (mtp) cc_final: 0.9129 (mtp) REVERT: A 496 ASN cc_start: 0.9677 (t0) cc_final: 0.8975 (t0) REVERT: A 499 SER cc_start: 0.9913 (t) cc_final: 0.9545 (p) REVERT: A 500 ILE cc_start: 0.9672 (mp) cc_final: 0.9224 (mp) REVERT: A 515 ASP cc_start: 0.9321 (m-30) cc_final: 0.9063 (m-30) REVERT: A 522 TYR cc_start: 0.9297 (m-80) cc_final: 0.8711 (m-10) REVERT: A 570 MET cc_start: 0.9401 (mtp) cc_final: 0.7719 (mtp) REVERT: A 575 ARG cc_start: 0.9370 (mtm110) cc_final: 0.9010 (ptp90) REVERT: A 586 TYR cc_start: 0.8937 (m-10) cc_final: 0.8699 (m-10) REVERT: A 602 GLU cc_start: 0.8194 (pt0) cc_final: 0.6775 (pt0) REVERT: A 615 MET cc_start: 0.8851 (mmp) cc_final: 0.8411 (mmp) REVERT: A 639 ASP cc_start: 0.9231 (m-30) cc_final: 0.8972 (m-30) REVERT: A 645 GLN cc_start: 0.9153 (tp40) cc_final: 0.8909 (tp-100) REVERT: A 650 GLN cc_start: 0.8810 (mt0) cc_final: 0.8498 (mt0) REVERT: A 657 PHE cc_start: 0.8559 (m-80) cc_final: 0.8307 (m-80) REVERT: B 15 GLU cc_start: 0.9220 (tp30) cc_final: 0.8738 (tp30) REVERT: B 29 ASP cc_start: 0.9450 (t70) cc_final: 0.9170 (t70) REVERT: B 51 LEU cc_start: 0.9447 (tp) cc_final: 0.9108 (tp) REVERT: B 87 LYS cc_start: 0.9178 (mtpt) cc_final: 0.8928 (mtpt) REVERT: B 95 MET cc_start: 0.9230 (tpp) cc_final: 0.8812 (tpp) REVERT: B 99 LYS cc_start: 0.9580 (mmmt) cc_final: 0.9161 (mmmt) REVERT: B 107 LYS cc_start: 0.9634 (mptt) cc_final: 0.9370 (mmtt) REVERT: B 136 LYS cc_start: 0.9635 (mmtp) cc_final: 0.9340 (mmmm) REVERT: B 144 MET cc_start: 0.9134 (mtm) cc_final: 0.8859 (mtm) REVERT: B 147 GLN cc_start: 0.9207 (mt0) cc_final: 0.8859 (mt0) REVERT: B 158 ASN cc_start: 0.9610 (m110) cc_final: 0.9197 (p0) REVERT: B 161 ARG cc_start: 0.8866 (ttm110) cc_final: 0.8260 (mtp85) REVERT: B 211 GLU cc_start: 0.8570 (mm-30) cc_final: 0.7923 (mm-30) REVERT: B 227 MET cc_start: 0.9369 (mtp) cc_final: 0.9153 (mtp) REVERT: B 251 LEU cc_start: 0.9423 (tp) cc_final: 0.9177 (tp) REVERT: B 286 ASP cc_start: 0.8808 (m-30) cc_final: 0.8090 (m-30) REVERT: B 296 LYS cc_start: 0.8990 (mmpt) cc_final: 0.8654 (mtmm) REVERT: B 312 GLN cc_start: 0.9222 (pm20) cc_final: 0.8422 (pm20) REVERT: B 322 MET cc_start: 0.8798 (mmm) cc_final: 0.8557 (mmm) REVERT: B 333 LYS cc_start: 0.9543 (ttmm) cc_final: 0.9248 (ttmm) REVERT: B 345 LYS cc_start: 0.9671 (tttt) cc_final: 0.9455 (tttt) REVERT: B 350 ARG cc_start: 0.8725 (mtp85) cc_final: 0.8111 (mtp85) REVERT: B 362 ASP cc_start: 0.9107 (m-30) cc_final: 0.8019 (m-30) REVERT: B 370 ASN cc_start: 0.9580 (m-40) cc_final: 0.9212 (m110) REVERT: B 373 ILE cc_start: 0.9676 (mt) cc_final: 0.9336 (mt) REVERT: B 375 LYS cc_start: 0.9208 (mmtm) cc_final: 0.8986 (mmtm) REVERT: B 393 SER cc_start: 0.9549 (t) cc_final: 0.8984 (t) REVERT: B 398 ASP cc_start: 0.8809 (t70) cc_final: 0.8535 (t70) REVERT: B 402 GLU cc_start: 0.8638 (mp0) cc_final: 0.8262 (mp0) REVERT: B 403 ILE cc_start: 0.9366 (mp) cc_final: 0.8884 (tp) REVERT: B 413 SER cc_start: 0.9501 (m) cc_final: 0.9061 (t) REVERT: B 440 SER cc_start: 0.9747 (t) cc_final: 0.9490 (p) REVERT: B 458 MET cc_start: 0.9506 (mmm) cc_final: 0.9200 (mmm) REVERT: B 494 MET cc_start: 0.9563 (mtt) cc_final: 0.8996 (mtt) REVERT: B 585 SER cc_start: 0.9144 (p) cc_final: 0.8748 (t) REVERT: B 591 THR cc_start: 0.9277 (p) cc_final: 0.8956 (p) REVERT: B 606 TYR cc_start: 0.8399 (m-80) cc_final: 0.8040 (m-10) REVERT: B 615 MET cc_start: 0.9030 (mmp) cc_final: 0.8713 (mmm) REVERT: B 631 ASP cc_start: 0.9275 (m-30) cc_final: 0.8992 (m-30) REVERT: B 632 MET cc_start: 0.8433 (mmp) cc_final: 0.8150 (mmm) REVERT: B 646 GLN cc_start: 0.9249 (pm20) cc_final: 0.9037 (pm20) REVERT: B 657 PHE cc_start: 0.9082 (m-80) cc_final: 0.8735 (m-80) REVERT: B 667 LEU cc_start: 0.9432 (tp) cc_final: 0.9140 (tp) REVERT: B 668 ASN cc_start: 0.9405 (m-40) cc_final: 0.8727 (m110) REVERT: B 671 ASP cc_start: 0.9338 (m-30) cc_final: 0.9134 (m-30) REVERT: B 677 ARG cc_start: 0.9625 (mmm160) cc_final: 0.9300 (mmm-85) REVERT: B 683 TYR cc_start: 0.9170 (t80) cc_final: 0.8767 (t80) REVERT: C 93 MET cc_start: 0.9301 (mtm) cc_final: 0.9034 (tpt) REVERT: C 98 ASN cc_start: 0.7058 (p0) cc_final: 0.6719 (p0) REVERT: C 124 TRP cc_start: 0.8647 (t60) cc_final: 0.8016 (t60) REVERT: C 125 VAL cc_start: 0.8419 (t) cc_final: 0.8218 (t) REVERT: C 136 GLN cc_start: -0.0777 (mt0) cc_final: -0.1271 (tp40) REVERT: D 91 ASN cc_start: 0.8436 (m110) cc_final: 0.8124 (m110) REVERT: D 93 MET cc_start: 0.9106 (mtm) cc_final: 0.8771 (mtm) REVERT: D 100 VAL cc_start: 0.4856 (t) cc_final: 0.4084 (p) REVERT: D 146 GLN cc_start: 0.9267 (mt0) cc_final: 0.9048 (tm-30) outliers start: 2 outliers final: 0 residues processed: 655 average time/residue: 0.1232 time to fit residues: 121.0047 Evaluate side-chains 563 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 563 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 8.9990 chunk 183 optimal weight: 20.0000 chunk 72 optimal weight: 1.9990 chunk 172 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 28 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 4 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 136 optimal weight: 4.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 GLN A 180 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 304 HIS B 447 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN D 186 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.138034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.093251 restraints weight = 46064.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.096413 restraints weight = 26635.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.098624 restraints weight = 17750.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.100143 restraints weight = 13005.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.101147 restraints weight = 10171.138| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3233 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3233 r_free = 0.3233 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3233 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.6643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16386 Z= 0.134 Angle : 0.585 7.672 22134 Z= 0.314 Chirality : 0.042 0.206 2360 Planarity : 0.003 0.049 2818 Dihedral : 8.528 134.771 2290 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 14.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.12 % Allowed : 1.17 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.19), residues: 1932 helix: 1.07 (0.15), residues: 1148 sheet: -0.56 (0.39), residues: 144 loop : 0.24 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 117 TYR 0.019 0.001 TYR C 174 PHE 0.029 0.002 PHE D 109 TRP 0.017 0.001 TRP C 124 HIS 0.017 0.002 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 (16386) covalent geometry : angle 0.58509 / 0.31 (22134) hydrogen bonds : bond 0.03801 / 2.40 ( 871) hydrogen bonds : angle 4.83436 / 3.46 ( 2571) *********************** 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 653 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 651 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9465 (t0) cc_final: 0.9008 (t70) REVERT: A 89 PHE cc_start: 0.9052 (t80) cc_final: 0.8743 (t80) REVERT: A 95 MET cc_start: 0.8980 (tpp) cc_final: 0.8435 (tpt) REVERT: A 116 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8463 (tt0) REVERT: A 117 ARG cc_start: 0.9236 (mtp180) cc_final: 0.8993 (mtt180) REVERT: A 119 GLU cc_start: 0.9197 (mp0) cc_final: 0.8095 (tm-30) REVERT: A 124 ILE cc_start: 0.9786 (mm) cc_final: 0.9573 (mm) REVERT: A 129 PHE cc_start: 0.9139 (m-80) cc_final: 0.8826 (m-80) REVERT: A 139 GLU cc_start: 0.9234 (mt-10) cc_final: 0.8984 (pt0) REVERT: A 172 LEU cc_start: 0.9277 (mp) cc_final: 0.8905 (mp) REVERT: A 176 ASN cc_start: 0.9046 (t0) cc_final: 0.8544 (m-40) REVERT: A 184 ARG cc_start: 0.9272 (mmm-85) cc_final: 0.9021 (mmm-85) REVERT: A 190 MET cc_start: 0.9470 (mmm) cc_final: 0.9202 (mmm) REVERT: A 195 LEU cc_start: 0.9586 (mt) cc_final: 0.9359 (mt) REVERT: A 204 SER cc_start: 0.9387 (m) cc_final: 0.8992 (p) REVERT: A 251 LEU cc_start: 0.9617 (tp) cc_final: 0.9388 (tp) REVERT: A 252 ASN cc_start: 0.9374 (t0) cc_final: 0.8766 (t0) REVERT: A 307 TYR cc_start: 0.9641 (t80) cc_final: 0.9161 (t80) REVERT: A 322 MET cc_start: 0.9142 (tpt) cc_final: 0.8876 (mmm) REVERT: A 344 GLU cc_start: 0.9294 (mt-10) cc_final: 0.9038 (mt-10) REVERT: A 345 LYS cc_start: 0.9706 (tttt) cc_final: 0.9425 (mttt) REVERT: A 348 MET cc_start: 0.9321 (ptp) cc_final: 0.9085 (ptp) REVERT: A 350 ARG cc_start: 0.8894 (mmm-85) cc_final: 0.8424 (mmm-85) REVERT: A 370 ASN cc_start: 0.9592 (m-40) cc_final: 0.9302 (m-40) REVERT: A 394 TYR cc_start: 0.9204 (m-80) cc_final: 0.8870 (m-80) REVERT: A 406 ASP cc_start: 0.8914 (m-30) cc_final: 0.8696 (m-30) REVERT: A 418 ASN cc_start: 0.9606 (m-40) cc_final: 0.9311 (m-40) REVERT: A 420 MET cc_start: 0.9618 (mmm) cc_final: 0.9349 (mmm) REVERT: A 421 GLU cc_start: 0.9189 (tm-30) cc_final: 0.8913 (tm-30) REVERT: A 447 ASN cc_start: 0.9120 (m-40) cc_final: 0.8757 (m-40) REVERT: A 459 LYS cc_start: 0.9233 (mttp) cc_final: 0.8521 (mtmt) REVERT: A 468 LEU cc_start: 0.9609 (tp) cc_final: 0.9300 (tp) REVERT: A 472 LEU cc_start: 0.9739 (mt) cc_final: 0.9499 (mt) REVERT: A 479 TYR cc_start: 0.8846 (t80) cc_final: 0.8134 (t80) REVERT: A 493 MET cc_start: 0.9158 (tmm) cc_final: 0.8802 (tmm) REVERT: A 494 MET cc_start: 0.9428 (mtp) cc_final: 0.9125 (mtp) REVERT: A 499 SER cc_start: 0.9920 (t) cc_final: 0.9406 (p) REVERT: A 500 ILE cc_start: 0.9664 (mp) cc_final: 0.8742 (mp) REVERT: A 515 ASP cc_start: 0.9301 (m-30) cc_final: 0.9017 (m-30) REVERT: A 522 TYR cc_start: 0.9303 (m-80) cc_final: 0.8965 (m-10) REVERT: A 550 MET cc_start: 0.7870 (mpp) cc_final: 0.7577 (mpp) REVERT: A 570 MET cc_start: 0.9424 (mtp) cc_final: 0.8043 (mtp) REVERT: A 575 ARG cc_start: 0.9407 (mtm110) cc_final: 0.8795 (mpp80) REVERT: A 598 MET cc_start: 0.9006 (mmm) cc_final: 0.8790 (mmm) REVERT: A 603 GLU cc_start: 0.9252 (mm-30) cc_final: 0.9038 (tp30) REVERT: A 615 MET cc_start: 0.8890 (mmp) cc_final: 0.8440 (mmp) REVERT: A 639 ASP cc_start: 0.9217 (m-30) cc_final: 0.8893 (m-30) REVERT: A 645 GLN cc_start: 0.9190 (tp40) cc_final: 0.8934 (tp-100) REVERT: A 650 GLN cc_start: 0.8817 (mt0) cc_final: 0.8597 (mt0) REVERT: A 657 PHE cc_start: 0.8535 (m-80) cc_final: 0.8227 (m-80) REVERT: B 15 GLU cc_start: 0.9268 (tp30) cc_final: 0.8793 (tp30) REVERT: B 29 ASP cc_start: 0.9462 (t70) cc_final: 0.9190 (t70) REVERT: B 51 LEU cc_start: 0.9359 (tp) cc_final: 0.9129 (tp) REVERT: B 95 MET cc_start: 0.9143 (tpp) cc_final: 0.8668 (mmm) REVERT: B 99 LYS cc_start: 0.9538 (mmmt) cc_final: 0.9113 (mmmt) REVERT: B 119 GLU cc_start: 0.9205 (mp0) cc_final: 0.8433 (tm-30) REVERT: B 136 LYS cc_start: 0.9651 (mmtp) cc_final: 0.9343 (mmmm) REVERT: B 144 MET cc_start: 0.9043 (mtm) cc_final: 0.8769 (mtm) REVERT: B 147 GLN cc_start: 0.9201 (mt0) cc_final: 0.8004 (mt0) REVERT: B 157 LEU cc_start: 0.9607 (tp) cc_final: 0.9375 (tp) REVERT: B 158 ASN cc_start: 0.9576 (m110) cc_final: 0.9168 (p0) REVERT: B 161 ARG cc_start: 0.8711 (ttm110) cc_final: 0.8175 (mtp85) REVERT: B 211 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7976 (mm-30) REVERT: B 218 ASN cc_start: 0.9557 (m110) cc_final: 0.9015 (t0) REVERT: B 251 LEU cc_start: 0.9460 (tp) cc_final: 0.9228 (tp) REVERT: B 258 ILE cc_start: 0.9492 (tp) cc_final: 0.9292 (tp) REVERT: B 286 ASP cc_start: 0.8773 (m-30) cc_final: 0.7925 (m-30) REVERT: B 296 LYS cc_start: 0.8944 (mmpt) cc_final: 0.8621 (mtmm) REVERT: B 312 GLN cc_start: 0.9224 (pm20) cc_final: 0.8056 (pm20) REVERT: B 322 MET cc_start: 0.8761 (mmm) cc_final: 0.8510 (mmm) REVERT: B 333 LYS cc_start: 0.9552 (ttmm) cc_final: 0.9255 (ttmm) REVERT: B 344 GLU cc_start: 0.9274 (mm-30) cc_final: 0.9062 (mm-30) REVERT: B 345 LYS cc_start: 0.9712 (tttt) cc_final: 0.9431 (tttt) REVERT: B 350 ARG cc_start: 0.8730 (mtp85) cc_final: 0.8197 (mtp85) REVERT: B 362 ASP cc_start: 0.9037 (m-30) cc_final: 0.7998 (m-30) REVERT: B 370 ASN cc_start: 0.9464 (m-40) cc_final: 0.9006 (m110) REVERT: B 373 ILE cc_start: 0.9675 (mt) cc_final: 0.9415 (mt) REVERT: B 375 LYS cc_start: 0.9181 (mmtm) cc_final: 0.8684 (mmtm) REVERT: B 390 GLN cc_start: 0.9341 (mt0) cc_final: 0.9038 (mm-40) REVERT: B 393 SER cc_start: 0.9558 (t) cc_final: 0.9052 (t) REVERT: B 398 ASP cc_start: 0.8815 (t70) cc_final: 0.8568 (t70) REVERT: B 399 GLU cc_start: 0.8878 (mp0) cc_final: 0.8491 (mp0) REVERT: B 402 GLU cc_start: 0.8631 (mp0) cc_final: 0.8261 (mp0) REVERT: B 403 ILE cc_start: 0.9355 (mp) cc_final: 0.8909 (tp) REVERT: B 410 ASN cc_start: 0.9358 (m-40) cc_final: 0.9122 (m-40) REVERT: B 447 ASN cc_start: 0.8745 (OUTLIER) cc_final: 0.8106 (t0) REVERT: B 458 MET cc_start: 0.9481 (mmm) cc_final: 0.9125 (mmm) REVERT: B 494 MET cc_start: 0.9541 (mtt) cc_final: 0.8959 (mtt) REVERT: B 585 SER cc_start: 0.9076 (p) cc_final: 0.8673 (t) REVERT: B 588 GLN cc_start: 0.9363 (mm-40) cc_final: 0.8951 (mm-40) REVERT: B 591 THR cc_start: 0.9215 (p) cc_final: 0.8866 (p) REVERT: B 606 TYR cc_start: 0.8321 (m-80) cc_final: 0.7967 (m-10) REVERT: B 615 MET cc_start: 0.9029 (mmp) cc_final: 0.8768 (mmm) REVERT: B 631 ASP cc_start: 0.9146 (m-30) cc_final: 0.8922 (m-30) REVERT: B 634 MET cc_start: 0.9472 (mmm) cc_final: 0.9255 (mmp) REVERT: B 657 PHE cc_start: 0.8978 (m-80) cc_final: 0.8340 (m-80) REVERT: B 667 LEU cc_start: 0.9416 (tp) cc_final: 0.9134 (tp) REVERT: B 668 ASN cc_start: 0.9455 (m-40) cc_final: 0.9065 (m-40) REVERT: B 671 ASP cc_start: 0.9332 (m-30) cc_final: 0.9131 (m-30) REVERT: B 677 ARG cc_start: 0.9593 (mmm160) cc_final: 0.9289 (mmm-85) REVERT: C 56 MET cc_start: -0.1291 (ttp) cc_final: -0.1799 (mmm) REVERT: C 93 MET cc_start: 0.9339 (mtm) cc_final: 0.9081 (tpt) REVERT: C 124 TRP cc_start: 0.8540 (t60) cc_final: 0.7973 (t60) REVERT: D 69 GLN cc_start: 0.9332 (tp40) cc_final: 0.8720 (tp40) REVERT: D 97 GLU cc_start: 0.6340 (pt0) cc_final: 0.5417 (pt0) REVERT: D 100 VAL cc_start: 0.4665 (t) cc_final: 0.4464 (t) outliers start: 2 outliers final: 0 residues processed: 652 average time/residue: 0.1090 time to fit residues: 106.4014 Evaluate side-chains 557 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 556 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 74 optimal weight: 0.0570 chunk 105 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 186 optimal weight: 1.9990 chunk 140 optimal weight: 9.9990 chunk 115 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 20.0000 overall best weight: 1.6102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN B 191 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 GLN ** 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 = 0.3777 r_free = 0.3777 target = 0.134533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.091315 restraints weight = 46530.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.094480 restraints weight = 27174.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.096526 restraints weight = 18047.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.097928 restraints weight = 13145.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.098872 restraints weight = 10314.469| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3228 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.6960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16386 Z= 0.149 Angle : 0.592 6.751 22134 Z= 0.321 Chirality : 0.043 0.188 2360 Planarity : 0.004 0.060 2818 Dihedral : 8.444 134.944 2290 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.06 % Allowed : 1.46 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.19), residues: 1932 helix: 1.03 (0.15), residues: 1146 sheet: -0.39 (0.39), residues: 140 loop : 0.12 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 117 TYR 0.020 0.002 TYR B 471 PHE 0.022 0.002 PHE B 81 TRP 0.014 0.001 TRP C 124 HIS 0.015 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.15 (16386) covalent geometry : angle 0.59243 / 0.32 (22134) hydrogen bonds : bond 0.03761 / 2.38 ( 871) hydrogen bonds : angle 4.91278 / 3.52 ( 2571) *********************** 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 635 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 634 time to evaluate : 0.715 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: A 29 ASP cc_start: 0.9447 (t0) cc_final: 0.8993 (t70) REVERT: A 95 MET cc_start: 0.8995 (tpp) cc_final: 0.8466 (tpt) REVERT: A 117 ARG cc_start: 0.9299 (mtp180) cc_final: 0.9093 (mtt180) REVERT: A 119 GLU cc_start: 0.9201 (mp0) cc_final: 0.7958 (tm-30) REVERT: A 124 ILE cc_start: 0.9790 (mm) cc_final: 0.9576 (mm) REVERT: A 129 PHE cc_start: 0.9136 (m-80) cc_final: 0.8822 (m-80) REVERT: A 139 GLU cc_start: 0.9223 (mt-10) cc_final: 0.8940 (pt0) REVERT: A 147 GLN cc_start: 0.9312 (mm-40) cc_final: 0.8703 (mm110) REVERT: A 172 LEU cc_start: 0.9279 (mp) cc_final: 0.8903 (mp) REVERT: A 173 LEU cc_start: 0.9404 (mt) cc_final: 0.9073 (mt) REVERT: A 176 ASN cc_start: 0.9093 (t0) cc_final: 0.8643 (m-40) REVERT: A 188 ILE cc_start: 0.9628 (mt) cc_final: 0.9416 (mt) REVERT: A 195 LEU cc_start: 0.9578 (mt) cc_final: 0.9367 (mt) REVERT: A 204 SER cc_start: 0.9377 (m) cc_final: 0.8994 (p) REVERT: A 227 MET cc_start: 0.9280 (mtm) cc_final: 0.9032 (mtm) REVERT: A 251 LEU cc_start: 0.9583 (tp) cc_final: 0.9377 (tp) REVERT: A 252 ASN cc_start: 0.9396 (t0) cc_final: 0.8831 (t0) REVERT: A 307 TYR cc_start: 0.9638 (t80) cc_final: 0.9151 (t80) REVERT: A 322 MET cc_start: 0.9091 (tpt) cc_final: 0.8834 (mmm) REVERT: A 348 MET cc_start: 0.9305 (ptp) cc_final: 0.9057 (ptp) REVERT: A 350 ARG cc_start: 0.8927 (mmm-85) cc_final: 0.8470 (mmm-85) REVERT: A 370 ASN cc_start: 0.9596 (m-40) cc_final: 0.9276 (m-40) REVERT: A 387 GLN cc_start: 0.9152 (mt0) cc_final: 0.8350 (mp10) REVERT: A 394 TYR cc_start: 0.9221 (m-80) cc_final: 0.8863 (m-80) REVERT: A 406 ASP cc_start: 0.8942 (m-30) cc_final: 0.8499 (m-30) REVERT: A 415 ASN cc_start: 0.9556 (t0) cc_final: 0.9304 (t0) REVERT: A 418 ASN cc_start: 0.9660 (m-40) cc_final: 0.8969 (t0) REVERT: A 420 MET cc_start: 0.9642 (mmm) cc_final: 0.9373 (mmm) REVERT: A 421 GLU cc_start: 0.9193 (tm-30) cc_final: 0.8905 (tm-30) REVERT: A 447 ASN cc_start: 0.9054 (m-40) cc_final: 0.8467 (t0) REVERT: A 459 LYS cc_start: 0.9268 (mttp) cc_final: 0.8303 (mtmm) REVERT: A 468 LEU cc_start: 0.9633 (tp) cc_final: 0.9353 (tp) REVERT: A 472 LEU cc_start: 0.9747 (mt) cc_final: 0.9510 (mt) REVERT: A 479 TYR cc_start: 0.8832 (t80) cc_final: 0.8055 (t80) REVERT: A 493 MET cc_start: 0.9146 (tmm) cc_final: 0.8758 (tmm) REVERT: A 494 MET cc_start: 0.9435 (mtp) cc_final: 0.9127 (mtp) REVERT: A 499 SER cc_start: 0.9904 (t) cc_final: 0.9309 (p) REVERT: A 500 ILE cc_start: 0.9671 (mp) cc_final: 0.8796 (mp) REVERT: A 515 ASP cc_start: 0.9344 (m-30) cc_final: 0.9105 (m-30) REVERT: A 522 TYR cc_start: 0.9309 (m-80) cc_final: 0.9006 (m-10) REVERT: A 550 MET cc_start: 0.7851 (mpp) cc_final: 0.7619 (mpp) REVERT: A 570 MET cc_start: 0.9405 (mtp) cc_final: 0.8311 (mtp) REVERT: A 575 ARG cc_start: 0.9416 (mtm110) cc_final: 0.8810 (mpp80) REVERT: A 598 MET cc_start: 0.9000 (mmm) cc_final: 0.8739 (mmm) REVERT: A 615 MET cc_start: 0.8899 (mmp) cc_final: 0.8472 (mmp) REVERT: A 639 ASP cc_start: 0.9241 (m-30) cc_final: 0.8919 (m-30) REVERT: A 645 GLN cc_start: 0.9161 (tp40) cc_final: 0.8888 (tp-100) REVERT: A 650 GLN cc_start: 0.8789 (mt0) cc_final: 0.7605 (mt0) REVERT: B 15 GLU cc_start: 0.9298 (tp30) cc_final: 0.8799 (tp30) REVERT: B 29 ASP cc_start: 0.9457 (t70) cc_final: 0.9140 (t0) REVERT: B 51 LEU cc_start: 0.9387 (tp) cc_final: 0.9172 (tp) REVERT: B 95 MET cc_start: 0.9168 (tpp) cc_final: 0.8753 (tpp) REVERT: B 99 LYS cc_start: 0.9557 (mmmt) cc_final: 0.9105 (mmmt) REVERT: B 119 GLU cc_start: 0.9234 (mp0) cc_final: 0.8879 (tm-30) REVERT: B 120 ASP cc_start: 0.9360 (m-30) cc_final: 0.8891 (m-30) REVERT: B 128 PHE cc_start: 0.9599 (t80) cc_final: 0.9355 (t80) REVERT: B 136 LYS cc_start: 0.9661 (mmtp) cc_final: 0.9321 (mmmm) REVERT: B 144 MET cc_start: 0.9085 (mtm) cc_final: 0.8813 (mtm) REVERT: B 147 GLN cc_start: 0.9194 (mt0) cc_final: 0.8285 (mt0) REVERT: B 157 LEU cc_start: 0.9551 (tp) cc_final: 0.9346 (tp) REVERT: B 158 ASN cc_start: 0.9576 (m110) cc_final: 0.9118 (p0) REVERT: B 161 ARG cc_start: 0.8738 (ttm110) cc_final: 0.8199 (mtp85) REVERT: B 200 SER cc_start: 0.8969 (t) cc_final: 0.8686 (t) REVERT: B 218 ASN cc_start: 0.9403 (m110) cc_final: 0.8923 (m-40) REVERT: B 251 LEU cc_start: 0.9457 (tp) cc_final: 0.9187 (tp) REVERT: B 286 ASP cc_start: 0.8717 (m-30) cc_final: 0.8153 (m-30) REVERT: B 290 GLU cc_start: 0.9181 (pp20) cc_final: 0.8606 (pp20) REVERT: B 291 LEU cc_start: 0.9597 (mt) cc_final: 0.9373 (mt) REVERT: B 296 LYS cc_start: 0.9062 (mmpt) cc_final: 0.8760 (mtmm) REVERT: B 312 GLN cc_start: 0.9187 (pm20) cc_final: 0.8866 (pm20) REVERT: B 322 MET cc_start: 0.8726 (mmm) cc_final: 0.8503 (mmm) REVERT: B 333 LYS cc_start: 0.9498 (ttmm) cc_final: 0.9197 (ttmm) REVERT: B 335 GLU cc_start: 0.9192 (pt0) cc_final: 0.8954 (pt0) REVERT: B 344 GLU cc_start: 0.9265 (mm-30) cc_final: 0.9010 (mm-30) REVERT: B 345 LYS cc_start: 0.9714 (tttt) cc_final: 0.9493 (tttt) REVERT: B 350 ARG cc_start: 0.8770 (mtp85) cc_final: 0.8071 (mtp85) REVERT: B 362 ASP cc_start: 0.9059 (m-30) cc_final: 0.8037 (m-30) REVERT: B 375 LYS cc_start: 0.9164 (mmtm) cc_final: 0.8722 (mmtm) REVERT: B 393 SER cc_start: 0.9553 (t) cc_final: 0.9022 (t) REVERT: B 398 ASP cc_start: 0.8792 (t70) cc_final: 0.8562 (t70) REVERT: B 399 GLU cc_start: 0.8834 (mp0) cc_final: 0.8500 (mp0) REVERT: B 402 GLU cc_start: 0.8643 (mp0) cc_final: 0.8352 (mp0) REVERT: B 410 ASN cc_start: 0.9319 (m-40) cc_final: 0.9106 (m-40) REVERT: B 413 SER cc_start: 0.9529 (m) cc_final: 0.9095 (t) REVERT: B 441 GLU cc_start: 0.9059 (pm20) cc_final: 0.8778 (pm20) REVERT: B 458 MET cc_start: 0.9467 (mmm) cc_final: 0.9183 (mmm) REVERT: B 494 MET cc_start: 0.9405 (mtt) cc_final: 0.8848 (mtt) REVERT: B 501 GLN cc_start: 0.9677 (tt0) cc_final: 0.9417 (mt0) REVERT: B 585 SER cc_start: 0.9212 (p) cc_final: 0.8829 (t) REVERT: B 588 GLN cc_start: 0.9450 (mm-40) cc_final: 0.9048 (mm110) REVERT: B 591 THR cc_start: 0.9267 (p) cc_final: 0.8920 (p) REVERT: B 598 MET cc_start: 0.8167 (tpt) cc_final: 0.7892 (tpt) REVERT: B 606 TYR cc_start: 0.8381 (m-80) cc_final: 0.8035 (m-10) REVERT: B 615 MET cc_start: 0.9091 (mmp) cc_final: 0.8804 (mmm) REVERT: B 631 ASP cc_start: 0.9149 (m-30) cc_final: 0.8919 (m-30) REVERT: B 657 PHE cc_start: 0.9066 (m-80) cc_final: 0.8782 (m-10) REVERT: B 667 LEU cc_start: 0.9420 (tp) cc_final: 0.9185 (tt) REVERT: B 668 ASN cc_start: 0.9404 (m-40) cc_final: 0.8998 (m-40) REVERT: B 671 ASP cc_start: 0.9303 (m-30) cc_final: 0.9097 (m-30) REVERT: B 677 ARG cc_start: 0.9582 (mmm160) cc_final: 0.9269 (mmm-85) REVERT: B 683 TYR cc_start: 0.9069 (t80) cc_final: 0.8576 (t80) REVERT: C 56 MET cc_start: -0.1095 (ttp) cc_final: -0.1418 (ttp) REVERT: C 124 TRP cc_start: 0.8608 (t60) cc_final: 0.8093 (t60) REVERT: D 25 ASN cc_start: 0.8121 (m-40) cc_final: 0.7891 (m-40) REVERT: D 69 GLN cc_start: 0.9374 (tp40) cc_final: 0.8933 (tp40) REVERT: D 74 MET cc_start: 0.8931 (mmp) cc_final: 0.8694 (mmp) REVERT: D 97 GLU cc_start: 0.5877 (pt0) cc_final: 0.5541 (pt0) outliers start: 1 outliers final: 0 residues processed: 634 average time/residue: 0.1279 time to fit residues: 122.4609 Evaluate side-chains 563 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 563 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 19 optimal weight: 7.9990 chunk 134 optimal weight: 0.9990 chunk 153 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 97 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 HIS ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN D 234 GLN ** D 238 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 = 0.3763 r_free = 0.3763 target = 0.132815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.090107 restraints weight = 46463.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.093285 restraints weight = 26975.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.095309 restraints weight = 17603.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.096728 restraints weight = 12854.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097726 restraints weight = 10067.524| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.7222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16386 Z= 0.169 Angle : 0.604 7.147 22134 Z= 0.328 Chirality : 0.043 0.186 2360 Planarity : 0.004 0.046 2818 Dihedral : 8.487 134.363 2290 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.19), residues: 1932 helix: 1.02 (0.15), residues: 1147 sheet: -0.48 (0.40), residues: 140 loop : 0.07 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 117 TYR 0.025 0.002 TYR B 101 PHE 0.023 0.002 PHE B 261 TRP 0.014 0.001 TRP C 124 HIS 0.012 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (16386) covalent geometry : angle 0.60393 / 0.33 (22134) hydrogen bonds : bond 0.03806 / 2.41 ( 871) hydrogen bonds : angle 4.90606 / 3.50 ( 2571) *********************** 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 610 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 610 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9468 (t0) cc_final: 0.9091 (t70) REVERT: A 95 MET cc_start: 0.9016 (tpp) cc_final: 0.8437 (tpt) REVERT: A 116 GLU cc_start: 0.8849 (tt0) cc_final: 0.8567 (tt0) REVERT: A 119 GLU cc_start: 0.9086 (mp0) cc_final: 0.8756 (mt-10) REVERT: A 129 PHE cc_start: 0.9214 (m-80) cc_final: 0.8903 (m-80) REVERT: A 139 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8799 (pt0) REVERT: A 147 GLN cc_start: 0.9336 (mm-40) cc_final: 0.8704 (mm110) REVERT: A 176 ASN cc_start: 0.9069 (t0) cc_final: 0.8586 (m-40) REVERT: A 195 LEU cc_start: 0.9557 (mt) cc_final: 0.9341 (mt) REVERT: A 204 SER cc_start: 0.9348 (m) cc_final: 0.8906 (p) REVERT: A 251 LEU cc_start: 0.9622 (tp) cc_final: 0.9412 (tp) REVERT: A 252 ASN cc_start: 0.9357 (t0) cc_final: 0.8902 (t0) REVERT: A 301 PHE cc_start: 0.9267 (m-10) cc_final: 0.8754 (m-10) REVERT: A 307 TYR cc_start: 0.9641 (t80) cc_final: 0.9133 (t80) REVERT: A 322 MET cc_start: 0.8987 (tpt) cc_final: 0.8660 (tpp) REVERT: A 350 ARG cc_start: 0.8967 (mmm-85) cc_final: 0.8542 (mmm-85) REVERT: A 370 ASN cc_start: 0.9636 (m-40) cc_final: 0.9343 (m-40) REVERT: A 387 GLN cc_start: 0.9159 (mt0) cc_final: 0.8594 (mp10) REVERT: A 394 TYR cc_start: 0.9234 (m-80) cc_final: 0.8743 (m-80) REVERT: A 418 ASN cc_start: 0.9671 (m-40) cc_final: 0.9195 (m-40) REVERT: A 421 GLU cc_start: 0.9186 (tm-30) cc_final: 0.8928 (tm-30) REVERT: A 447 ASN cc_start: 0.9130 (m-40) cc_final: 0.8557 (t0) REVERT: A 459 LYS cc_start: 0.9224 (mttp) cc_final: 0.8272 (mtmm) REVERT: A 468 LEU cc_start: 0.9659 (tp) cc_final: 0.9379 (tp) REVERT: A 472 LEU cc_start: 0.9747 (mt) cc_final: 0.9503 (mt) REVERT: A 479 TYR cc_start: 0.8843 (t80) cc_final: 0.8166 (t80) REVERT: A 493 MET cc_start: 0.9156 (tmm) cc_final: 0.8770 (tmm) REVERT: A 494 MET cc_start: 0.9406 (mtp) cc_final: 0.9094 (mtp) REVERT: A 499 SER cc_start: 0.9892 (t) cc_final: 0.9312 (p) REVERT: A 500 ILE cc_start: 0.9704 (mp) cc_final: 0.8827 (mp) REVERT: A 515 ASP cc_start: 0.9332 (m-30) cc_final: 0.9075 (m-30) REVERT: A 570 MET cc_start: 0.9349 (mtp) cc_final: 0.8290 (mtp) REVERT: A 575 ARG cc_start: 0.9452 (mtm110) cc_final: 0.8827 (mpp80) REVERT: A 586 TYR cc_start: 0.8828 (m-10) cc_final: 0.8497 (m-10) REVERT: A 602 GLU cc_start: 0.8134 (pt0) cc_final: 0.6105 (pt0) REVERT: A 615 MET cc_start: 0.9059 (mmp) cc_final: 0.8633 (mmp) REVERT: A 639 ASP cc_start: 0.9257 (m-30) cc_final: 0.8941 (m-30) REVERT: A 640 MET cc_start: 0.9111 (tpp) cc_final: 0.8833 (tpp) REVERT: A 645 GLN cc_start: 0.9179 (tp40) cc_final: 0.8915 (tp-100) REVERT: A 650 GLN cc_start: 0.8842 (mt0) cc_final: 0.7566 (mt0) REVERT: B 15 GLU cc_start: 0.9344 (tp30) cc_final: 0.8860 (tp30) REVERT: B 29 ASP cc_start: 0.9407 (t70) cc_final: 0.9097 (t0) REVERT: B 81 PHE cc_start: 0.9424 (m-80) cc_final: 0.9178 (m-80) REVERT: B 95 MET cc_start: 0.9203 (tpp) cc_final: 0.8946 (tpp) REVERT: B 99 LYS cc_start: 0.9554 (mmmt) cc_final: 0.9115 (mmmt) REVERT: B 119 GLU cc_start: 0.9252 (mp0) cc_final: 0.8938 (tm-30) REVERT: B 120 ASP cc_start: 0.9312 (m-30) cc_final: 0.8597 (m-30) REVERT: B 128 PHE cc_start: 0.9573 (t80) cc_final: 0.9354 (t80) REVERT: B 136 LYS cc_start: 0.9684 (mmtp) cc_final: 0.9320 (mmmm) REVERT: B 144 MET cc_start: 0.9107 (mtm) cc_final: 0.8809 (mtm) REVERT: B 147 GLN cc_start: 0.9258 (mt0) cc_final: 0.8713 (mt0) REVERT: B 200 SER cc_start: 0.9029 (t) cc_final: 0.8776 (t) REVERT: B 227 MET cc_start: 0.9390 (mtm) cc_final: 0.9085 (mtm) REVERT: B 251 LEU cc_start: 0.9497 (tp) cc_final: 0.9280 (tp) REVERT: B 286 ASP cc_start: 0.8685 (m-30) cc_final: 0.8113 (m-30) REVERT: B 290 GLU cc_start: 0.9211 (pp20) cc_final: 0.8394 (pp20) REVERT: B 291 LEU cc_start: 0.9601 (mt) cc_final: 0.9329 (mt) REVERT: B 294 GLU cc_start: 0.9480 (mp0) cc_final: 0.9082 (mp0) REVERT: B 296 LYS cc_start: 0.9110 (mmpt) cc_final: 0.8795 (mtmm) REVERT: B 322 MET cc_start: 0.8681 (mmm) cc_final: 0.8418 (mmm) REVERT: B 333 LYS cc_start: 0.9476 (ttmm) cc_final: 0.9165 (ttmm) REVERT: B 335 GLU cc_start: 0.9185 (pt0) cc_final: 0.8964 (pt0) REVERT: B 345 LYS cc_start: 0.9726 (tttt) cc_final: 0.9442 (tttt) REVERT: B 350 ARG cc_start: 0.8828 (mtp85) cc_final: 0.8114 (mtp85) REVERT: B 362 ASP cc_start: 0.9071 (m-30) cc_final: 0.8057 (m-30) REVERT: B 375 LYS cc_start: 0.9163 (mmtm) cc_final: 0.8740 (mmtm) REVERT: B 393 SER cc_start: 0.9518 (t) cc_final: 0.8856 (t) REVERT: B 398 ASP cc_start: 0.8800 (t70) cc_final: 0.8541 (t70) REVERT: B 399 GLU cc_start: 0.8863 (mp0) cc_final: 0.8521 (mp0) REVERT: B 402 GLU cc_start: 0.8648 (mp0) cc_final: 0.8297 (mp0) REVERT: B 458 MET cc_start: 0.9481 (mmm) cc_final: 0.9161 (mmm) REVERT: B 494 MET cc_start: 0.9398 (mtt) cc_final: 0.8796 (mtt) REVERT: B 501 GLN cc_start: 0.9685 (tt0) cc_final: 0.9470 (mt0) REVERT: B 585 SER cc_start: 0.9194 (p) cc_final: 0.8842 (t) REVERT: B 591 THR cc_start: 0.9246 (p) cc_final: 0.8875 (p) REVERT: B 598 MET cc_start: 0.8101 (tpt) cc_final: 0.7645 (tpt) REVERT: B 615 MET cc_start: 0.8931 (mmp) cc_final: 0.8668 (mmp) REVERT: B 631 ASP cc_start: 0.9113 (m-30) cc_final: 0.8862 (m-30) REVERT: B 636 LYS cc_start: 0.9718 (mptt) cc_final: 0.9511 (mmmt) REVERT: B 639 ASP cc_start: 0.9304 (m-30) cc_final: 0.8972 (m-30) REVERT: B 657 PHE cc_start: 0.9078 (m-80) cc_final: 0.8831 (m-10) REVERT: B 667 LEU cc_start: 0.9454 (tp) cc_final: 0.9241 (tt) REVERT: B 668 ASN cc_start: 0.9423 (m-40) cc_final: 0.8998 (m-40) REVERT: B 677 ARG cc_start: 0.9575 (mmm160) cc_final: 0.9289 (mmm-85) REVERT: B 683 TYR cc_start: 0.9008 (t80) cc_final: 0.8249 (t80) REVERT: C 56 MET cc_start: -0.1165 (ttp) cc_final: -0.1458 (ttp) REVERT: C 124 TRP cc_start: 0.8629 (t60) cc_final: 0.8189 (t60) REVERT: D 69 GLN cc_start: 0.9417 (tp40) cc_final: 0.8966 (tp40) REVERT: D 74 MET cc_start: 0.8964 (mmp) cc_final: 0.8719 (mmp) REVERT: D 91 ASN cc_start: 0.8402 (m110) cc_final: 0.7971 (m110) REVERT: D 93 MET cc_start: 0.9006 (mtm) cc_final: 0.8755 (mtm) REVERT: D 97 GLU cc_start: 0.6369 (pt0) cc_final: 0.5989 (pt0) outliers start: 0 outliers final: 0 residues processed: 610 average time/residue: 0.1211 time to fit residues: 111.7291 Evaluate side-chains 553 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 553 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 0.9990 chunk 133 optimal weight: 0.2980 chunk 149 optimal weight: 0.3980 chunk 16 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN B 150 GLN B 191 GLN ** B 650 GLN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.138521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.094915 restraints weight = 45662.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.098163 restraints weight = 26394.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.100222 restraints weight = 17377.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.101750 restraints weight = 12714.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.102888 restraints weight = 9858.214| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3252 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.7439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16386 Z= 0.133 Angle : 0.626 9.045 22134 Z= 0.334 Chirality : 0.044 0.369 2360 Planarity : 0.004 0.054 2818 Dihedral : 8.442 134.349 2290 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.19), residues: 1932 helix: 1.02 (0.15), residues: 1134 sheet: 0.17 (0.47), residues: 110 loop : -0.13 (0.23), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 161 TYR 0.043 0.002 TYR C 142 PHE 0.025 0.002 PHE B 487 TRP 0.011 0.001 TRP C 124 HIS 0.011 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (16386) covalent geometry : angle 0.62565 / 0.33 (22134) hydrogen bonds : bond 0.03754 / 2.36 ( 871) hydrogen bonds : angle 4.89897 / 3.50 ( 2571) *********************** 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 622 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 622 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9489 (t0) cc_final: 0.9111 (t70) REVERT: A 95 MET cc_start: 0.9065 (tpp) cc_final: 0.8508 (tpt) REVERT: A 116 GLU cc_start: 0.8631 (tt0) cc_final: 0.7837 (tt0) REVERT: A 119 GLU cc_start: 0.9012 (mp0) cc_final: 0.8337 (mt-10) REVERT: A 129 PHE cc_start: 0.9070 (m-80) cc_final: 0.8820 (m-80) REVERT: A 139 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8939 (pt0) REVERT: A 147 GLN cc_start: 0.9297 (mm-40) cc_final: 0.8952 (mm110) REVERT: A 176 ASN cc_start: 0.9114 (t0) cc_final: 0.8691 (m-40) REVERT: A 180 ASN cc_start: 0.9132 (m-40) cc_final: 0.8664 (t0) REVERT: A 188 ILE cc_start: 0.9610 (mt) cc_final: 0.9405 (mt) REVERT: A 195 LEU cc_start: 0.9523 (mt) cc_final: 0.9303 (mt) REVERT: A 204 SER cc_start: 0.9349 (m) cc_final: 0.9003 (p) REVERT: A 252 ASN cc_start: 0.9345 (t0) cc_final: 0.8985 (t0) REVERT: A 307 TYR cc_start: 0.9623 (t80) cc_final: 0.9119 (t80) REVERT: A 322 MET cc_start: 0.9015 (tpt) cc_final: 0.8694 (mmm) REVERT: A 342 LEU cc_start: 0.9656 (tp) cc_final: 0.9454 (tp) REVERT: A 350 ARG cc_start: 0.8970 (mmm-85) cc_final: 0.8504 (mmm-85) REVERT: A 370 ASN cc_start: 0.9567 (m-40) cc_final: 0.9239 (m-40) REVERT: A 387 GLN cc_start: 0.9099 (mt0) cc_final: 0.8440 (mp10) REVERT: A 394 TYR cc_start: 0.9198 (m-80) cc_final: 0.8603 (m-80) REVERT: A 418 ASN cc_start: 0.9667 (m-40) cc_final: 0.8960 (t0) REVERT: A 421 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8917 (tm-30) REVERT: A 447 ASN cc_start: 0.9092 (m-40) cc_final: 0.8509 (t0) REVERT: A 459 LYS cc_start: 0.9265 (mttp) cc_final: 0.8767 (mtmm) REVERT: A 468 LEU cc_start: 0.9595 (tp) cc_final: 0.9361 (tp) REVERT: A 472 LEU cc_start: 0.9737 (mt) cc_final: 0.9507 (mt) REVERT: A 493 MET cc_start: 0.9153 (tmm) cc_final: 0.8763 (tmm) REVERT: A 494 MET cc_start: 0.9382 (mtp) cc_final: 0.9052 (mtp) REVERT: A 499 SER cc_start: 0.9903 (t) cc_final: 0.9333 (p) REVERT: A 500 ILE cc_start: 0.9605 (mp) cc_final: 0.8702 (mp) REVERT: A 515 ASP cc_start: 0.9324 (m-30) cc_final: 0.9089 (m-30) REVERT: A 522 TYR cc_start: 0.9312 (m-10) cc_final: 0.8843 (m-10) REVERT: A 570 MET cc_start: 0.9191 (mtp) cc_final: 0.7867 (mtp) REVERT: A 575 ARG cc_start: 0.9283 (mtm110) cc_final: 0.8582 (mpp80) REVERT: A 615 MET cc_start: 0.8996 (mmp) cc_final: 0.8584 (mmp) REVERT: A 639 ASP cc_start: 0.9290 (m-30) cc_final: 0.8965 (m-30) REVERT: A 645 GLN cc_start: 0.9243 (tp40) cc_final: 0.8977 (tp-100) REVERT: A 650 GLN cc_start: 0.8793 (mt0) cc_final: 0.7638 (mt0) REVERT: A 654 PHE cc_start: 0.9373 (t80) cc_final: 0.9141 (t80) REVERT: A 655 THR cc_start: 0.8741 (m) cc_final: 0.8262 (m) REVERT: A 657 PHE cc_start: 0.8656 (m-80) cc_final: 0.8232 (m-80) REVERT: A 664 THR cc_start: 0.9307 (p) cc_final: 0.9083 (p) REVERT: A 668 ASN cc_start: 0.9615 (m110) cc_final: 0.9356 (m-40) REVERT: B 15 GLU cc_start: 0.9297 (tp30) cc_final: 0.8831 (tp30) REVERT: B 29 ASP cc_start: 0.9387 (t70) cc_final: 0.9162 (t70) REVERT: B 81 PHE cc_start: 0.9366 (m-80) cc_final: 0.9166 (m-80) REVERT: B 95 MET cc_start: 0.9036 (tpp) cc_final: 0.8603 (tpp) REVERT: B 99 LYS cc_start: 0.9472 (mmmt) cc_final: 0.9065 (mmmt) REVERT: B 119 GLU cc_start: 0.9205 (mp0) cc_final: 0.8467 (tm-30) REVERT: B 120 ASP cc_start: 0.9203 (m-30) cc_final: 0.8975 (m-30) REVERT: B 128 PHE cc_start: 0.9575 (t80) cc_final: 0.9340 (t80) REVERT: B 136 LYS cc_start: 0.9672 (mmtp) cc_final: 0.9300 (mmmm) REVERT: B 144 MET cc_start: 0.8954 (mtm) cc_final: 0.8687 (mtm) REVERT: B 147 GLN cc_start: 0.9289 (mt0) cc_final: 0.8823 (mt0) REVERT: B 157 LEU cc_start: 0.9547 (tp) cc_final: 0.9175 (tp) REVERT: B 161 ARG cc_start: 0.8569 (ttm110) cc_final: 0.8231 (mtp85) REVERT: B 200 SER cc_start: 0.8962 (t) cc_final: 0.8654 (t) REVERT: B 217 GLU cc_start: 0.8267 (tp30) cc_final: 0.7925 (tp30) REVERT: B 218 ASN cc_start: 0.9319 (m-40) cc_final: 0.8865 (m-40) REVERT: B 227 MET cc_start: 0.9349 (mtm) cc_final: 0.9108 (mtm) REVERT: B 251 LEU cc_start: 0.9516 (tp) cc_final: 0.9280 (tp) REVERT: B 286 ASP cc_start: 0.8593 (m-30) cc_final: 0.7964 (m-30) REVERT: B 290 GLU cc_start: 0.9171 (pp20) cc_final: 0.8292 (pp20) REVERT: B 291 LEU cc_start: 0.9600 (mt) cc_final: 0.9318 (mt) REVERT: B 294 GLU cc_start: 0.9497 (mp0) cc_final: 0.9088 (mp0) REVERT: B 296 LYS cc_start: 0.8961 (mmpt) cc_final: 0.8647 (mtmm) REVERT: B 322 MET cc_start: 0.8669 (mmm) cc_final: 0.8400 (mmm) REVERT: B 333 LYS cc_start: 0.9470 (ttmm) cc_final: 0.9178 (ttmm) REVERT: B 344 GLU cc_start: 0.9309 (mm-30) cc_final: 0.9000 (mm-30) REVERT: B 345 LYS cc_start: 0.9730 (tttt) cc_final: 0.9477 (tttt) REVERT: B 350 ARG cc_start: 0.8841 (mtp85) cc_final: 0.8254 (mtp85) REVERT: B 362 ASP cc_start: 0.9064 (m-30) cc_final: 0.8044 (m-30) REVERT: B 375 LYS cc_start: 0.9103 (mmtm) cc_final: 0.8658 (mmtm) REVERT: B 393 SER cc_start: 0.9543 (t) cc_final: 0.9028 (t) REVERT: B 398 ASP cc_start: 0.8800 (t70) cc_final: 0.8550 (t70) REVERT: B 399 GLU cc_start: 0.8854 (mp0) cc_final: 0.8495 (mp0) REVERT: B 402 GLU cc_start: 0.8655 (mp0) cc_final: 0.8320 (mp0) REVERT: B 413 SER cc_start: 0.9547 (m) cc_final: 0.9129 (t) REVERT: B 414 LEU cc_start: 0.9748 (mt) cc_final: 0.9526 (mt) REVERT: B 452 ARG cc_start: 0.9337 (ttp80) cc_final: 0.9051 (mmm-85) REVERT: B 458 MET cc_start: 0.9407 (mmm) cc_final: 0.9101 (mmm) REVERT: B 494 MET cc_start: 0.9381 (mtt) cc_final: 0.8780 (mtt) REVERT: B 585 SER cc_start: 0.9168 (p) cc_final: 0.8812 (t) REVERT: B 588 GLN cc_start: 0.9440 (mm110) cc_final: 0.9223 (mm110) REVERT: B 591 THR cc_start: 0.9160 (p) cc_final: 0.8783 (p) REVERT: B 606 TYR cc_start: 0.8273 (m-80) cc_final: 0.7920 (m-10) REVERT: B 612 TYR cc_start: 0.9118 (m-10) cc_final: 0.8741 (m-10) REVERT: B 615 MET cc_start: 0.9000 (mmp) cc_final: 0.8786 (mmm) REVERT: B 631 ASP cc_start: 0.9037 (m-30) cc_final: 0.8802 (m-30) REVERT: B 636 LYS cc_start: 0.9703 (mptt) cc_final: 0.9440 (mmmt) REVERT: B 639 ASP cc_start: 0.9332 (m-30) cc_final: 0.8936 (m-30) REVERT: B 667 LEU cc_start: 0.9491 (tp) cc_final: 0.9255 (tt) REVERT: B 668 ASN cc_start: 0.9340 (m-40) cc_final: 0.8879 (m-40) REVERT: B 677 ARG cc_start: 0.9577 (mmm160) cc_final: 0.9323 (mmm-85) REVERT: B 683 TYR cc_start: 0.8931 (t80) cc_final: 0.8508 (t80) REVERT: C 56 MET cc_start: -0.0952 (ttp) cc_final: -0.1289 (ttp) REVERT: C 100 VAL cc_start: 0.8697 (t) cc_final: 0.8292 (p) REVERT: C 124 TRP cc_start: 0.8514 (t60) cc_final: 0.8181 (t60) REVERT: D 68 GLU cc_start: 0.8277 (mp0) cc_final: 0.8035 (mp0) REVERT: D 69 GLN cc_start: 0.9389 (tp40) cc_final: 0.8868 (tp40) REVERT: D 74 MET cc_start: 0.8814 (mmp) cc_final: 0.8592 (mmp) REVERT: D 93 MET cc_start: 0.8913 (mtm) cc_final: 0.8689 (mtm) REVERT: D 97 GLU cc_start: 0.6306 (pt0) cc_final: 0.5713 (pt0) REVERT: D 211 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8536 (mt-10) outliers start: 0 outliers final: 0 residues processed: 622 average time/residue: 0.1268 time to fit residues: 119.2381 Evaluate side-chains 561 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 561 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 189 optimal weight: 7.9990 chunk 181 optimal weight: 10.0000 chunk 165 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 54 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN A 158 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN C 186 GLN D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.133665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.090903 restraints weight = 47451.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.094040 restraints weight = 27552.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.096096 restraints weight = 18229.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.097441 restraints weight = 13207.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.098543 restraints weight = 10364.420| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.7615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16386 Z= 0.199 Angle : 0.653 8.766 22134 Z= 0.351 Chirality : 0.044 0.323 2360 Planarity : 0.004 0.056 2818 Dihedral : 8.526 134.702 2290 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.06 % Allowed : 0.41 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.19), residues: 1932 helix: 0.98 (0.15), residues: 1146 sheet: 0.21 (0.48), residues: 110 loop : -0.28 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 161 TYR 0.044 0.002 TYR C 142 PHE 0.022 0.002 PHE D 109 TRP 0.014 0.002 TRP C 124 HIS 0.011 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.20 (16386) covalent geometry : angle 0.65298 / 0.35 (22134) hydrogen bonds : bond 0.03839 / 2.43 ( 871) hydrogen bonds : angle 5.03318 / 3.57 ( 2571) ********************** 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 612 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 611 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9505 (t0) cc_final: 0.9140 (t70) REVERT: A 95 MET cc_start: 0.9079 (tpp) cc_final: 0.8496 (tpt) REVERT: A 117 ARG cc_start: 0.9234 (mtp180) cc_final: 0.9008 (mtt180) REVERT: A 119 GLU cc_start: 0.9112 (mp0) cc_final: 0.8525 (mt-10) REVERT: A 129 PHE cc_start: 0.9237 (m-80) cc_final: 0.8916 (m-80) REVERT: A 147 GLN cc_start: 0.9365 (mm-40) cc_final: 0.8834 (mm110) REVERT: A 176 ASN cc_start: 0.9093 (t0) cc_final: 0.8701 (m-40) REVERT: A 195 LEU cc_start: 0.9575 (mt) cc_final: 0.9363 (mt) REVERT: A 204 SER cc_start: 0.9386 (m) cc_final: 0.9070 (p) REVERT: A 235 ARG cc_start: 0.8831 (mtm110) cc_final: 0.8424 (mtm180) REVERT: A 251 LEU cc_start: 0.9629 (tp) cc_final: 0.9309 (tp) REVERT: A 252 ASN cc_start: 0.9363 (t0) cc_final: 0.8971 (t0) REVERT: A 307 TYR cc_start: 0.9620 (t80) cc_final: 0.9125 (t80) REVERT: A 322 MET cc_start: 0.8950 (tpt) cc_final: 0.8619 (mmm) REVERT: A 350 ARG cc_start: 0.8984 (mmm-85) cc_final: 0.8499 (mmm-85) REVERT: A 394 TYR cc_start: 0.9271 (m-80) cc_final: 0.8658 (m-80) REVERT: A 418 ASN cc_start: 0.9693 (m-40) cc_final: 0.8968 (t0) REVERT: A 421 GLU cc_start: 0.9233 (tm-30) cc_final: 0.8962 (tm-30) REVERT: A 447 ASN cc_start: 0.9138 (m-40) cc_final: 0.8638 (t0) REVERT: A 459 LYS cc_start: 0.9283 (mttp) cc_final: 0.8114 (mtmm) REVERT: A 468 LEU cc_start: 0.9668 (tp) cc_final: 0.9440 (tp) REVERT: A 472 LEU cc_start: 0.9769 (mt) cc_final: 0.9533 (mt) REVERT: A 493 MET cc_start: 0.9140 (tmm) cc_final: 0.8732 (tmm) REVERT: A 494 MET cc_start: 0.9394 (mtp) cc_final: 0.9089 (mtp) REVERT: A 499 SER cc_start: 0.9886 (t) cc_final: 0.9344 (p) REVERT: A 500 ILE cc_start: 0.9668 (mp) cc_final: 0.8782 (mp) REVERT: A 515 ASP cc_start: 0.9355 (m-30) cc_final: 0.9129 (m-30) REVERT: A 522 TYR cc_start: 0.9255 (m-10) cc_final: 0.8948 (m-10) REVERT: A 570 MET cc_start: 0.9309 (mtp) cc_final: 0.8056 (mtp) REVERT: A 571 TYR cc_start: 0.9291 (t80) cc_final: 0.8182 (t80) REVERT: A 575 ARG cc_start: 0.9448 (mtm110) cc_final: 0.8783 (mpp80) REVERT: A 586 TYR cc_start: 0.8851 (m-10) cc_final: 0.8566 (m-10) REVERT: A 599 GLU cc_start: 0.9192 (tm-30) cc_final: 0.8696 (tm-30) REVERT: A 602 GLU cc_start: 0.8164 (pt0) cc_final: 0.6816 (pt0) REVERT: A 615 MET cc_start: 0.8976 (mmp) cc_final: 0.8532 (mmp) REVERT: A 639 ASP cc_start: 0.9321 (m-30) cc_final: 0.9079 (m-30) REVERT: A 645 GLN cc_start: 0.9226 (tp40) cc_final: 0.8947 (tp-100) REVERT: B 15 GLU cc_start: 0.9312 (tp30) cc_final: 0.8804 (tp30) REVERT: B 51 LEU cc_start: 0.9294 (tp) cc_final: 0.9022 (tp) REVERT: B 95 MET cc_start: 0.9210 (tpp) cc_final: 0.8779 (tpp) REVERT: B 99 LYS cc_start: 0.9524 (mmmt) cc_final: 0.9101 (mmmt) REVERT: B 128 PHE cc_start: 0.9551 (t80) cc_final: 0.9320 (t80) REVERT: B 136 LYS cc_start: 0.9688 (mmtp) cc_final: 0.9297 (mmmm) REVERT: B 144 MET cc_start: 0.9023 (mtm) cc_final: 0.8752 (mtm) REVERT: B 147 GLN cc_start: 0.9353 (mt0) cc_final: 0.8892 (mt0) REVERT: B 157 LEU cc_start: 0.9545 (tp) cc_final: 0.9162 (tp) REVERT: B 161 ARG cc_start: 0.8653 (ttm110) cc_final: 0.7975 (mtp85) REVERT: B 200 SER cc_start: 0.8994 (t) cc_final: 0.8708 (t) REVERT: B 218 ASN cc_start: 0.9299 (m-40) cc_final: 0.8914 (m110) REVERT: B 251 LEU cc_start: 0.9517 (tp) cc_final: 0.9227 (tp) REVERT: B 286 ASP cc_start: 0.8657 (m-30) cc_final: 0.8036 (m-30) REVERT: B 290 GLU cc_start: 0.9193 (pp20) cc_final: 0.8392 (pp20) REVERT: B 291 LEU cc_start: 0.9602 (mt) cc_final: 0.9315 (mt) REVERT: B 294 GLU cc_start: 0.9474 (mp0) cc_final: 0.9090 (mp0) REVERT: B 296 LYS cc_start: 0.9088 (mmpt) cc_final: 0.8781 (mtmm) REVERT: B 322 MET cc_start: 0.8691 (mmm) cc_final: 0.8412 (mmm) REVERT: B 333 LYS cc_start: 0.9451 (ttmm) cc_final: 0.9160 (ttmm) REVERT: B 335 GLU cc_start: 0.9026 (pt0) cc_final: 0.8636 (pp20) REVERT: B 337 ILE cc_start: 0.9480 (mp) cc_final: 0.8853 (mp) REVERT: B 342 LEU cc_start: 0.9757 (tp) cc_final: 0.9488 (tp) REVERT: B 344 GLU cc_start: 0.9309 (mm-30) cc_final: 0.9013 (mm-30) REVERT: B 348 MET cc_start: 0.9504 (tpp) cc_final: 0.9052 (tpp) REVERT: B 350 ARG cc_start: 0.8892 (mtp85) cc_final: 0.8140 (mtp85) REVERT: B 357 TYR cc_start: 0.9061 (m-80) cc_final: 0.8809 (m-80) REVERT: B 362 ASP cc_start: 0.9041 (m-30) cc_final: 0.8004 (m-30) REVERT: B 375 LYS cc_start: 0.9154 (mmtm) cc_final: 0.8682 (mmtm) REVERT: B 393 SER cc_start: 0.9506 (t) cc_final: 0.8805 (t) REVERT: B 398 ASP cc_start: 0.8880 (t70) cc_final: 0.8583 (t70) REVERT: B 402 GLU cc_start: 0.8620 (mp0) cc_final: 0.8201 (mp0) REVERT: B 403 ILE cc_start: 0.9209 (mm) cc_final: 0.8793 (tp) REVERT: B 407 ILE cc_start: 0.8992 (mt) cc_final: 0.8700 (mt) REVERT: B 413 SER cc_start: 0.9540 (m) cc_final: 0.9171 (t) REVERT: B 414 LEU cc_start: 0.9760 (mt) cc_final: 0.9504 (mt) REVERT: B 458 MET cc_start: 0.9461 (mmm) cc_final: 0.9140 (mmm) REVERT: B 494 MET cc_start: 0.9368 (mtt) cc_final: 0.8756 (mtt) REVERT: B 606 TYR cc_start: 0.8431 (m-80) cc_final: 0.7983 (m-10) REVERT: B 612 TYR cc_start: 0.9162 (m-10) cc_final: 0.8541 (m-10) REVERT: B 615 MET cc_start: 0.9077 (mmp) cc_final: 0.8812 (mmm) REVERT: B 631 ASP cc_start: 0.9094 (m-30) cc_final: 0.8847 (m-30) REVERT: B 636 LYS cc_start: 0.9686 (mptt) cc_final: 0.9437 (mmmt) REVERT: B 639 ASP cc_start: 0.9321 (m-30) cc_final: 0.8947 (m-30) REVERT: B 667 LEU cc_start: 0.9478 (tp) cc_final: 0.9211 (tt) REVERT: B 668 ASN cc_start: 0.9387 (m-40) cc_final: 0.8873 (m-40) REVERT: B 677 ARG cc_start: 0.9598 (mmm160) cc_final: 0.9340 (mmm-85) REVERT: B 683 TYR cc_start: 0.8885 (t80) cc_final: 0.8537 (t80) REVERT: C 56 MET cc_start: -0.0921 (ttp) cc_final: -0.1247 (ttp) REVERT: C 100 VAL cc_start: 0.8551 (t) cc_final: 0.8237 (p) REVERT: C 124 TRP cc_start: 0.8509 (t60) cc_final: 0.8185 (t60) REVERT: D 69 GLN cc_start: 0.9395 (tp40) cc_final: 0.8931 (tp40) REVERT: D 91 ASN cc_start: 0.8587 (m110) cc_final: 0.8172 (m110) REVERT: D 97 GLU cc_start: 0.6336 (pt0) cc_final: 0.6105 (pt0) REVERT: D 205 VAL cc_start: 0.9243 (t) cc_final: 0.9042 (t) outliers start: 1 outliers final: 0 residues processed: 611 average time/residue: 0.1249 time to fit residues: 114.9185 Evaluate side-chains 543 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 543 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 8.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 GLN A 158 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.135777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.092916 restraints weight = 46255.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.096089 restraints weight = 26822.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.098145 restraints weight = 17822.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.099481 restraints weight = 12945.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.100600 restraints weight = 10247.195| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.7757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16386 Z= 0.163 Angle : 0.656 12.249 22134 Z= 0.354 Chirality : 0.044 0.282 2360 Planarity : 0.004 0.055 2818 Dihedral : 8.428 136.190 2290 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.06 % Allowed : 0.41 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.19), residues: 1932 helix: 0.92 (0.15), residues: 1145 sheet: 0.20 (0.48), residues: 110 loop : -0.27 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 161 TYR 0.042 0.002 TYR C 142 PHE 0.022 0.002 PHE D 109 TRP 0.014 0.002 TRP D 44 HIS 0.011 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (16386) covalent geometry : angle 0.65603 / 0.35 (22134) hydrogen bonds : bond 0.03907 / 2.48 ( 871) hydrogen bonds : angle 5.04717 / 3.58 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3518.78 seconds wall clock time: 61 minutes 45.50 seconds (3705.50 seconds total)