Starting phenix.real_space_refine on Fri Jul 3 19:48:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz3_45052/07_2026/9bz3_45052_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz3_45052/07_2026/9bz3_45052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bz3_45052/07_2026/9bz3_45052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz3_45052/07_2026/9bz3_45052.map" model { file = "/net/cci-nas-00/data/ceres_data/9bz3_45052/07_2026/9bz3_45052_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz3_45052/07_2026/9bz3_45052_neut.cif" } resolution = 4.01 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 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: 2.95, per 1000 atoms: 0.18 Number of scatterers: 16038 At special positions: 0 Unit cell: (96.615, 129.159, 132.21, 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: 1.11 Conformation dependent library (CDL) restraints added in 663.3 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: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.986A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.954A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.665A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A 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: 3.694A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.628A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.118A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.676A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A 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: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.027A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.068A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.936A 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: 6.359A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.479A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.192A 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: 6.382A 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: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.50 Time building geometry restraints manager: 1.53 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: 4851 1.34 - 1.46: 3061 1.46 - 1.58: 8293 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.81e+01 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 4.80e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.25e-02 6.40e+03 2.39e+01 bond pdb=" O3A TTP A 803 " pdb=" PB TTP A 803 " ideal model delta sigma weight residual 1.675 1.605 0.070 2.00e-02 2.50e+03 1.22e+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 1.15e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21531 2.09 - 4.18: 522 4.18 - 6.27: 63 6.27 - 8.36: 9 8.36 - 10.45: 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 110.54 116.63 -6.09 1.36e+00 5.41e-01 2.00e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.17 -4.46 1.15e+00 7.56e-01 1.50e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.25 -3.97 1.09e+00 8.42e-01 1.33e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.85 -4.35 1.23e+00 6.61e-01 1.25e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.71 -4.00 1.15e+00 7.56e-01 1.21e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.06: 9088 25.06 - 50.12: 656 50.12 - 75.17: 126 75.17 - 100.23: 26 100.23 - 125.29: 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 -98.27 125.29 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 -95.61 122.63 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 -134.27 12.27 0 2.50e+00 1.60e-01 2.41e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2144 0.094 - 0.187: 183 0.187 - 0.281: 29 0.281 - 0.375: 2 0.375 - 0.469: 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 5.49e+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 4.56e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " 0.017 2.00e-02 2.50e+03 1.12e-02 2.18e+00 pdb=" CG PHE D 92 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.001 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 D 179 " -0.017 2.00e-02 2.50e+03 9.83e-03 1.93e+00 pdb=" CG TYR D 179 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR D 179 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR D 179 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR D 179 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 179 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 179 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 179 " -0.005 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 129 2.51 - 3.11: 11559 3.11 - 3.70: 27043 3.70 - 4.30: 41517 4.30 - 4.90: 65377 Nonbonded interactions: 145625 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 3.060 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 3.060 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 3.060 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.012 3.040 ... (remaining 145620 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: 1.050 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: 13.920 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 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 10.455 22134 Z= 0.472 Chirality : 0.058 0.469 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.680 125.289 6202 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.34 % Allowed : 15.27 % Favored : 83.39 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.58 (0.14), residues: 1151 sheet: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 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 0.78792 / 0.47 (22134) hydrogen bonds : bond 0.15421 / 9.51 ( 871) hydrogen bonds : angle 6.51731 / 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 822 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 799 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8448 (t0) cc_final: 0.8229 (t70) REVERT: A 68 PHE cc_start: 0.8635 (p90) cc_final: 0.8319 (p90) REVERT: A 106 LEU cc_start: 0.9003 (tp) cc_final: 0.8700 (tp) REVERT: A 120 ASP cc_start: 0.7014 (m-30) cc_final: 0.6684 (m-30) REVERT: A 122 ILE cc_start: 0.9216 (mt) cc_final: 0.8933 (mt) REVERT: A 134 THR cc_start: 0.7929 (t) cc_final: 0.7579 (t) REVERT: A 186 ILE cc_start: 0.9310 (mt) cc_final: 0.9047 (mt) REVERT: A 200 SER cc_start: 0.9120 (t) cc_final: 0.8887 (p) REVERT: A 202 ASN cc_start: 0.9124 (t0) cc_final: 0.8612 (t0) REVERT: A 204 SER cc_start: 0.8970 (m) cc_final: 0.8634 (p) REVERT: A 227 MET cc_start: 0.8293 (mtp) cc_final: 0.7903 (mtp) REVERT: A 322 MET cc_start: 0.8217 (mmp) cc_final: 0.7951 (mmp) REVERT: A 362 ASP cc_start: 0.6331 (m-30) cc_final: 0.6105 (m-30) REVERT: A 367 VAL cc_start: 0.9095 (m) cc_final: 0.8712 (p) REVERT: A 417 LEU cc_start: 0.8510 (tt) cc_final: 0.7871 (tt) REVERT: A 425 ILE cc_start: 0.8978 (mt) cc_final: 0.8494 (mt) REVERT: A 436 LEU cc_start: 0.9194 (mt) cc_final: 0.8976 (mm) REVERT: A 447 ASN cc_start: 0.7972 (m-40) cc_final: 0.7770 (m-40) REVERT: A 458 MET cc_start: 0.8831 (mmm) cc_final: 0.8310 (mtm) REVERT: A 576 LEU cc_start: 0.8899 (mt) cc_final: 0.8672 (mt) REVERT: A 606 TYR cc_start: 0.6769 (m-80) cc_final: 0.6552 (m-80) REVERT: A 618 LEU cc_start: 0.9218 (tp) cc_final: 0.8984 (tp) REVERT: A 630 TYR cc_start: 0.7538 (m-80) cc_final: 0.6524 (m-80) REVERT: A 634 MET cc_start: 0.8587 (mmp) cc_final: 0.8325 (mmm) REVERT: A 640 MET cc_start: 0.7738 (tpp) cc_final: 0.7285 (tpp) REVERT: A 670 ILE cc_start: 0.9244 (mt) cc_final: 0.9024 (mt) REVERT: B 51 LEU cc_start: 0.8434 (tp) cc_final: 0.8202 (tp) REVERT: B 116 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7303 (mt-10) REVERT: B 156 PHE cc_start: 0.8455 (t80) cc_final: 0.8208 (t80) REVERT: B 167 LEU cc_start: 0.8207 (mt) cc_final: 0.7970 (mt) REVERT: B 190 MET cc_start: 0.8381 (mtm) cc_final: 0.8127 (mtm) REVERT: B 322 MET cc_start: 0.8152 (mmm) cc_final: 0.7789 (tpp) REVERT: B 362 ASP cc_start: 0.6823 (m-30) cc_final: 0.6117 (m-30) REVERT: B 373 ILE cc_start: 0.8899 (mt) cc_final: 0.8612 (mt) REVERT: B 466 MET cc_start: 0.8431 (ptp) cc_final: 0.8107 (ptm) REVERT: B 467 ASN cc_start: 0.8888 (t0) cc_final: 0.8478 (t0) REVERT: B 471 TYR cc_start: 0.8362 (t80) cc_final: 0.8153 (t80) REVERT: B 500 ILE cc_start: 0.9270 (mt) cc_final: 0.9049 (mt) REVERT: B 522 TYR cc_start: 0.8492 (m-80) cc_final: 0.8094 (m-10) REVERT: B 550 MET cc_start: 0.8179 (mtm) cc_final: 0.7348 (mtp) REVERT: B 570 MET cc_start: 0.7240 (mtm) cc_final: 0.6754 (mtm) REVERT: B 576 LEU cc_start: 0.9117 (mt) cc_final: 0.8820 (mt) REVERT: B 590 SER cc_start: 0.8861 (p) cc_final: 0.8207 (t) REVERT: B 591 THR cc_start: 0.9291 (p) cc_final: 0.8600 (m) REVERT: B 597 ILE cc_start: 0.9135 (pt) cc_final: 0.8769 (pt) REVERT: C 31 LEU cc_start: 0.5709 (mt) cc_final: 0.5442 (mt) REVERT: C 155 LYS cc_start: 0.7170 (mttt) cc_final: 0.6918 (mttm) REVERT: D 130 TYR cc_start: 0.1601 (m-80) cc_final: 0.0661 (m-10) REVERT: D 136 GLN cc_start: 0.1071 (mm-40) cc_final: 0.0602 (tm-30) REVERT: D 137 MET cc_start: -0.0170 (mtp) cc_final: -0.0759 (mtp) REVERT: D 256 VAL cc_start: 0.5301 (t) cc_final: 0.4484 (t) outliers start: 23 outliers final: 6 residues processed: 810 average time/residue: 0.1213 time to fit residues: 144.1693 Evaluate side-chains 549 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 543 time to evaluate : 0.496 ------------------------------------------------------------------------------- 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: 4.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN A 242 GLN A 320 ASN A 370 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 410 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN B 668 ASN C 85 GLN C 201 HIS D 71 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.162216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.109933 restraints weight = 33509.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.113591 restraints weight = 16141.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.115985 restraints weight = 9672.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.117480 restraints weight = 6649.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.118477 restraints weight = 5045.764| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3347 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16386 Z= 0.220 Angle : 0.612 7.882 22134 Z= 0.330 Chirality : 0.043 0.313 2360 Planarity : 0.004 0.031 2818 Dihedral : 9.417 131.403 2290 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.12 % Allowed : 3.26 % Favored : 96.62 % 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: 1.39 (0.19), residues: 1932 helix: 1.40 (0.15), residues: 1128 sheet: -0.05 (0.41), residues: 146 loop : 0.52 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 256 TYR 0.021 0.002 TYR A 522 PHE 0.034 0.002 PHE C 227 TRP 0.014 0.002 TRP A 623 HIS 0.008 0.001 HIS A 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.22 (16386) covalent geometry : angle 0.61208 / 0.33 (22134) hydrogen bonds : bond 0.04744 / 2.95 ( 871) hydrogen bonds : angle 5.07912 / 3.60 ( 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 626 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 624 time to evaluate : 0.428 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: A 106 LEU cc_start: 0.9364 (tp) cc_final: 0.9160 (tp) REVERT: A 122 ILE cc_start: 0.9332 (mt) cc_final: 0.9053 (mt) REVERT: A 156 PHE cc_start: 0.9468 (t80) cc_final: 0.9075 (t80) REVERT: A 179 LEU cc_start: 0.9345 (tp) cc_final: 0.9073 (tp) REVERT: A 188 ILE cc_start: 0.9604 (mt) cc_final: 0.9366 (mm) REVERT: A 202 ASN cc_start: 0.9288 (t0) cc_final: 0.9049 (t0) REVERT: A 204 SER cc_start: 0.9157 (m) cc_final: 0.8614 (t) REVERT: A 232 ASN cc_start: 0.8504 (m-40) cc_final: 0.8254 (m110) REVERT: A 286 ASP cc_start: 0.8043 (m-30) cc_final: 0.7690 (m-30) REVERT: A 308 LYS cc_start: 0.9588 (mtmt) cc_final: 0.9343 (mtmm) REVERT: A 362 ASP cc_start: 0.7315 (m-30) cc_final: 0.7044 (m-30) REVERT: A 367 VAL cc_start: 0.9702 (m) cc_final: 0.9477 (p) REVERT: A 447 ASN cc_start: 0.8408 (m-40) cc_final: 0.7278 (m-40) REVERT: A 458 MET cc_start: 0.9321 (mmm) cc_final: 0.8486 (mmm) REVERT: A 485 ARG cc_start: 0.8354 (mtm-85) cc_final: 0.7390 (mtm-85) REVERT: A 494 MET cc_start: 0.8756 (mtp) cc_final: 0.8400 (mtp) REVERT: A 576 LEU cc_start: 0.9012 (mt) cc_final: 0.8759 (mt) REVERT: A 583 SER cc_start: 0.9124 (m) cc_final: 0.8724 (t) REVERT: A 586 TYR cc_start: 0.8471 (m-80) cc_final: 0.8167 (m-10) REVERT: A 590 SER cc_start: 0.9235 (t) cc_final: 0.8786 (m) REVERT: A 602 GLU cc_start: 0.7208 (pt0) cc_final: 0.6557 (pt0) REVERT: A 606 TYR cc_start: 0.7950 (m-80) cc_final: 0.7680 (m-10) REVERT: A 630 TYR cc_start: 0.8562 (m-80) cc_final: 0.8357 (m-80) REVERT: A 640 MET cc_start: 0.9043 (tpp) cc_final: 0.8624 (tpp) REVERT: A 662 MET cc_start: 0.8458 (pmm) cc_final: 0.8227 (pmm) REVERT: A 667 LEU cc_start: 0.9058 (tt) cc_final: 0.8358 (tt) REVERT: A 668 ASN cc_start: 0.8907 (m110) cc_final: 0.8518 (m110) REVERT: B 108 THR cc_start: 0.8937 (OUTLIER) cc_final: 0.8655 (p) REVERT: B 115 LEU cc_start: 0.9233 (mp) cc_final: 0.8967 (mp) REVERT: B 156 PHE cc_start: 0.9224 (t80) cc_final: 0.8966 (t80) REVERT: B 190 MET cc_start: 0.9292 (mtm) cc_final: 0.8987 (mtm) REVERT: B 253 ILE cc_start: 0.9443 (tt) cc_final: 0.9203 (tt) REVERT: B 257 ASP cc_start: 0.8968 (m-30) cc_final: 0.8689 (m-30) REVERT: B 288 PHE cc_start: 0.9428 (t80) cc_final: 0.9188 (t80) REVERT: B 318 ASP cc_start: 0.8799 (t0) cc_final: 0.8544 (p0) REVERT: B 333 LYS cc_start: 0.8798 (tptp) cc_final: 0.8470 (tppt) REVERT: B 358 ILE cc_start: 0.9440 (mm) cc_final: 0.9164 (mm) REVERT: B 362 ASP cc_start: 0.8202 (m-30) cc_final: 0.7515 (m-30) REVERT: B 396 ASP cc_start: 0.8074 (m-30) cc_final: 0.7861 (m-30) REVERT: B 471 TYR cc_start: 0.9041 (t80) cc_final: 0.8609 (t80) REVERT: B 493 MET cc_start: 0.9344 (tmm) cc_final: 0.9030 (tmm) REVERT: B 512 GLU cc_start: 0.8553 (pt0) cc_final: 0.8271 (pt0) REVERT: B 550 MET cc_start: 0.8370 (mtm) cc_final: 0.8102 (mtp) REVERT: B 561 LEU cc_start: 0.9371 (tp) cc_final: 0.9084 (tp) REVERT: B 615 MET cc_start: 0.9107 (mmp) cc_final: 0.8849 (mmm) REVERT: B 627 LYS cc_start: 0.9135 (tttt) cc_final: 0.8749 (tttp) REVERT: B 662 MET cc_start: 0.8238 (ptp) cc_final: 0.7950 (ptp) REVERT: C 74 MET cc_start: 0.6080 (mtt) cc_final: 0.5500 (mtt) REVERT: C 154 PHE cc_start: 0.8610 (t80) cc_final: 0.8312 (t80) REVERT: C 239 GLU cc_start: 0.9032 (tp30) cc_final: 0.8653 (tp30) REVERT: D 95 MET cc_start: 0.6984 (ttp) cc_final: 0.6710 (ttp) REVERT: D 242 TYR cc_start: 0.7812 (t80) cc_final: 0.7407 (t80) REVERT: D 245 ASP cc_start: 0.5048 (t0) cc_final: 0.4751 (m-30) outliers start: 2 outliers final: 0 residues processed: 625 average time/residue: 0.1085 time to fit residues: 101.8726 Evaluate side-chains 474 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 473 time to evaluate : 0.563 ------------------------------------------------------------------------------- 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: 2.9990 chunk 131 optimal weight: 0.6980 chunk 164 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 182 optimal weight: 10.0000 chunk 159 optimal weight: 6.9990 chunk 91 optimal weight: 10.0000 chunk 150 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 158 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 313 HIS A 676 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.162657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.112414 restraints weight = 33480.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.116150 restraints weight = 15958.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.118406 restraints weight = 9471.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.119975 restraints weight = 6443.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.121016 restraints weight = 4802.169| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.4474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 16386 Z= 0.149 Angle : 0.557 8.784 22134 Z= 0.297 Chirality : 0.041 0.186 2360 Planarity : 0.003 0.043 2818 Dihedral : 8.934 130.899 2290 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.06 % Allowed : 2.62 % Favored : 97.32 % 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: 1.52 (0.15), residues: 1132 sheet: -0.19 (0.40), residues: 146 loop : 0.49 (0.24), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 293 TYR 0.022 0.002 TYR D 22 PHE 0.038 0.002 PHE C 109 TRP 0.009 0.001 TRP B 9 HIS 0.013 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (16386) covalent geometry : angle 0.55668 / 0.30 (22134) hydrogen bonds : bond 0.04047 / 2.54 ( 871) hydrogen bonds : angle 4.76913 / 3.37 ( 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 595 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 594 time to evaluate : 0.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 ASP cc_start: 0.8295 (m-30) cc_final: 0.8019 (m-30) REVERT: A 128 PHE cc_start: 0.8848 (t80) cc_final: 0.8609 (t80) REVERT: A 158 ASN cc_start: 0.9018 (m110) cc_final: 0.8707 (m-40) REVERT: A 204 SER cc_start: 0.9179 (m) cc_final: 0.8617 (t) REVERT: A 232 ASN cc_start: 0.8400 (m-40) cc_final: 0.8129 (m110) REVERT: A 286 ASP cc_start: 0.8205 (m-30) cc_final: 0.7639 (m-30) REVERT: A 308 LYS cc_start: 0.9560 (mtmt) cc_final: 0.9342 (mtmm) REVERT: A 362 ASP cc_start: 0.7317 (m-30) cc_final: 0.7050 (m-30) REVERT: A 417 LEU cc_start: 0.9356 (tt) cc_final: 0.8461 (tt) REVERT: A 447 ASN cc_start: 0.8242 (m-40) cc_final: 0.7751 (m-40) REVERT: A 456 LYS cc_start: 0.9174 (pttm) cc_final: 0.8968 (ptpp) REVERT: A 458 MET cc_start: 0.9242 (mmm) cc_final: 0.8323 (mtm) REVERT: A 466 MET cc_start: 0.8948 (ptt) cc_final: 0.8635 (ptt) REVERT: A 576 LEU cc_start: 0.9065 (mt) cc_final: 0.8854 (mt) REVERT: A 583 SER cc_start: 0.9092 (m) cc_final: 0.8858 (t) REVERT: A 586 TYR cc_start: 0.8445 (m-80) cc_final: 0.8109 (m-10) REVERT: A 590 SER cc_start: 0.8692 (t) cc_final: 0.8470 (t) REVERT: A 602 GLU cc_start: 0.6968 (pt0) cc_final: 0.5948 (pt0) REVERT: A 604 ARG cc_start: 0.8422 (tpp-160) cc_final: 0.8170 (tpp-160) REVERT: A 640 MET cc_start: 0.9003 (tpp) cc_final: 0.8683 (tpp) REVERT: A 667 LEU cc_start: 0.9162 (tt) cc_final: 0.8574 (tt) REVERT: B 51 LEU cc_start: 0.8940 (tp) cc_final: 0.8674 (tp) REVERT: B 120 ASP cc_start: 0.8564 (m-30) cc_final: 0.8335 (m-30) REVERT: B 156 PHE cc_start: 0.9137 (t80) cc_final: 0.8906 (t80) REVERT: B 190 MET cc_start: 0.9274 (mtm) cc_final: 0.9012 (mtm) REVERT: B 253 ILE cc_start: 0.9455 (tt) cc_final: 0.9252 (tt) REVERT: B 276 LYS cc_start: 0.8789 (ptmt) cc_final: 0.8343 (ptpp) REVERT: B 288 PHE cc_start: 0.9445 (t80) cc_final: 0.9156 (t80) REVERT: B 291 LEU cc_start: 0.9546 (mt) cc_final: 0.9318 (mt) REVERT: B 348 MET cc_start: 0.7816 (tpp) cc_final: 0.7604 (tpp) REVERT: B 362 ASP cc_start: 0.8205 (m-30) cc_final: 0.7399 (m-30) REVERT: B 393 SER cc_start: 0.9484 (m) cc_final: 0.9238 (p) REVERT: B 471 TYR cc_start: 0.9036 (t80) cc_final: 0.8708 (t80) REVERT: B 493 MET cc_start: 0.9326 (tmm) cc_final: 0.9029 (tmm) REVERT: B 550 MET cc_start: 0.8409 (mtm) cc_final: 0.8112 (mtp) REVERT: B 561 LEU cc_start: 0.9425 (tp) cc_final: 0.9147 (tp) REVERT: B 615 MET cc_start: 0.9132 (mmp) cc_final: 0.8902 (mmm) REVERT: B 627 LYS cc_start: 0.9352 (tttt) cc_final: 0.8971 (tttp) REVERT: B 640 MET cc_start: 0.8917 (tpp) cc_final: 0.8426 (tpp) REVERT: B 662 MET cc_start: 0.8522 (ptp) cc_final: 0.8236 (ptp) REVERT: C 74 MET cc_start: 0.6639 (mtt) cc_final: 0.6049 (mtt) REVERT: C 89 VAL cc_start: 0.6034 (t) cc_final: 0.5780 (t) REVERT: C 154 PHE cc_start: 0.8513 (t80) cc_final: 0.8178 (t80) REVERT: C 239 GLU cc_start: 0.8960 (tp30) cc_final: 0.8543 (tp30) REVERT: D 21 PHE cc_start: 0.8454 (m-10) cc_final: 0.8172 (m-10) REVERT: D 68 GLU cc_start: 0.3869 (tp30) cc_final: 0.2709 (mm-30) REVERT: D 117 THR cc_start: 0.8520 (p) cc_final: 0.8261 (p) REVERT: D 242 TYR cc_start: 0.7722 (t80) cc_final: 0.7397 (t80) outliers start: 1 outliers final: 0 residues processed: 594 average time/residue: 0.1058 time to fit residues: 94.5807 Evaluate side-chains 473 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 473 time to evaluate : 0.577 ------------------------------------------------------------------------------- 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: 2.9990 chunk 157 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 89 optimal weight: 8.9990 chunk 127 optimal weight: 3.9990 chunk 60 optimal weight: 8.9990 chunk 185 optimal weight: 6.9990 chunk 191 optimal weight: 20.0000 chunk 159 optimal weight: 6.9990 chunk 182 optimal weight: 30.0000 chunk 93 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN A 370 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN B 11 GLN B 25 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.152445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.103396 restraints weight = 34667.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.106663 restraints weight = 16980.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.108717 restraints weight = 10218.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.110062 restraints weight = 7030.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.111057 restraints weight = 5329.381| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3203 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3203 r_free = 0.3203 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (13 function evaluations) r_final: 0.3203 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.5268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.100 16386 Z= 0.392 Angle : 0.745 7.282 22134 Z= 0.394 Chirality : 0.047 0.281 2360 Planarity : 0.004 0.046 2818 Dihedral : 9.238 133.727 2290 Min Nonbonded Distance : 1.692 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.17 % Allowed : 3.26 % Favored : 96.56 % 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: 0.98 (0.19), residues: 1932 helix: 1.09 (0.15), residues: 1131 sheet: -0.65 (0.40), residues: 140 loop : 0.41 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 453 TYR 0.027 0.002 TYR B 612 PHE 0.028 0.003 PHE B 68 TRP 0.024 0.003 TRP A 623 HIS 0.014 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00847 / 0.39 (16386) covalent geometry : angle 0.74456 / 0.39 (22134) hydrogen bonds : bond 0.04482 / 2.83 ( 871) hydrogen bonds : angle 5.02516 / 3.55 ( 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 511 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 508 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8445 (mm-30) cc_final: 0.7857 (mp0) REVERT: A 122 ILE cc_start: 0.9226 (mt) cc_final: 0.8997 (mt) REVERT: A 139 GLU cc_start: 0.8134 (mp0) cc_final: 0.7906 (mp0) REVERT: A 144 MET cc_start: 0.8963 (mtm) cc_final: 0.8659 (mtm) REVERT: A 188 ILE cc_start: 0.9636 (mt) cc_final: 0.9345 (mm) REVERT: A 204 SER cc_start: 0.9222 (m) cc_final: 0.8828 (t) REVERT: A 250 TYR cc_start: 0.8937 (m-80) cc_final: 0.8735 (m-80) REVERT: A 286 ASP cc_start: 0.7923 (m-30) cc_final: 0.7552 (m-30) REVERT: A 308 LYS cc_start: 0.9598 (mtmt) cc_final: 0.9378 (mtmm) REVERT: A 344 GLU cc_start: 0.8822 (pt0) cc_final: 0.8511 (pt0) REVERT: A 362 ASP cc_start: 0.7486 (m-30) cc_final: 0.7102 (m-30) REVERT: A 383 SER cc_start: 0.8699 (p) cc_final: 0.8253 (t) REVERT: A 406 ASP cc_start: 0.8619 (m-30) cc_final: 0.8360 (m-30) REVERT: A 447 ASN cc_start: 0.8175 (m-40) cc_final: 0.7368 (m-40) REVERT: A 458 MET cc_start: 0.9236 (mmm) cc_final: 0.8471 (mtm) REVERT: A 494 MET cc_start: 0.8774 (mtp) cc_final: 0.8450 (mtp) REVERT: A 576 LEU cc_start: 0.9106 (mt) cc_final: 0.8866 (mt) REVERT: A 583 SER cc_start: 0.9178 (m) cc_final: 0.8740 (t) REVERT: A 584 ILE cc_start: 0.9057 (pt) cc_final: 0.8854 (pt) REVERT: A 602 GLU cc_start: 0.7277 (pt0) cc_final: 0.6935 (pt0) REVERT: A 604 ARG cc_start: 0.8490 (tpp-160) cc_final: 0.7839 (ttm-80) REVERT: A 606 TYR cc_start: 0.7958 (m-10) cc_final: 0.7648 (m-10) REVERT: A 645 GLN cc_start: 0.9006 (tp40) cc_final: 0.8731 (tp-100) REVERT: A 667 LEU cc_start: 0.9369 (tt) cc_final: 0.8797 (tt) REVERT: B 51 LEU cc_start: 0.9145 (tp) cc_final: 0.8911 (tp) REVERT: B 102 ASN cc_start: 0.9254 (m110) cc_final: 0.8954 (m110) REVERT: B 117 ARG cc_start: 0.8683 (mtt-85) cc_final: 0.8155 (mmm-85) REVERT: B 120 ASP cc_start: 0.8816 (m-30) cc_final: 0.8569 (m-30) REVERT: B 214 LYS cc_start: 0.8074 (mmtm) cc_final: 0.7741 (mmtt) REVERT: B 276 LYS cc_start: 0.8912 (ptmt) cc_final: 0.8496 (ptpp) REVERT: B 286 ASP cc_start: 0.8395 (m-30) cc_final: 0.8179 (m-30) REVERT: B 358 ILE cc_start: 0.9402 (mm) cc_final: 0.9200 (mm) REVERT: B 393 SER cc_start: 0.9455 (m) cc_final: 0.9250 (p) REVERT: B 396 ASP cc_start: 0.8161 (m-30) cc_final: 0.7957 (m-30) REVERT: B 410 ASN cc_start: 0.9064 (m-40) cc_final: 0.8860 (m-40) REVERT: B 458 MET cc_start: 0.9025 (mmp) cc_final: 0.8823 (mmm) REVERT: B 467 ASN cc_start: 0.9459 (t0) cc_final: 0.9094 (t0) REVERT: B 512 GLU cc_start: 0.8782 (pt0) cc_final: 0.8511 (pt0) REVERT: B 604 ARG cc_start: 0.8680 (tpp80) cc_final: 0.8253 (tpp80) REVERT: B 627 LYS cc_start: 0.9337 (tttt) cc_final: 0.8991 (tttp) REVERT: B 640 MET cc_start: 0.8895 (tpp) cc_final: 0.8387 (tpp) REVERT: B 650 GLN cc_start: 0.7973 (mt0) cc_final: 0.7733 (mt0) REVERT: B 662 MET cc_start: 0.8460 (ptp) cc_final: 0.8258 (ptp) REVERT: C 74 MET cc_start: 0.7464 (mtt) cc_final: 0.6861 (mtt) REVERT: C 95 MET cc_start: 0.7324 (tmm) cc_final: 0.6932 (ptm) REVERT: D 173 TYR cc_start: 0.6994 (t80) cc_final: 0.6573 (t80) outliers start: 3 outliers final: 0 residues processed: 509 average time/residue: 0.1078 time to fit residues: 83.0298 Evaluate side-chains 416 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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: 0.7980 chunk 120 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 126 optimal weight: 0.9990 chunk 129 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 157 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN A 232 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 28 GLN C 69 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.160403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.110640 restraints weight = 33765.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.114164 restraints weight = 16290.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.116478 restraints weight = 9613.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.117902 restraints weight = 6453.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.119034 restraints weight = 4854.638| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3325 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3325 r_free = 0.3325 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3325 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.5393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 16386 Z= 0.134 Angle : 0.565 7.340 22134 Z= 0.302 Chirality : 0.041 0.199 2360 Planarity : 0.003 0.038 2818 Dihedral : 8.669 130.078 2290 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.06 % Allowed : 2.27 % Favored : 97.67 % 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: 1.15 (0.19), residues: 1932 helix: 1.28 (0.15), residues: 1157 sheet: 0.01 (0.44), residues: 116 loop : 0.15 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 686 TYR 0.026 0.001 TYR D 130 PHE 0.041 0.002 PHE C 109 TRP 0.038 0.002 TRP D 124 HIS 0.011 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (16386) covalent geometry : angle 0.56482 / 0.30 (22134) hydrogen bonds : bond 0.03856 / 2.44 ( 871) hydrogen bonds : angle 4.73617 / 3.37 ( 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 549 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 548 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.8723 (m-10) cc_final: 0.8324 (m-10) REVERT: A 65 GLU cc_start: 0.8345 (mm-30) cc_final: 0.7797 (mp0) REVERT: A 144 MET cc_start: 0.8794 (mtm) cc_final: 0.8494 (mtm) REVERT: A 188 ILE cc_start: 0.9611 (mt) cc_final: 0.9366 (mm) REVERT: A 204 SER cc_start: 0.9208 (m) cc_final: 0.8679 (t) REVERT: A 228 LYS cc_start: 0.9003 (mmmt) cc_final: 0.8711 (mmtt) REVERT: A 231 ASP cc_start: 0.8558 (t0) cc_final: 0.8325 (t0) REVERT: A 257 ASP cc_start: 0.8964 (m-30) cc_final: 0.8744 (m-30) REVERT: A 290 GLU cc_start: 0.8723 (mm-30) cc_final: 0.8351 (mm-30) REVERT: A 308 LYS cc_start: 0.9551 (mtmt) cc_final: 0.9331 (mtmm) REVERT: A 344 GLU cc_start: 0.8856 (pt0) cc_final: 0.8506 (pt0) REVERT: A 406 ASP cc_start: 0.8562 (m-30) cc_final: 0.8189 (m-30) REVERT: A 458 MET cc_start: 0.9171 (mmm) cc_final: 0.8351 (mtm) REVERT: A 576 LEU cc_start: 0.9078 (mt) cc_final: 0.8819 (mt) REVERT: A 602 GLU cc_start: 0.7056 (pt0) cc_final: 0.6703 (pt0) REVERT: A 604 ARG cc_start: 0.8341 (tpp-160) cc_final: 0.7592 (ttm-80) REVERT: A 667 LEU cc_start: 0.9188 (tt) cc_final: 0.8578 (tt) REVERT: B 51 LEU cc_start: 0.8933 (tp) cc_final: 0.8666 (tp) REVERT: B 102 ASN cc_start: 0.9304 (m110) cc_final: 0.8951 (m110) REVERT: B 117 ARG cc_start: 0.8679 (mtt-85) cc_final: 0.8124 (mmm-85) REVERT: B 120 ASP cc_start: 0.8690 (m-30) cc_final: 0.8428 (m-30) REVERT: B 156 PHE cc_start: 0.9085 (t80) cc_final: 0.8792 (t80) REVERT: B 179 LEU cc_start: 0.9523 (tp) cc_final: 0.9276 (tp) REVERT: B 190 MET cc_start: 0.9301 (mtm) cc_final: 0.9061 (mtm) REVERT: B 191 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8300 (mm-40) REVERT: B 218 ASN cc_start: 0.8820 (t0) cc_final: 0.8482 (t0) REVERT: B 235 ARG cc_start: 0.8588 (ttm110) cc_final: 0.8184 (mtm110) REVERT: B 276 LYS cc_start: 0.8836 (ptmt) cc_final: 0.8484 (ptpp) REVERT: B 286 ASP cc_start: 0.8493 (m-30) cc_final: 0.8226 (m-30) REVERT: B 288 PHE cc_start: 0.9497 (t80) cc_final: 0.9205 (t80) REVERT: B 358 ILE cc_start: 0.9456 (mm) cc_final: 0.9210 (mm) REVERT: B 379 SER cc_start: 0.8856 (t) cc_final: 0.8653 (t) REVERT: B 393 SER cc_start: 0.9463 (m) cc_final: 0.9137 (p) REVERT: B 427 LYS cc_start: 0.9444 (pttt) cc_final: 0.9206 (pttt) REVERT: B 458 MET cc_start: 0.9008 (mmp) cc_final: 0.8804 (mmm) REVERT: B 467 ASN cc_start: 0.9296 (t0) cc_final: 0.8782 (t0) REVERT: B 471 TYR cc_start: 0.9264 (t80) cc_final: 0.8790 (t80) REVERT: B 512 GLU cc_start: 0.8713 (pt0) cc_final: 0.8451 (pt0) REVERT: B 604 ARG cc_start: 0.8651 (tpp80) cc_final: 0.8081 (tpp80) REVERT: B 627 LYS cc_start: 0.9382 (tttt) cc_final: 0.9061 (tttp) REVERT: B 640 MET cc_start: 0.8929 (tpp) cc_final: 0.8382 (tpp) REVERT: B 683 TYR cc_start: 0.8279 (t80) cc_final: 0.7917 (t80) REVERT: C 89 VAL cc_start: 0.6630 (t) cc_final: 0.6165 (t) REVERT: C 208 LEU cc_start: 0.9342 (mt) cc_final: 0.9139 (mt) REVERT: D 68 GLU cc_start: 0.3892 (tp30) cc_final: 0.2894 (mm-30) REVERT: D 95 MET cc_start: 0.6493 (ttt) cc_final: 0.6179 (ttt) REVERT: D 173 TYR cc_start: 0.7125 (t80) cc_final: 0.6766 (t80) outliers start: 1 outliers final: 0 residues processed: 549 average time/residue: 0.1118 time to fit residues: 92.8276 Evaluate side-chains 446 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 446 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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: 5.9990 chunk 183 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 172 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 4 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 27 optimal weight: 0.0370 chunk 136 optimal weight: 6.9990 overall best weight: 1.5662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN A 232 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN B 232 ASN B 361 GLN B 501 GLN B 668 ASN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.159018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.109967 restraints weight = 33797.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.113481 restraints weight = 16123.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.115602 restraints weight = 9534.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.117065 restraints weight = 6485.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.117922 restraints weight = 4837.423| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3316 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3316 r_free = 0.3316 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3316 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16386 Z= 0.162 Angle : 0.569 7.700 22134 Z= 0.307 Chirality : 0.042 0.160 2360 Planarity : 0.003 0.038 2818 Dihedral : 8.467 132.583 2290 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % 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: 1.12 (0.19), residues: 1932 helix: 1.32 (0.15), residues: 1141 sheet: 0.02 (0.45), residues: 110 loop : 0.02 (0.23), residues: 681 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 686 TYR 0.023 0.002 TYR D 130 PHE 0.042 0.002 PHE C 109 TRP 0.041 0.002 TRP D 124 HIS 0.010 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (16386) covalent geometry : angle 0.56863 / 0.31 (22134) hydrogen bonds : bond 0.03793 / 2.41 ( 871) hydrogen bonds : angle 4.78516 / 3.40 ( 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 532 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 532 time to evaluate : 0.682 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: A 65 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7927 (mp0) REVERT: A 150 GLN cc_start: 0.9077 (tm-30) cc_final: 0.8811 (tm-30) REVERT: A 172 LEU cc_start: 0.9013 (mp) cc_final: 0.8735 (mp) REVERT: A 188 ILE cc_start: 0.9630 (mt) cc_final: 0.9398 (mm) REVERT: A 214 LYS cc_start: 0.8154 (tppt) cc_final: 0.7715 (mmtp) REVERT: A 228 LYS cc_start: 0.8984 (mmmt) cc_final: 0.8758 (mmtt) REVERT: A 290 GLU cc_start: 0.8705 (mm-30) cc_final: 0.8473 (mm-30) REVERT: A 308 LYS cc_start: 0.9548 (mtmt) cc_final: 0.9315 (mtmm) REVERT: A 319 MET cc_start: 0.9187 (tpp) cc_final: 0.8716 (tpp) REVERT: A 406 ASP cc_start: 0.8521 (m-30) cc_final: 0.8258 (m-30) REVERT: A 458 MET cc_start: 0.9178 (mmm) cc_final: 0.8452 (mtm) REVERT: A 576 LEU cc_start: 0.9038 (mt) cc_final: 0.8772 (mt) REVERT: A 606 TYR cc_start: 0.7877 (m-10) cc_final: 0.7244 (m-10) REVERT: A 667 LEU cc_start: 0.9248 (tt) cc_final: 0.8635 (tt) REVERT: B 51 LEU cc_start: 0.8947 (tp) cc_final: 0.8689 (tp) REVERT: B 102 ASN cc_start: 0.9275 (m110) cc_final: 0.8949 (m110) REVERT: B 120 ASP cc_start: 0.8680 (m-30) cc_final: 0.8469 (m-30) REVERT: B 147 GLN cc_start: 0.9134 (mt0) cc_final: 0.8771 (mt0) REVERT: B 156 PHE cc_start: 0.9124 (t80) cc_final: 0.8880 (t80) REVERT: B 190 MET cc_start: 0.9282 (mtm) cc_final: 0.9064 (mtm) REVERT: B 191 GLN cc_start: 0.8897 (mm-40) cc_final: 0.8217 (mm-40) REVERT: B 214 LYS cc_start: 0.7956 (mmtt) cc_final: 0.7663 (mmtt) REVERT: B 218 ASN cc_start: 0.8851 (t0) cc_final: 0.8509 (t0) REVERT: B 235 ARG cc_start: 0.8590 (ttm110) cc_final: 0.8129 (mtm110) REVERT: B 253 ILE cc_start: 0.9394 (tt) cc_final: 0.9152 (tt) REVERT: B 258 ILE cc_start: 0.9508 (tp) cc_final: 0.9307 (tp) REVERT: B 262 LEU cc_start: 0.9491 (mm) cc_final: 0.9277 (mm) REVERT: B 276 LYS cc_start: 0.8804 (ptmt) cc_final: 0.8460 (ptpp) REVERT: B 288 PHE cc_start: 0.9446 (t80) cc_final: 0.9154 (t80) REVERT: B 348 MET cc_start: 0.7925 (tpp) cc_final: 0.7712 (tpp) REVERT: B 362 ASP cc_start: 0.8021 (m-30) cc_final: 0.7053 (m-30) REVERT: B 392 SER cc_start: 0.9275 (m) cc_final: 0.8928 (m) REVERT: B 393 SER cc_start: 0.9531 (m) cc_final: 0.9201 (p) REVERT: B 396 ASP cc_start: 0.8096 (m-30) cc_final: 0.7892 (m-30) REVERT: B 427 LYS cc_start: 0.9451 (pttt) cc_final: 0.9214 (pttt) REVERT: B 467 ASN cc_start: 0.9269 (t0) cc_final: 0.8794 (t0) REVERT: B 471 TYR cc_start: 0.9295 (t80) cc_final: 0.8791 (t80) REVERT: B 512 GLU cc_start: 0.8691 (pt0) cc_final: 0.8413 (pt0) REVERT: B 561 LEU cc_start: 0.9414 (tp) cc_final: 0.9202 (tp) REVERT: B 588 GLN cc_start: 0.8971 (mm-40) cc_final: 0.8703 (mm-40) REVERT: B 604 ARG cc_start: 0.8659 (tpp80) cc_final: 0.7853 (tpp80) REVERT: B 627 LYS cc_start: 0.9291 (tttt) cc_final: 0.8919 (tttp) REVERT: B 640 MET cc_start: 0.8950 (tpp) cc_final: 0.8254 (tpp) REVERT: C 74 MET cc_start: 0.8163 (mtt) cc_final: 0.7853 (mtp) REVERT: C 89 VAL cc_start: 0.6901 (t) cc_final: 0.6482 (t) REVERT: C 95 MET cc_start: 0.6780 (tmm) cc_final: 0.6116 (ptm) REVERT: D 108 ILE cc_start: 0.8357 (tp) cc_final: 0.8060 (pt) outliers start: 0 outliers final: 0 residues processed: 532 average time/residue: 0.1106 time to fit residues: 88.8380 Evaluate side-chains 443 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 443 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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: 0.0870 chunk 51 optimal weight: 8.9990 chunk 74 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 186 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 0.2980 overall best weight: 2.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 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 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.157794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.107919 restraints weight = 33794.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.111405 restraints weight = 16362.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.113607 restraints weight = 9745.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.115066 restraints weight = 6641.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.116082 restraints weight = 5012.440| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3306 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3306 r_free = 0.3306 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3306 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.5881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16386 Z= 0.190 Angle : 0.601 11.465 22134 Z= 0.322 Chirality : 0.043 0.160 2360 Planarity : 0.003 0.040 2818 Dihedral : 8.323 133.479 2290 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.00 (0.19), residues: 1932 helix: 1.29 (0.15), residues: 1129 sheet: -0.40 (0.43), residues: 126 loop : -0.05 (0.23), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 686 TYR 0.030 0.002 TYR A 571 PHE 0.042 0.002 PHE C 109 TRP 0.045 0.002 TRP D 124 HIS 0.011 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.19 (16386) covalent geometry : angle 0.60086 / 0.32 (22134) hydrogen bonds : bond 0.03898 / 2.48 ( 871) hydrogen bonds : angle 4.82929 / 3.43 ( 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 523 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 523 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8430 (mm-30) cc_final: 0.7945 (mp0) REVERT: A 158 ASN cc_start: 0.8983 (m110) cc_final: 0.8780 (m-40) REVERT: A 172 LEU cc_start: 0.9212 (mp) cc_final: 0.8834 (mp) REVERT: A 188 ILE cc_start: 0.9623 (mt) cc_final: 0.9418 (mm) REVERT: A 228 LYS cc_start: 0.8983 (mmmt) cc_final: 0.8702 (mmtt) REVERT: A 290 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8432 (mm-30) REVERT: A 308 LYS cc_start: 0.9551 (mtmt) cc_final: 0.9309 (mtmm) REVERT: A 319 MET cc_start: 0.9273 (tpp) cc_final: 0.8891 (tpp) REVERT: A 344 GLU cc_start: 0.8873 (pt0) cc_final: 0.8531 (pt0) REVERT: A 406 ASP cc_start: 0.8500 (m-30) cc_final: 0.8275 (m-30) REVERT: A 458 MET cc_start: 0.9216 (mmm) cc_final: 0.8515 (mtm) REVERT: A 557 ASP cc_start: 0.8756 (m-30) cc_final: 0.8541 (m-30) REVERT: A 576 LEU cc_start: 0.9055 (mt) cc_final: 0.8846 (mt) REVERT: A 584 ILE cc_start: 0.8889 (pt) cc_final: 0.8653 (pt) REVERT: A 667 LEU cc_start: 0.9267 (tt) cc_final: 0.8665 (tt) REVERT: A 686 ARG cc_start: 0.8397 (mtp-110) cc_final: 0.7802 (mtp-110) REVERT: B 51 LEU cc_start: 0.8978 (tp) cc_final: 0.8732 (tp) REVERT: B 102 ASN cc_start: 0.9255 (m110) cc_final: 0.8909 (m110) REVERT: B 156 PHE cc_start: 0.9183 (t80) cc_final: 0.8976 (t80) REVERT: B 214 LYS cc_start: 0.8065 (mmtt) cc_final: 0.7770 (mmtt) REVERT: B 218 ASN cc_start: 0.8927 (t0) cc_final: 0.8561 (t0) REVERT: B 253 ILE cc_start: 0.9389 (tt) cc_final: 0.9174 (tt) REVERT: B 258 ILE cc_start: 0.9511 (tp) cc_final: 0.9281 (tp) REVERT: B 262 LEU cc_start: 0.9502 (mm) cc_final: 0.9235 (mm) REVERT: B 276 LYS cc_start: 0.8869 (ptmt) cc_final: 0.8498 (ptpp) REVERT: B 286 ASP cc_start: 0.8388 (m-30) cc_final: 0.8130 (m-30) REVERT: B 288 PHE cc_start: 0.9478 (t80) cc_final: 0.9186 (t80) REVERT: B 348 MET cc_start: 0.7900 (tpp) cc_final: 0.7069 (tpp) REVERT: B 358 ILE cc_start: 0.9414 (mm) cc_final: 0.9176 (mm) REVERT: B 392 SER cc_start: 0.9289 (m) cc_final: 0.9024 (m) REVERT: B 414 LEU cc_start: 0.9324 (mt) cc_final: 0.9048 (mt) REVERT: B 427 LYS cc_start: 0.9429 (pttt) cc_final: 0.9180 (pttt) REVERT: B 467 ASN cc_start: 0.9280 (t0) cc_final: 0.8783 (t0) REVERT: B 512 GLU cc_start: 0.8739 (pt0) cc_final: 0.8471 (pt0) REVERT: B 561 LEU cc_start: 0.9428 (tp) cc_final: 0.9228 (tp) REVERT: B 576 LEU cc_start: 0.9240 (mt) cc_final: 0.9031 (mt) REVERT: B 588 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8661 (mm-40) REVERT: B 604 ARG cc_start: 0.8676 (tpp80) cc_final: 0.7816 (tpp80) REVERT: B 627 LYS cc_start: 0.9302 (tttt) cc_final: 0.8921 (tttp) REVERT: B 640 MET cc_start: 0.8939 (tpp) cc_final: 0.8215 (tpp) REVERT: C 89 VAL cc_start: 0.6927 (t) cc_final: 0.6476 (t) REVERT: D 108 ILE cc_start: 0.8324 (tp) cc_final: 0.8060 (pt) outliers start: 0 outliers final: 0 residues processed: 523 average time/residue: 0.1079 time to fit residues: 85.0224 Evaluate side-chains 437 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 0.511 ------------------------------------------------------------------------------- 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: 5.9990 chunk 99 optimal weight: 0.8980 chunk 61 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 134 optimal weight: 6.9990 chunk 153 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 97 optimal weight: 0.9990 chunk 151 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN A 645 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 69 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.156225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.107638 restraints weight = 34336.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.111072 restraints weight = 16487.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.113266 restraints weight = 9784.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.114667 restraints weight = 6657.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.115560 restraints weight = 4980.720| |-----------------------------------------------------------------------------| r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 16386 Z= 0.221 Angle : 0.628 10.125 22134 Z= 0.334 Chirality : 0.044 0.161 2360 Planarity : 0.004 0.041 2818 Dihedral : 8.300 133.707 2290 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: 0.92 (0.19), residues: 1932 helix: 1.23 (0.15), residues: 1141 sheet: -0.60 (0.42), residues: 126 loop : -0.09 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 256 TYR 0.026 0.002 TYR B 612 PHE 0.044 0.002 PHE C 109 TRP 0.046 0.002 TRP D 124 HIS 0.010 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.22 (16386) covalent geometry : angle 0.62774 / 0.33 (22134) hydrogen bonds : bond 0.03943 / 2.50 ( 871) hydrogen bonds : angle 4.83686 / 3.43 ( 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 489 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 489 time to evaluate : 0.656 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: A 65 GLU cc_start: 0.8421 (mm-30) cc_final: 0.7987 (mp0) REVERT: A 188 ILE cc_start: 0.9608 (mt) cc_final: 0.9374 (mm) REVERT: A 286 ASP cc_start: 0.8099 (m-30) cc_final: 0.7761 (m-30) REVERT: A 290 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8439 (mm-30) REVERT: A 308 LYS cc_start: 0.9551 (mtmt) cc_final: 0.9325 (mtmm) REVERT: A 319 MET cc_start: 0.9243 (tpp) cc_final: 0.8819 (tpp) REVERT: A 362 ASP cc_start: 0.7261 (m-30) cc_final: 0.6879 (m-30) REVERT: A 447 ASN cc_start: 0.8292 (m110) cc_final: 0.7576 (m110) REVERT: A 458 MET cc_start: 0.9212 (mmm) cc_final: 0.8481 (mtm) REVERT: A 557 ASP cc_start: 0.8697 (m-30) cc_final: 0.8493 (m-30) REVERT: A 576 LEU cc_start: 0.9034 (mt) cc_final: 0.8789 (mt) REVERT: A 584 ILE cc_start: 0.8886 (pt) cc_final: 0.8658 (pt) REVERT: A 639 ASP cc_start: 0.8811 (m-30) cc_final: 0.8455 (m-30) REVERT: A 667 LEU cc_start: 0.9320 (tt) cc_final: 0.8673 (tt) REVERT: A 671 ASP cc_start: 0.8404 (m-30) cc_final: 0.8186 (m-30) REVERT: A 686 ARG cc_start: 0.8512 (mtp-110) cc_final: 0.7888 (mtp-110) REVERT: B 51 LEU cc_start: 0.9017 (tp) cc_final: 0.8767 (tp) REVERT: B 102 ASN cc_start: 0.9242 (m110) cc_final: 0.8890 (m110) REVERT: B 120 ASP cc_start: 0.8807 (m-30) cc_final: 0.8461 (m-30) REVERT: B 147 GLN cc_start: 0.9053 (mt0) cc_final: 0.8718 (mt0) REVERT: B 213 ILE cc_start: 0.8799 (mp) cc_final: 0.8495 (mm) REVERT: B 214 LYS cc_start: 0.8104 (mmtt) cc_final: 0.7800 (mmtt) REVERT: B 218 ASN cc_start: 0.8935 (t0) cc_final: 0.8548 (t0) REVERT: B 235 ARG cc_start: 0.8456 (ttm110) cc_final: 0.7972 (mtm110) REVERT: B 253 ILE cc_start: 0.9400 (tt) cc_final: 0.9156 (tt) REVERT: B 258 ILE cc_start: 0.9535 (tp) cc_final: 0.9307 (tp) REVERT: B 262 LEU cc_start: 0.9486 (mm) cc_final: 0.9201 (mm) REVERT: B 276 LYS cc_start: 0.9028 (ptmt) cc_final: 0.8659 (ptpp) REVERT: B 286 ASP cc_start: 0.8369 (m-30) cc_final: 0.8149 (m-30) REVERT: B 288 PHE cc_start: 0.9512 (t80) cc_final: 0.9234 (t80) REVERT: B 348 MET cc_start: 0.7850 (tpp) cc_final: 0.7423 (tpp) REVERT: B 392 SER cc_start: 0.9257 (m) cc_final: 0.9018 (m) REVERT: B 396 ASP cc_start: 0.8265 (m-30) cc_final: 0.8052 (m-30) REVERT: B 427 LYS cc_start: 0.9453 (pttt) cc_final: 0.9175 (pttt) REVERT: B 447 ASN cc_start: 0.8682 (m-40) cc_final: 0.8448 (m-40) REVERT: B 467 ASN cc_start: 0.9284 (t0) cc_final: 0.8849 (t0) REVERT: B 512 GLU cc_start: 0.8736 (pt0) cc_final: 0.8448 (pt0) REVERT: B 576 LEU cc_start: 0.9234 (mt) cc_final: 0.8939 (mt) REVERT: B 586 TYR cc_start: 0.8489 (m-10) cc_final: 0.8095 (m-10) REVERT: B 602 GLU cc_start: 0.7307 (pt0) cc_final: 0.7098 (pt0) REVERT: B 604 ARG cc_start: 0.8662 (tpp80) cc_final: 0.7786 (tpp80) REVERT: B 627 LYS cc_start: 0.9285 (tttt) cc_final: 0.8901 (tttp) REVERT: B 640 MET cc_start: 0.8888 (tpp) cc_final: 0.8185 (tpp) REVERT: C 89 VAL cc_start: 0.6840 (t) cc_final: 0.6353 (t) REVERT: C 154 PHE cc_start: 0.8457 (t80) cc_final: 0.7786 (t80) REVERT: D 108 ILE cc_start: 0.8387 (tp) cc_final: 0.8158 (pt) REVERT: D 173 TYR cc_start: 0.6035 (t80) cc_final: 0.5711 (t80) outliers start: 0 outliers final: 0 residues processed: 489 average time/residue: 0.1292 time to fit residues: 95.4821 Evaluate side-chains 434 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 434 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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: 7.9990 chunk 133 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN A 645 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.157327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.108961 restraints weight = 33915.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.112372 restraints weight = 16426.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.114637 restraints weight = 9772.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.116002 restraints weight = 6619.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.117084 restraints weight = 5009.327| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3315 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.6160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 16386 Z= 0.172 Angle : 0.610 8.947 22134 Z= 0.326 Chirality : 0.043 0.250 2360 Planarity : 0.003 0.039 2818 Dihedral : 8.114 133.012 2290 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % 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: 0.96 (0.19), residues: 1932 helix: 1.26 (0.15), residues: 1129 sheet: -0.01 (0.46), residues: 110 loop : -0.16 (0.23), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 686 TYR 0.028 0.002 TYR A 571 PHE 0.050 0.002 PHE C 109 TRP 0.051 0.002 TRP D 124 HIS 0.009 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (16386) covalent geometry : angle 0.61024 / 0.33 (22134) hydrogen bonds : bond 0.03908 / 2.50 ( 871) hydrogen bonds : angle 4.85781 / 3.46 ( 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 496 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 496 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8021 (mp0) REVERT: A 158 ASN cc_start: 0.8951 (m110) cc_final: 0.8731 (m-40) REVERT: A 172 LEU cc_start: 0.9181 (mp) cc_final: 0.8778 (mp) REVERT: A 188 ILE cc_start: 0.9596 (mt) cc_final: 0.9314 (mm) REVERT: A 228 LYS cc_start: 0.8989 (mmmt) cc_final: 0.8639 (mmtt) REVERT: A 231 ASP cc_start: 0.8586 (t0) cc_final: 0.8360 (t0) REVERT: A 286 ASP cc_start: 0.8209 (m-30) cc_final: 0.7922 (m-30) REVERT: A 290 GLU cc_start: 0.8660 (mm-30) cc_final: 0.8434 (mm-30) REVERT: A 308 LYS cc_start: 0.9533 (mtmt) cc_final: 0.9316 (mtmm) REVERT: A 319 MET cc_start: 0.9263 (tpp) cc_final: 0.8862 (tpp) REVERT: A 362 ASP cc_start: 0.7267 (m-30) cc_final: 0.6941 (m-30) REVERT: A 447 ASN cc_start: 0.8274 (m-40) cc_final: 0.7502 (m110) REVERT: A 458 MET cc_start: 0.9206 (mmm) cc_final: 0.8523 (mtm) REVERT: A 576 LEU cc_start: 0.9062 (mt) cc_final: 0.8844 (mt) REVERT: A 630 TYR cc_start: 0.8564 (m-80) cc_final: 0.8351 (m-80) REVERT: A 639 ASP cc_start: 0.8787 (m-30) cc_final: 0.8381 (m-30) REVERT: A 667 LEU cc_start: 0.9296 (tt) cc_final: 0.8623 (tt) REVERT: A 671 ASP cc_start: 0.8304 (m-30) cc_final: 0.8098 (m-30) REVERT: A 686 ARG cc_start: 0.8510 (mtp-110) cc_final: 0.8090 (mtp-110) REVERT: B 51 LEU cc_start: 0.8989 (tp) cc_final: 0.8746 (tp) REVERT: B 102 ASN cc_start: 0.9257 (m110) cc_final: 0.8874 (m110) REVERT: B 120 ASP cc_start: 0.8709 (m-30) cc_final: 0.8409 (m-30) REVERT: B 147 GLN cc_start: 0.9025 (mt0) cc_final: 0.8541 (mt0) REVERT: B 213 ILE cc_start: 0.8769 (mp) cc_final: 0.8451 (mm) REVERT: B 214 LYS cc_start: 0.8078 (mmtt) cc_final: 0.7777 (mmtt) REVERT: B 235 ARG cc_start: 0.8432 (ttm110) cc_final: 0.7960 (mtm110) REVERT: B 253 ILE cc_start: 0.9378 (tt) cc_final: 0.9171 (tt) REVERT: B 262 LEU cc_start: 0.9458 (mm) cc_final: 0.9198 (mm) REVERT: B 274 ARG cc_start: 0.8153 (ttm-80) cc_final: 0.7529 (ttm-80) REVERT: B 276 LYS cc_start: 0.9031 (ptmt) cc_final: 0.8676 (ptpp) REVERT: B 286 ASP cc_start: 0.8359 (m-30) cc_final: 0.8096 (m-30) REVERT: B 288 PHE cc_start: 0.9501 (t80) cc_final: 0.9240 (t80) REVERT: B 392 SER cc_start: 0.9238 (m) cc_final: 0.9021 (m) REVERT: B 427 LYS cc_start: 0.9453 (pttt) cc_final: 0.9221 (pttt) REVERT: B 447 ASN cc_start: 0.8665 (m-40) cc_final: 0.8463 (m-40) REVERT: B 467 ASN cc_start: 0.9264 (t0) cc_final: 0.8788 (t0) REVERT: B 471 TYR cc_start: 0.9287 (t80) cc_final: 0.8926 (t80) REVERT: B 512 GLU cc_start: 0.8735 (pt0) cc_final: 0.8448 (pt0) REVERT: B 576 LEU cc_start: 0.9242 (mt) cc_final: 0.8950 (mt) REVERT: B 588 GLN cc_start: 0.8931 (mm-40) cc_final: 0.8700 (mm-40) REVERT: B 604 ARG cc_start: 0.8592 (tpp80) cc_final: 0.7641 (tpp80) REVERT: B 627 LYS cc_start: 0.9253 (tttt) cc_final: 0.8867 (tttp) REVERT: B 640 MET cc_start: 0.8926 (tpp) cc_final: 0.8225 (tpp) REVERT: C 89 VAL cc_start: 0.6928 (t) cc_final: 0.6402 (t) REVERT: C 134 LYS cc_start: 0.7891 (mtmm) cc_final: 0.7438 (mmtm) REVERT: D 42 LEU cc_start: 0.5426 (tp) cc_final: 0.5142 (mm) REVERT: D 108 ILE cc_start: 0.8376 (tp) cc_final: 0.8101 (pt) REVERT: D 173 TYR cc_start: 0.5890 (t80) cc_final: 0.5495 (t80) REVERT: D 256 VAL cc_start: 0.3478 (t) cc_final: 0.3201 (t) outliers start: 0 outliers final: 0 residues processed: 496 average time/residue: 0.1311 time to fit residues: 98.1941 Evaluate side-chains 441 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 441 time to evaluate : 0.676 ------------------------------------------------------------------------------- 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: 6.9990 chunk 62 optimal weight: 0.8980 chunk 33 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 189 optimal weight: 9.9990 chunk 181 optimal weight: 5.9990 chunk 165 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 132 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.160043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.112698 restraints weight = 33638.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.116112 restraints weight = 16046.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.118303 restraints weight = 9458.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.119701 restraints weight = 6368.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.120749 restraints weight = 4750.200| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.6306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16386 Z= 0.136 Angle : 0.600 8.753 22134 Z= 0.320 Chirality : 0.042 0.168 2360 Planarity : 0.003 0.036 2818 Dihedral : 7.881 132.579 2290 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: 0.96 (0.19), residues: 1932 helix: 1.28 (0.15), residues: 1129 sheet: 0.12 (0.46), residues: 106 loop : -0.21 (0.23), residues: 697 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 686 TYR 0.028 0.001 TYR A 571 PHE 0.048 0.002 PHE C 109 TRP 0.049 0.002 TRP D 124 HIS 0.009 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (16386) covalent geometry : angle 0.59980 / 0.32 (22134) hydrogen bonds : bond 0.03809 / 2.40 ( 871) hydrogen bonds : angle 4.84702 / 3.45 ( 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 523 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 523 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 TRP cc_start: 0.9193 (p90) cc_final: 0.8934 (p90) REVERT: A 158 ASN cc_start: 0.8951 (m110) cc_final: 0.8715 (m-40) REVERT: A 172 LEU cc_start: 0.9125 (mp) cc_final: 0.8784 (mp) REVERT: A 228 LYS cc_start: 0.9005 (mmmt) cc_final: 0.8628 (mmtt) REVERT: A 286 ASP cc_start: 0.8197 (m-30) cc_final: 0.7978 (m-30) REVERT: A 290 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8464 (mm-30) REVERT: A 357 TYR cc_start: 0.8194 (m-80) cc_final: 0.7868 (m-80) REVERT: A 362 ASP cc_start: 0.7142 (m-30) cc_final: 0.6926 (m-30) REVERT: A 447 ASN cc_start: 0.8554 (m-40) cc_final: 0.7582 (m-40) REVERT: A 458 MET cc_start: 0.9196 (mmm) cc_final: 0.8485 (mtm) REVERT: A 492 PHE cc_start: 0.9295 (m-80) cc_final: 0.9090 (m-10) REVERT: A 576 LEU cc_start: 0.9199 (mt) cc_final: 0.8981 (mt) REVERT: A 584 ILE cc_start: 0.8886 (pt) cc_final: 0.8679 (pt) REVERT: A 630 TYR cc_start: 0.8451 (m-80) cc_final: 0.8090 (m-80) REVERT: A 639 ASP cc_start: 0.8690 (m-30) cc_final: 0.8329 (m-30) REVERT: A 667 LEU cc_start: 0.9314 (tt) cc_final: 0.8651 (tt) REVERT: A 683 TYR cc_start: 0.8275 (t80) cc_final: 0.7380 (t80) REVERT: A 686 ARG cc_start: 0.8523 (mtp-110) cc_final: 0.8298 (mtp-110) REVERT: B 51 LEU cc_start: 0.8916 (tp) cc_final: 0.8675 (tp) REVERT: B 117 ARG cc_start: 0.8684 (mtt-85) cc_final: 0.8237 (mtt-85) REVERT: B 119 GLU cc_start: 0.8947 (mp0) cc_final: 0.8728 (mp0) REVERT: B 120 ASP cc_start: 0.8619 (m-30) cc_final: 0.8350 (m-30) REVERT: B 147 GLN cc_start: 0.8991 (mt0) cc_final: 0.8473 (mt0) REVERT: B 156 PHE cc_start: 0.9048 (t80) cc_final: 0.8816 (t80) REVERT: B 190 MET cc_start: 0.9279 (mtm) cc_final: 0.9034 (mtm) REVERT: B 214 LYS cc_start: 0.8033 (mmtt) cc_final: 0.7744 (mmtt) REVERT: B 235 ARG cc_start: 0.8411 (ttm110) cc_final: 0.7846 (mtm110) REVERT: B 253 ILE cc_start: 0.9385 (tt) cc_final: 0.9091 (tt) REVERT: B 274 ARG cc_start: 0.8121 (ttm-80) cc_final: 0.7551 (ttm-80) REVERT: B 276 LYS cc_start: 0.8919 (ptmt) cc_final: 0.8434 (ptpp) REVERT: B 286 ASP cc_start: 0.8293 (m-30) cc_final: 0.8063 (m-30) REVERT: B 288 PHE cc_start: 0.9442 (t80) cc_final: 0.9158 (t80) REVERT: B 392 SER cc_start: 0.9244 (m) cc_final: 0.8841 (m) REVERT: B 410 ASN cc_start: 0.9043 (m-40) cc_final: 0.8618 (m-40) REVERT: B 414 LEU cc_start: 0.9210 (mt) cc_final: 0.8917 (mt) REVERT: B 467 ASN cc_start: 0.9230 (t0) cc_final: 0.8765 (t0) REVERT: B 471 TYR cc_start: 0.9222 (t80) cc_final: 0.8702 (t80) REVERT: B 512 GLU cc_start: 0.8674 (pt0) cc_final: 0.8394 (pt0) REVERT: B 576 LEU cc_start: 0.9205 (mt) cc_final: 0.8917 (mt) REVERT: B 588 GLN cc_start: 0.8918 (mm-40) cc_final: 0.8703 (mm-40) REVERT: B 604 ARG cc_start: 0.8527 (tpp80) cc_final: 0.7519 (tpp80) REVERT: B 627 LYS cc_start: 0.9253 (tttt) cc_final: 0.8940 (tttp) REVERT: B 640 MET cc_start: 0.8916 (tpp) cc_final: 0.8220 (tpp) REVERT: C 74 MET cc_start: 0.8111 (mtt) cc_final: 0.7807 (mtp) REVERT: C 89 VAL cc_start: 0.6931 (t) cc_final: 0.6519 (t) REVERT: C 117 THR cc_start: 0.3056 (m) cc_final: 0.2831 (p) REVERT: C 134 LYS cc_start: 0.7840 (mtmm) cc_final: 0.7524 (mmpt) REVERT: C 154 PHE cc_start: 0.8627 (t80) cc_final: 0.7810 (t80) REVERT: D 108 ILE cc_start: 0.8366 (tp) cc_final: 0.8113 (pt) REVERT: D 173 TYR cc_start: 0.6014 (t80) cc_final: 0.5643 (t80) REVERT: D 256 VAL cc_start: 0.3496 (t) cc_final: 0.3193 (t) outliers start: 0 outliers final: 0 residues processed: 523 average time/residue: 0.1260 time to fit residues: 100.3140 Evaluate side-chains 449 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 449 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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: 0.1980 chunk 1 optimal weight: 10.0000 chunk 48 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 148 optimal weight: 7.9990 chunk 125 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.163100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.115642 restraints weight = 33469.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.119160 restraints weight = 16045.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.121426 restraints weight = 9441.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.122864 restraints weight = 6351.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.123780 restraints weight = 4711.914| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3391 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3391 r_free = 0.3391 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3391 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.6454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16386 Z= 0.129 Angle : 0.596 8.833 22134 Z= 0.319 Chirality : 0.042 0.156 2360 Planarity : 0.003 0.035 2818 Dihedral : 7.709 132.546 2290 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.99 (0.19), residues: 1932 helix: 1.25 (0.15), residues: 1142 sheet: 0.32 (0.49), residues: 96 loop : -0.17 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 686 TYR 0.041 0.001 TYR B 118 PHE 0.050 0.002 PHE C 109 TRP 0.048 0.002 TRP D 124 HIS 0.010 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (16386) covalent geometry : angle 0.59629 / 0.32 (22134) hydrogen bonds : bond 0.03764 / 2.40 ( 871) hydrogen bonds : angle 4.84506 / 3.43 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3192.66 seconds wall clock time: 56 minutes 6.43 seconds (3366.43 seconds total)