Starting phenix.real_space_refine on Fri Jul 3 19:52:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byy_45048/07_2026/9byy_45048_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byy_45048/07_2026/9byy_45048.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9byy_45048/07_2026/9byy_45048_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byy_45048/07_2026/9byy_45048_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9byy_45048/07_2026/9byy_45048.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byy_45048/07_2026/9byy_45048.map" } resolution = 4.07 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: (97.632, 124.074, 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: 0.91 Conformation dependent library (CDL) restraints added in 527.2 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: 0.36 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: 3.516A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.985A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.954A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.665A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.695A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A 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: 3.627A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.016A 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: 4.073A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.677A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.878A 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: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.567A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.668A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.360A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.715A 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: 6.477A 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: 7.228A 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: 7.907A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.25 Time building geometry restraints manager: 1.33 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: 4819 1.34 - 1.46: 3057 1.46 - 1.58: 8329 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 4.82e+01 bond pdb=" O3B TTP A 803 " pdb=" PG TTP A 803 " ideal model delta sigma weight residual 1.748 1.610 0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.600 -0.060 1.25e-02 6.40e+03 2.29e+01 bond pdb=" O3A TTP A 803 " pdb=" PB TTP A 803 " ideal model delta sigma weight residual 1.675 1.606 0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.14e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21528 2.09 - 4.18: 525 4.18 - 6.27: 64 6.27 - 8.36: 8 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 2.01e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.14 -4.43 1.15e+00 7.56e-01 1.48e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.20 -3.92 1.09e+00 8.42e-01 1.29e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.81 -4.31 1.23e+00 6.61e-01 1.23e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.68 -3.97 1.15e+00 7.56e-01 1.19e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.05: 9088 25.05 - 50.10: 657 50.10 - 75.16: 125 75.16 - 100.21: 26 100.21 - 125.26: 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 -98.24 125.26 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 -95.59 122.61 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 -134.34 12.34 0 2.50e+00 1.60e-01 2.44e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2139 0.093 - 0.186: 189 0.186 - 0.279: 27 0.279 - 0.372: 3 0.372 - 0.465: 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 5.42e+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 4.67e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.01e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.10e-02 2.68e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " 0.017 2.00e-02 2.50e+03 1.11e-02 2.14e+00 pdb=" CG PHE D 92 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 169 " 0.017 2.00e-02 2.50e+03 9.71e-03 1.88e+00 pdb=" CG TYR C 169 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 169 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 169 " 0.008 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 129 2.51 - 3.11: 11557 3.11 - 3.70: 27052 3.70 - 4.30: 41529 4.30 - 4.90: 65421 Nonbonded interactions: 145688 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 1.961 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 3.060 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.991 3.060 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.012 3.040 ... (remaining 145683 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: 1.410 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.030 Find NCS groups from input model: 0.230 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 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 : 0.787 10.449 22134 Z= 0.471 Chirality : 0.058 0.465 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.680 125.261 6202 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.34 % Allowed : 15.33 % Favored : 83.33 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.18), residues: 1932 helix: 0.59 (0.14), residues: 1151 sheet: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.009 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 0.78748 / 0.47 (22134) hydrogen bonds : bond 0.15421 / 9.51 ( 871) hydrogen bonds : angle 6.51807 / 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 883 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 860 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.8904 (mm) cc_final: 0.8689 (mm) REVERT: A 109 ASN cc_start: 0.8043 (m-40) cc_final: 0.7604 (p0) REVERT: A 116 GLU cc_start: 0.7208 (mt-10) cc_final: 0.6837 (mt-10) REVERT: A 118 TYR cc_start: 0.8114 (t80) cc_final: 0.7889 (t80) REVERT: A 147 GLN cc_start: 0.8293 (mt0) cc_final: 0.7243 (mt0) REVERT: A 149 TYR cc_start: 0.8380 (t80) cc_final: 0.8010 (t80) REVERT: A 155 THR cc_start: 0.9239 (m) cc_final: 0.8920 (m) REVERT: A 162 LYS cc_start: 0.7625 (ttpt) cc_final: 0.7293 (ttmm) REVERT: A 190 MET cc_start: 0.8182 (mtt) cc_final: 0.7777 (mtt) REVERT: A 192 LEU cc_start: 0.9213 (mt) cc_final: 0.8681 (mt) REVERT: A 204 SER cc_start: 0.9231 (m) cc_final: 0.8698 (t) REVERT: A 227 MET cc_start: 0.8479 (mtp) cc_final: 0.8231 (mtp) REVERT: A 345 LYS cc_start: 0.8579 (tttt) cc_final: 0.8187 (tttt) REVERT: A 373 ILE cc_start: 0.8878 (mt) cc_final: 0.8625 (mt) REVERT: A 377 LYS cc_start: 0.8860 (mttt) cc_final: 0.8375 (mttp) REVERT: A 436 LEU cc_start: 0.8997 (mt) cc_final: 0.8616 (mm) REVERT: A 500 ILE cc_start: 0.9355 (mt) cc_final: 0.9153 (mt) REVERT: A 588 GLN cc_start: 0.7615 (mm-40) cc_final: 0.7289 (mm-40) REVERT: A 598 MET cc_start: 0.7525 (mtm) cc_final: 0.6965 (mtm) REVERT: A 606 TYR cc_start: 0.6927 (m-80) cc_final: 0.6616 (m-10) REVERT: A 610 LYS cc_start: 0.7099 (ttmm) cc_final: 0.6876 (ttmm) REVERT: A 634 MET cc_start: 0.8405 (mmp) cc_final: 0.8098 (mmm) REVERT: B 12 LEU cc_start: 0.8929 (mt) cc_final: 0.8462 (mt) REVERT: B 51 LEU cc_start: 0.8151 (tp) cc_final: 0.7910 (tp) REVERT: B 99 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8632 (mmtt) REVERT: B 147 GLN cc_start: 0.8068 (mt0) cc_final: 0.7384 (mt0) REVERT: B 161 ARG cc_start: 0.7152 (mtt180) cc_final: 0.6931 (mtt180) REVERT: B 181 ASP cc_start: 0.8428 (m-30) cc_final: 0.8063 (m-30) REVERT: B 211 GLU cc_start: 0.7667 (mt-10) cc_final: 0.7301 (mm-30) REVERT: B 264 THR cc_start: 0.8338 (p) cc_final: 0.8067 (p) REVERT: B 286 ASP cc_start: 0.6259 (OUTLIER) cc_final: 0.5864 (m-30) REVERT: B 288 PHE cc_start: 0.7852 (t80) cc_final: 0.7546 (t80) REVERT: B 319 MET cc_start: 0.8079 (tpp) cc_final: 0.7482 (tpp) REVERT: B 394 TYR cc_start: 0.8003 (m-80) cc_final: 0.7679 (m-80) REVERT: B 425 ILE cc_start: 0.9175 (mt) cc_final: 0.8898 (mt) REVERT: B 436 LEU cc_start: 0.9111 (mt) cc_final: 0.8900 (mt) REVERT: B 460 SER cc_start: 0.8467 (t) cc_final: 0.8144 (p) REVERT: B 570 MET cc_start: 0.7289 (mtm) cc_final: 0.6929 (mtm) REVERT: B 584 ILE cc_start: 0.8989 (tp) cc_final: 0.8771 (tp) REVERT: B 585 SER cc_start: 0.9094 (p) cc_final: 0.8611 (t) REVERT: B 588 GLN cc_start: 0.7635 (mm-40) cc_final: 0.6500 (mm-40) REVERT: B 589 SER cc_start: 0.7889 (m) cc_final: 0.7527 (m) REVERT: B 640 MET cc_start: 0.7717 (tpp) cc_final: 0.7082 (tpp) REVERT: B 644 ILE cc_start: 0.8889 (mt) cc_final: 0.8582 (mt) outliers start: 23 outliers final: 7 residues processed: 874 average time/residue: 0.1216 time to fit residues: 152.8988 Evaluate side-chains 587 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 579 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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: 0.0370 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.9980 overall best weight: 2.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 239 GLN A 259 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 HIS B 313 HIS B 387 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN B 676 HIS ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN C 201 HIS C 210 GLN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN D 80 HIS D 127 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.134245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.098316 restraints weight = 37024.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.101822 restraints weight = 18717.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.104182 restraints weight = 11444.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.105765 restraints weight = 7862.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.106789 restraints weight = 5910.679| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (14 function evaluations) r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.4190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16386 Z= 0.213 Angle : 0.659 11.804 22134 Z= 0.351 Chirality : 0.044 0.333 2360 Planarity : 0.004 0.045 2818 Dihedral : 9.455 130.653 2290 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.17 % Allowed : 3.09 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.19), residues: 1932 helix: 1.30 (0.15), residues: 1126 sheet: 0.22 (0.43), residues: 138 loop : 0.54 (0.23), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 350 TYR 0.023 0.002 TYR A 522 PHE 0.031 0.002 PHE D 320 TRP 0.012 0.002 TRP B 9 HIS 0.008 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.21 (16386) covalent geometry : angle 0.65861 / 0.35 (22134) hydrogen bonds : bond 0.04827 / 3.04 ( 871) hydrogen bonds : angle 5.07113 / 3.62 ( 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 684 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 681 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ARG cc_start: 0.8397 (mtp85) cc_final: 0.8185 (mtp85) REVERT: A 147 GLN cc_start: 0.8734 (mt0) cc_final: 0.8238 (mt0) REVERT: A 221 LYS cc_start: 0.9578 (mmmm) cc_final: 0.8754 (mppt) REVERT: A 266 LYS cc_start: 0.8608 (mtmm) cc_final: 0.8137 (mtmm) REVERT: A 276 LYS cc_start: 0.9214 (pttp) cc_final: 0.8962 (ptpp) REVERT: A 444 ASP cc_start: 0.8251 (t0) cc_final: 0.7343 (t0) REVERT: A 446 ARG cc_start: 0.7758 (mmm160) cc_final: 0.6921 (mmt180) REVERT: A 493 MET cc_start: 0.8978 (tmm) cc_final: 0.8661 (tmm) REVERT: A 588 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8294 (mm-40) REVERT: A 640 MET cc_start: 0.9149 (ttm) cc_final: 0.8575 (ttm) REVERT: A 683 TYR cc_start: 0.8455 (t80) cc_final: 0.8194 (t80) REVERT: B 8 LYS cc_start: 0.8793 (tptp) cc_final: 0.8143 (tppt) REVERT: B 12 LEU cc_start: 0.9505 (mt) cc_final: 0.9115 (mt) REVERT: B 95 MET cc_start: 0.8783 (tpp) cc_final: 0.8578 (mmm) REVERT: B 96 SER cc_start: 0.9513 (m) cc_final: 0.9247 (p) REVERT: B 147 GLN cc_start: 0.8856 (mt0) cc_final: 0.8215 (mt0) REVERT: B 181 ASP cc_start: 0.8838 (m-30) cc_final: 0.8159 (m-30) REVERT: B 200 SER cc_start: 0.8945 (t) cc_final: 0.8672 (t) REVERT: B 253 ILE cc_start: 0.9526 (tt) cc_final: 0.9276 (tt) REVERT: B 263 ASP cc_start: 0.9048 (m-30) cc_final: 0.8728 (m-30) REVERT: B 276 LYS cc_start: 0.9204 (pttt) cc_final: 0.8793 (pttm) REVERT: B 282 VAL cc_start: 0.9549 (t) cc_final: 0.9337 (m) REVERT: B 288 PHE cc_start: 0.9268 (t80) cc_final: 0.8904 (t80) REVERT: B 291 LEU cc_start: 0.9466 (mt) cc_final: 0.8901 (mt) REVERT: B 312 GLN cc_start: 0.8777 (mt0) cc_final: 0.8255 (mt0) REVERT: B 348 MET cc_start: 0.8015 (tpt) cc_final: 0.7326 (tpp) REVERT: B 386 LEU cc_start: 0.9185 (mt) cc_final: 0.8976 (mt) REVERT: B 393 SER cc_start: 0.9470 (m) cc_final: 0.8991 (p) REVERT: B 394 TYR cc_start: 0.8857 (m-80) cc_final: 0.7907 (m-80) REVERT: B 425 ILE cc_start: 0.9623 (mt) cc_final: 0.9405 (mt) REVERT: B 493 MET cc_start: 0.9457 (tmm) cc_final: 0.9191 (tmm) REVERT: B 526 GLU cc_start: 0.8072 (tp30) cc_final: 0.7696 (tp30) REVERT: B 550 MET cc_start: 0.7812 (mtp) cc_final: 0.7440 (ttm) REVERT: B 588 GLN cc_start: 0.9137 (mm-40) cc_final: 0.8407 (mm-40) REVERT: B 589 SER cc_start: 0.9267 (m) cc_final: 0.9020 (p) REVERT: B 602 GLU cc_start: 0.8023 (pt0) cc_final: 0.7495 (pt0) REVERT: B 640 MET cc_start: 0.9077 (tpp) cc_final: 0.8622 (tpp) REVERT: B 667 LEU cc_start: 0.9548 (tp) cc_final: 0.9344 (tp) REVERT: C 154 PHE cc_start: 0.8217 (t80) cc_final: 0.7985 (t80) REVERT: C 212 ILE cc_start: 0.8526 (mm) cc_final: 0.8031 (mm) REVERT: C 247 TYR cc_start: 0.7856 (m-10) cc_final: 0.7469 (m-80) REVERT: D 95 MET cc_start: 0.9241 (tmm) cc_final: 0.8936 (tmm) REVERT: D 96 MET cc_start: 0.7770 (mmm) cc_final: 0.7555 (mmt) REVERT: D 149 ASP cc_start: 0.8508 (m-30) cc_final: 0.8280 (m-30) REVERT: D 178 PHE cc_start: 0.8350 (m-80) cc_final: 0.8129 (m-80) REVERT: D 189 GLU cc_start: 0.7294 (tm-30) cc_final: 0.6538 (pt0) REVERT: D 224 LEU cc_start: 0.8531 (mt) cc_final: 0.8327 (mt) REVERT: D 235 LEU cc_start: 0.9084 (mt) cc_final: 0.8667 (pp) REVERT: D 259 PHE cc_start: 0.7706 (t80) cc_final: 0.7300 (t80) REVERT: D 318 ASP cc_start: 0.8414 (m-30) cc_final: 0.7904 (m-30) outliers start: 3 outliers final: 1 residues processed: 682 average time/residue: 0.1097 time to fit residues: 112.0290 Evaluate side-chains 544 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 543 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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: 10.0000 chunk 131 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 182 optimal weight: 7.9990 chunk 159 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 150 optimal weight: 20.0000 chunk 63 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 158 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN B 61 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN C 233 ASN D 23 ASN D 28 GLN D 71 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.124673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.089746 restraints weight = 39102.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.092988 restraints weight = 20035.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.095071 restraints weight = 12272.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.096650 restraints weight = 8610.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.097690 restraints weight = 6497.653| |-----------------------------------------------------------------------------| r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.5491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 16386 Z= 0.368 Angle : 0.763 13.499 22134 Z= 0.406 Chirality : 0.047 0.285 2360 Planarity : 0.005 0.056 2818 Dihedral : 9.575 136.945 2290 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 15.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.17 % Allowed : 3.44 % Favored : 96.39 % 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: 0.72 (0.19), residues: 1932 helix: 0.80 (0.15), residues: 1139 sheet: -0.12 (0.43), residues: 134 loop : 0.29 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 196 TYR 0.031 0.002 TYR C 169 PHE 0.032 0.003 PHE B 37 TRP 0.044 0.003 TRP D 124 HIS 0.017 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00787 / 0.37 (16386) covalent geometry : angle 0.76281 / 0.41 (22134) hydrogen bonds : bond 0.04719 / 2.98 ( 871) hydrogen bonds : angle 5.23611 / 3.74 ( 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 611 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 608 time to evaluate : 0.599 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 37 PHE cc_start: 0.8781 (m-10) cc_final: 0.8373 (m-10) REVERT: A 40 TYR cc_start: 0.8971 (t80) cc_final: 0.8374 (t80) REVERT: A 99 LYS cc_start: 0.9001 (mmtm) cc_final: 0.8756 (mmtp) REVERT: A 117 ARG cc_start: 0.8596 (mtp85) cc_final: 0.8365 (mtp85) REVERT: A 147 GLN cc_start: 0.8934 (mt0) cc_final: 0.8636 (mt0) REVERT: A 204 SER cc_start: 0.9378 (t) cc_final: 0.9002 (t) REVERT: A 266 LYS cc_start: 0.8508 (mttp) cc_final: 0.8253 (mttp) REVERT: A 348 MET cc_start: 0.8340 (tpt) cc_final: 0.7968 (tpt) REVERT: A 352 GLU cc_start: 0.8488 (mt-10) cc_final: 0.7853 (mt-10) REVERT: A 437 THR cc_start: 0.9379 (m) cc_final: 0.9117 (p) REVERT: A 458 MET cc_start: 0.9256 (mmm) cc_final: 0.8709 (mmm) REVERT: A 493 MET cc_start: 0.8973 (tmm) cc_final: 0.8525 (tmm) REVERT: A 573 SER cc_start: 0.9325 (p) cc_final: 0.8839 (p) REVERT: B 119 GLU cc_start: 0.8960 (mp0) cc_final: 0.8513 (mp0) REVERT: B 147 GLN cc_start: 0.9042 (mt0) cc_final: 0.8785 (mt0) REVERT: B 150 GLN cc_start: 0.9102 (tp40) cc_final: 0.8886 (tp-100) REVERT: B 157 LEU cc_start: 0.9192 (tp) cc_final: 0.8815 (tp) REVERT: B 211 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7497 (mm-30) REVERT: B 259 ASN cc_start: 0.9168 (m-40) cc_final: 0.8801 (m-40) REVERT: B 263 ASP cc_start: 0.9012 (m-30) cc_final: 0.8787 (m-30) REVERT: B 276 LYS cc_start: 0.9273 (pttt) cc_final: 0.8994 (pttt) REVERT: B 282 VAL cc_start: 0.9626 (t) cc_final: 0.9352 (m) REVERT: B 288 PHE cc_start: 0.9437 (t80) cc_final: 0.9141 (t80) REVERT: B 322 MET cc_start: 0.8883 (mmm) cc_final: 0.8527 (tpp) REVERT: B 348 MET cc_start: 0.7952 (tpt) cc_final: 0.7204 (tpp) REVERT: B 359 MET cc_start: 0.8776 (ttp) cc_final: 0.8509 (tmm) REVERT: B 373 ILE cc_start: 0.9673 (mt) cc_final: 0.9322 (mt) REVERT: B 394 TYR cc_start: 0.8981 (m-80) cc_final: 0.8214 (m-80) REVERT: B 413 SER cc_start: 0.7831 (p) cc_final: 0.6590 (t) REVERT: B 425 ILE cc_start: 0.9642 (mt) cc_final: 0.9422 (mt) REVERT: B 467 ASN cc_start: 0.9346 (t0) cc_final: 0.8484 (t0) REVERT: B 493 MET cc_start: 0.9446 (tmm) cc_final: 0.9137 (tmm) REVERT: B 526 GLU cc_start: 0.8022 (tp30) cc_final: 0.7552 (tp30) REVERT: B 543 ILE cc_start: 0.9558 (mp) cc_final: 0.9350 (mp) REVERT: B 584 ILE cc_start: 0.9400 (tp) cc_final: 0.9170 (tp) REVERT: B 590 SER cc_start: 0.9022 (p) cc_final: 0.8440 (t) REVERT: B 599 GLU cc_start: 0.8475 (pt0) cc_final: 0.8261 (pt0) REVERT: B 640 MET cc_start: 0.9193 (tpp) cc_final: 0.8521 (tpp) REVERT: B 667 LEU cc_start: 0.9518 (tp) cc_final: 0.9213 (tp) REVERT: B 668 ASN cc_start: 0.9219 (m-40) cc_final: 0.8982 (m-40) REVERT: B 671 ASP cc_start: 0.8653 (m-30) cc_final: 0.8417 (m-30) REVERT: C 27 LYS cc_start: 0.9012 (mtmm) cc_final: 0.8635 (tptt) REVERT: C 154 PHE cc_start: 0.8417 (t80) cc_final: 0.7974 (t80) REVERT: C 212 ILE cc_start: 0.8624 (mm) cc_final: 0.8186 (mm) REVERT: C 247 TYR cc_start: 0.8151 (m-80) cc_final: 0.7797 (m-80) REVERT: D 16 ASP cc_start: 0.4749 (m-30) cc_final: 0.4254 (t0) REVERT: D 23 ASN cc_start: 0.9372 (m110) cc_final: 0.9158 (m-40) REVERT: D 24 GLN cc_start: 0.8294 (mp-120) cc_final: 0.7585 (tp-100) REVERT: D 46 TYR cc_start: 0.8523 (m-80) cc_final: 0.8194 (m-80) REVERT: D 56 MET cc_start: 0.6138 (mpp) cc_final: 0.5746 (mpp) REVERT: D 149 ASP cc_start: 0.8564 (m-30) cc_final: 0.8268 (m-30) REVERT: D 185 MET cc_start: 0.7483 (mmm) cc_final: 0.7282 (mmm) REVERT: D 195 LEU cc_start: 0.8676 (tt) cc_final: 0.7970 (tt) REVERT: D 233 ASN cc_start: 0.8722 (m110) cc_final: 0.8481 (m110) REVERT: D 240 LEU cc_start: 0.8781 (mt) cc_final: 0.8525 (mt) REVERT: D 259 PHE cc_start: 0.7615 (t80) cc_final: 0.7204 (t80) outliers start: 3 outliers final: 0 residues processed: 609 average time/residue: 0.1083 time to fit residues: 99.7179 Evaluate side-chains 474 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 474 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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: 8.9990 chunk 168 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 185 optimal weight: 20.0000 chunk 191 optimal weight: 20.0000 chunk 159 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 93 optimal weight: 0.6980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 338 ASN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN B 14 ASN B 218 ASN B 232 ASN B 312 GLN B 370 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN D 91 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.128275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.093495 restraints weight = 37916.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.096777 restraints weight = 19192.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.099004 restraints weight = 11789.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.100502 restraints weight = 8086.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.101482 restraints weight = 6119.526| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3226 r_free = 0.3226 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3226 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.5838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16386 Z= 0.196 Angle : 0.619 10.147 22134 Z= 0.331 Chirality : 0.043 0.161 2360 Planarity : 0.004 0.044 2818 Dihedral : 9.038 134.203 2290 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.23 % Allowed : 2.86 % Favored : 96.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.19), residues: 1932 helix: 0.89 (0.15), residues: 1129 sheet: -0.31 (0.43), residues: 134 loop : 0.26 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 164 TYR 0.023 0.002 TYR A 118 PHE 0.026 0.002 PHE D 109 TRP 0.039 0.002 TRP D 124 HIS 0.011 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (16386) covalent geometry : angle 0.61925 / 0.33 (22134) hydrogen bonds : bond 0.04155 / 2.59 ( 871) hydrogen bonds : angle 4.98547 / 3.58 ( 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 614 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 610 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ILE cc_start: 0.9663 (mm) cc_final: 0.9311 (mm) REVERT: A 37 PHE cc_start: 0.8666 (m-10) cc_final: 0.8353 (m-10) REVERT: A 40 TYR cc_start: 0.8929 (t80) cc_final: 0.8398 (t80) REVERT: A 91 PHE cc_start: 0.9288 (m-80) cc_final: 0.8986 (m-80) REVERT: A 99 LYS cc_start: 0.8997 (mmtm) cc_final: 0.8788 (mmtp) REVERT: A 117 ARG cc_start: 0.8581 (mtp85) cc_final: 0.8305 (mtp85) REVERT: A 131 ASN cc_start: 0.9041 (t0) cc_final: 0.8707 (t0) REVERT: A 147 GLN cc_start: 0.8815 (mt0) cc_final: 0.8510 (mt0) REVERT: A 150 GLN cc_start: 0.8902 (tp40) cc_final: 0.8079 (tm-30) REVERT: A 156 PHE cc_start: 0.9360 (t80) cc_final: 0.9047 (t80) REVERT: A 204 SER cc_start: 0.9234 (t) cc_final: 0.8866 (t) REVERT: A 348 MET cc_start: 0.8121 (tpt) cc_final: 0.7761 (tpt) REVERT: A 352 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7690 (mt-10) REVERT: A 360 PHE cc_start: 0.8673 (m-80) cc_final: 0.8377 (m-80) REVERT: A 436 LEU cc_start: 0.9080 (mp) cc_final: 0.8727 (mt) REVERT: A 493 MET cc_start: 0.8971 (tmm) cc_final: 0.8583 (tmm) REVERT: B 119 GLU cc_start: 0.8904 (mp0) cc_final: 0.8493 (mp0) REVERT: B 147 GLN cc_start: 0.8966 (mt0) cc_final: 0.8308 (mt0) REVERT: B 157 LEU cc_start: 0.9161 (tp) cc_final: 0.8769 (tp) REVERT: B 158 ASN cc_start: 0.8983 (m110) cc_final: 0.8662 (m-40) REVERT: B 211 GLU cc_start: 0.7849 (mm-30) cc_final: 0.7445 (mm-30) REVERT: B 232 ASN cc_start: 0.7907 (t0) cc_final: 0.7683 (t0) REVERT: B 253 ILE cc_start: 0.9572 (tt) cc_final: 0.9272 (tt) REVERT: B 263 ASP cc_start: 0.9007 (m-30) cc_final: 0.8746 (m-30) REVERT: B 282 VAL cc_start: 0.9643 (t) cc_final: 0.9394 (m) REVERT: B 288 PHE cc_start: 0.9333 (t80) cc_final: 0.8976 (t80) REVERT: B 348 MET cc_start: 0.7864 (tpt) cc_final: 0.7186 (tpp) REVERT: B 349 LEU cc_start: 0.9231 (mp) cc_final: 0.8943 (mt) REVERT: B 359 MET cc_start: 0.8881 (ttp) cc_final: 0.8672 (tmm) REVERT: B 373 ILE cc_start: 0.9673 (mt) cc_final: 0.9328 (mt) REVERT: B 393 SER cc_start: 0.9395 (m) cc_final: 0.8514 (p) REVERT: B 394 TYR cc_start: 0.9041 (m-80) cc_final: 0.8378 (m-80) REVERT: B 425 ILE cc_start: 0.9605 (mt) cc_final: 0.9352 (mt) REVERT: B 467 ASN cc_start: 0.9244 (t0) cc_final: 0.8340 (t0) REVERT: B 493 MET cc_start: 0.9468 (tmm) cc_final: 0.9124 (tmm) REVERT: B 526 GLU cc_start: 0.7958 (tp30) cc_final: 0.7486 (tp30) REVERT: B 588 GLN cc_start: 0.9177 (mm-40) cc_final: 0.8546 (mm-40) REVERT: B 590 SER cc_start: 0.9071 (p) cc_final: 0.8405 (t) REVERT: B 615 MET cc_start: 0.9494 (mmm) cc_final: 0.9290 (mmm) REVERT: B 667 LEU cc_start: 0.9437 (tp) cc_final: 0.9138 (tp) REVERT: C 27 LYS cc_start: 0.9004 (mtmm) cc_final: 0.8729 (tptt) REVERT: C 55 TYR cc_start: 0.7078 (t80) cc_final: 0.6187 (t80) REVERT: C 154 PHE cc_start: 0.8518 (t80) cc_final: 0.8208 (t80) REVERT: C 243 THR cc_start: 0.7241 (p) cc_final: 0.6682 (t) REVERT: C 247 TYR cc_start: 0.8077 (m-80) cc_final: 0.7666 (m-80) REVERT: D 20 MET cc_start: 0.8800 (ptp) cc_final: 0.8477 (ptp) REVERT: D 23 ASN cc_start: 0.9406 (m110) cc_final: 0.9203 (m-40) REVERT: D 24 GLN cc_start: 0.8211 (mp-120) cc_final: 0.7512 (tp-100) REVERT: D 42 LEU cc_start: 0.5987 (pp) cc_final: 0.5610 (pp) REVERT: D 46 TYR cc_start: 0.8574 (m-80) cc_final: 0.8252 (m-80) REVERT: D 149 ASP cc_start: 0.8462 (m-30) cc_final: 0.8184 (m-30) REVERT: D 154 PHE cc_start: 0.8558 (t80) cc_final: 0.8327 (t80) REVERT: D 224 LEU cc_start: 0.8752 (mt) cc_final: 0.8545 (mt) REVERT: D 233 ASN cc_start: 0.8683 (m110) cc_final: 0.8450 (m110) REVERT: D 259 PHE cc_start: 0.7460 (t80) cc_final: 0.7123 (t80) outliers start: 4 outliers final: 0 residues processed: 612 average time/residue: 0.1115 time to fit residues: 103.2718 Evaluate side-chains 482 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 482 time to evaluate : 0.420 ------------------------------------------------------------------------------- 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: 0.9980 chunk 120 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 126 optimal weight: 0.1980 chunk 129 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 115 optimal weight: 0.7980 chunk 168 optimal weight: 9.9990 chunk 157 optimal weight: 20.0000 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 365 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN B 180 ASN B 218 ASN B 232 ASN B 361 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 25 ASN C 98 ASN D 91 ASN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.131450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.096308 restraints weight = 37800.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.099773 restraints weight = 19203.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.101930 restraints weight = 11666.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.103501 restraints weight = 8091.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.104511 restraints weight = 6074.248| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.6145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16386 Z= 0.134 Angle : 0.593 13.142 22134 Z= 0.314 Chirality : 0.042 0.155 2360 Planarity : 0.003 0.036 2818 Dihedral : 8.701 135.183 2290 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.17 % Allowed : 2.21 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.84 (0.19), residues: 1932 helix: 1.01 (0.15), residues: 1123 sheet: -0.77 (0.40), residues: 144 loop : 0.32 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 686 TYR 0.035 0.001 TYR A 118 PHE 0.030 0.002 PHE A 129 TRP 0.043 0.001 TRP D 124 HIS 0.012 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (16386) covalent geometry : angle 0.59285 / 0.31 (22134) hydrogen bonds : bond 0.03956 / 2.49 ( 871) hydrogen bonds : angle 4.93048 / 3.55 ( 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 633 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 630 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8937 (t80) cc_final: 0.8380 (t80) REVERT: A 99 LYS cc_start: 0.8921 (mmtm) cc_final: 0.8675 (mmtp) REVERT: A 131 ASN cc_start: 0.9135 (t0) cc_final: 0.8849 (t0) REVERT: A 147 GLN cc_start: 0.8614 (mt0) cc_final: 0.8281 (mt0) REVERT: A 150 GLN cc_start: 0.8769 (tp40) cc_final: 0.8091 (tm-30) REVERT: A 204 SER cc_start: 0.9418 (t) cc_final: 0.8845 (t) REVERT: A 263 ASP cc_start: 0.8339 (m-30) cc_final: 0.8117 (m-30) REVERT: A 278 LEU cc_start: 0.9166 (tp) cc_final: 0.8868 (tp) REVERT: A 348 MET cc_start: 0.8106 (tpt) cc_final: 0.7663 (tpt) REVERT: A 352 GLU cc_start: 0.8419 (mt-10) cc_final: 0.7734 (mt-10) REVERT: A 361 GLN cc_start: 0.8223 (tp40) cc_final: 0.7966 (tp-100) REVERT: A 444 ASP cc_start: 0.8330 (t70) cc_final: 0.8021 (t0) REVERT: A 493 MET cc_start: 0.8965 (tmm) cc_final: 0.8561 (tmm) REVERT: A 634 MET cc_start: 0.8941 (mmm) cc_final: 0.8672 (mmm) REVERT: A 640 MET cc_start: 0.9051 (ttm) cc_final: 0.8580 (ttm) REVERT: B 8 LYS cc_start: 0.8909 (tptp) cc_final: 0.8529 (tppt) REVERT: B 12 LEU cc_start: 0.9511 (mt) cc_final: 0.9218 (mt) REVERT: B 119 GLU cc_start: 0.8778 (mp0) cc_final: 0.8409 (mp0) REVERT: B 127 LEU cc_start: 0.9499 (mm) cc_final: 0.9222 (mm) REVERT: B 147 GLN cc_start: 0.8817 (mt0) cc_final: 0.8014 (mt0) REVERT: B 157 LEU cc_start: 0.9151 (tp) cc_final: 0.8774 (tp) REVERT: B 158 ASN cc_start: 0.8914 (m110) cc_final: 0.8636 (m-40) REVERT: B 211 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7351 (mm-30) REVERT: B 217 GLU cc_start: 0.8199 (tm-30) cc_final: 0.7790 (tm-30) REVERT: B 253 ILE cc_start: 0.9581 (tt) cc_final: 0.9325 (tt) REVERT: B 263 ASP cc_start: 0.8996 (m-30) cc_final: 0.8608 (m-30) REVERT: B 266 LYS cc_start: 0.9304 (mtpp) cc_final: 0.8896 (mttp) REVERT: B 282 VAL cc_start: 0.9611 (t) cc_final: 0.9387 (m) REVERT: B 288 PHE cc_start: 0.9231 (t80) cc_final: 0.8896 (t80) REVERT: B 322 MET cc_start: 0.8801 (tpp) cc_final: 0.8360 (mmm) REVERT: B 348 MET cc_start: 0.7938 (tpt) cc_final: 0.7187 (tpp) REVERT: B 359 MET cc_start: 0.8745 (ttp) cc_final: 0.8431 (tmm) REVERT: B 373 ILE cc_start: 0.9590 (mt) cc_final: 0.9198 (mt) REVERT: B 379 SER cc_start: 0.8786 (t) cc_final: 0.8566 (t) REVERT: B 393 SER cc_start: 0.9373 (m) cc_final: 0.8683 (p) REVERT: B 394 TYR cc_start: 0.9062 (m-80) cc_final: 0.8307 (m-80) REVERT: B 425 ILE cc_start: 0.9588 (mt) cc_final: 0.9386 (mt) REVERT: B 467 ASN cc_start: 0.9274 (t0) cc_final: 0.8405 (t0) REVERT: B 493 MET cc_start: 0.9445 (tmm) cc_final: 0.9087 (tmm) REVERT: B 526 GLU cc_start: 0.7876 (tp30) cc_final: 0.7355 (tp30) REVERT: B 588 GLN cc_start: 0.9108 (mm-40) cc_final: 0.8358 (mm-40) REVERT: B 590 SER cc_start: 0.9070 (p) cc_final: 0.8293 (t) REVERT: B 601 ILE cc_start: 0.9189 (mm) cc_final: 0.8987 (mm) REVERT: B 615 MET cc_start: 0.9442 (mmm) cc_final: 0.9202 (mmm) REVERT: B 667 LEU cc_start: 0.9482 (tp) cc_final: 0.9136 (tp) REVERT: C 27 LYS cc_start: 0.9050 (mtmm) cc_final: 0.8656 (tptp) REVERT: C 243 THR cc_start: 0.7169 (p) cc_final: 0.6670 (t) REVERT: C 247 TYR cc_start: 0.7993 (m-80) cc_final: 0.7697 (m-80) REVERT: C 313 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8587 (mt-10) REVERT: D 42 LEU cc_start: 0.5928 (pp) cc_final: 0.5554 (pp) REVERT: D 46 TYR cc_start: 0.8566 (m-80) cc_final: 0.8223 (m-80) REVERT: D 56 MET cc_start: 0.6088 (mpp) cc_final: 0.5699 (mpp) REVERT: D 95 MET cc_start: 0.9077 (tmm) cc_final: 0.8726 (tmm) REVERT: D 96 MET cc_start: 0.8396 (mmm) cc_final: 0.7276 (mmm) REVERT: D 119 ASN cc_start: 0.9252 (m-40) cc_final: 0.8866 (t0) REVERT: D 149 ASP cc_start: 0.8445 (m-30) cc_final: 0.8164 (m-30) REVERT: D 154 PHE cc_start: 0.8424 (t80) cc_final: 0.7853 (t80) REVERT: D 185 MET cc_start: 0.7927 (mmm) cc_final: 0.6520 (pmm) REVERT: D 192 ASN cc_start: 0.8673 (t0) cc_final: 0.8105 (m-40) REVERT: D 196 ARG cc_start: 0.8223 (tpm170) cc_final: 0.8003 (tpm170) REVERT: D 198 GLU cc_start: 0.8549 (pt0) cc_final: 0.7112 (mm-30) REVERT: D 233 ASN cc_start: 0.8687 (m110) cc_final: 0.8443 (m110) REVERT: D 259 PHE cc_start: 0.7688 (t80) cc_final: 0.7282 (t80) outliers start: 3 outliers final: 0 residues processed: 632 average time/residue: 0.1109 time to fit residues: 105.6050 Evaluate side-chains 517 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 517 time to evaluate : 0.483 ------------------------------------------------------------------------------- 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: 6.9990 chunk 183 optimal weight: 9.9990 chunk 72 optimal weight: 5.9990 chunk 172 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 4 optimal weight: 0.2980 chunk 77 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN A 645 GLN B 180 ASN B 232 ASN B 312 GLN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN C 24 GLN D 23 ASN D 132 GLN ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.127146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.092056 restraints weight = 38676.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.095270 restraints weight = 19698.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.097465 restraints weight = 12096.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.099038 restraints weight = 8423.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.099963 restraints weight = 6352.384| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3200 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.6375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 16386 Z= 0.253 Angle : 0.664 11.151 22134 Z= 0.352 Chirality : 0.044 0.168 2360 Planarity : 0.004 0.050 2818 Dihedral : 8.808 138.441 2290 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.23 % Allowed : 2.27 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.70 (0.19), residues: 1932 helix: 0.86 (0.15), residues: 1131 sheet: -0.64 (0.42), residues: 142 loop : 0.27 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 256 TYR 0.026 0.002 TYR D 174 PHE 0.030 0.002 PHE A 129 TRP 0.055 0.002 TRP D 124 HIS 0.009 0.002 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.25 (16386) covalent geometry : angle 0.66427 / 0.35 (22134) hydrogen bonds : bond 0.04077 / 2.55 ( 871) hydrogen bonds : angle 5.08210 / 3.66 ( 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 574 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 570 time to evaluate : 0.574 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 15 GLU cc_start: 0.8911 (mp0) cc_final: 0.8698 (mp0) REVERT: A 40 TYR cc_start: 0.8988 (t80) cc_final: 0.8350 (t80) REVERT: A 131 ASN cc_start: 0.9127 (t0) cc_final: 0.8887 (t0) REVERT: A 147 GLN cc_start: 0.8867 (mt0) cc_final: 0.8492 (mt0) REVERT: A 150 GLN cc_start: 0.8919 (tp40) cc_final: 0.7987 (tm-30) REVERT: A 204 SER cc_start: 0.9355 (t) cc_final: 0.8797 (t) REVERT: A 263 ASP cc_start: 0.8339 (m-30) cc_final: 0.8092 (m-30) REVERT: A 286 ASP cc_start: 0.8895 (m-30) cc_final: 0.8598 (m-30) REVERT: A 290 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8278 (pm20) REVERT: A 348 MET cc_start: 0.8233 (tpt) cc_final: 0.7758 (tpt) REVERT: A 352 GLU cc_start: 0.8397 (mt-10) cc_final: 0.8012 (mt-10) REVERT: A 493 MET cc_start: 0.9019 (tmm) cc_final: 0.8556 (tmm) REVERT: A 494 MET cc_start: 0.8840 (mtm) cc_final: 0.8010 (ptp) REVERT: A 640 MET cc_start: 0.9245 (ttm) cc_final: 0.8745 (ttm) REVERT: B 31 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8659 (mt-10) REVERT: B 60 GLU cc_start: 0.8855 (OUTLIER) cc_final: 0.8483 (mp0) REVERT: B 119 GLU cc_start: 0.8922 (mp0) cc_final: 0.8507 (mp0) REVERT: B 147 GLN cc_start: 0.8896 (mt0) cc_final: 0.8090 (mt0) REVERT: B 157 LEU cc_start: 0.9143 (tp) cc_final: 0.8767 (tp) REVERT: B 158 ASN cc_start: 0.8962 (m110) cc_final: 0.8684 (m-40) REVERT: B 211 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7522 (mm-30) REVERT: B 217 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7801 (tm-30) REVERT: B 232 ASN cc_start: 0.7815 (t160) cc_final: 0.7529 (t0) REVERT: B 253 ILE cc_start: 0.9582 (tt) cc_final: 0.9343 (tt) REVERT: B 263 ASP cc_start: 0.9039 (m-30) cc_final: 0.8709 (m-30) REVERT: B 288 PHE cc_start: 0.9439 (t80) cc_final: 0.9089 (t80) REVERT: B 348 MET cc_start: 0.7895 (tpt) cc_final: 0.7157 (tpp) REVERT: B 373 ILE cc_start: 0.9641 (mt) cc_final: 0.9282 (mt) REVERT: B 393 SER cc_start: 0.9420 (m) cc_final: 0.8936 (m) REVERT: B 394 TYR cc_start: 0.9097 (m-80) cc_final: 0.8340 (m-80) REVERT: B 425 ILE cc_start: 0.9613 (mt) cc_final: 0.9346 (mt) REVERT: B 441 GLU cc_start: 0.8685 (mp0) cc_final: 0.8480 (mp0) REVERT: B 467 ASN cc_start: 0.9318 (t0) cc_final: 0.8423 (t0) REVERT: B 493 MET cc_start: 0.9456 (tmm) cc_final: 0.9128 (tmm) REVERT: B 526 GLU cc_start: 0.7975 (tp30) cc_final: 0.7462 (tp30) REVERT: B 588 GLN cc_start: 0.9136 (mm-40) cc_final: 0.8349 (mm-40) REVERT: B 590 SER cc_start: 0.9186 (p) cc_final: 0.8423 (t) REVERT: B 595 MET cc_start: 0.8919 (mmm) cc_final: 0.8344 (mmm) REVERT: B 610 LYS cc_start: 0.9259 (ttpt) cc_final: 0.8968 (tmtt) REVERT: B 667 LEU cc_start: 0.9426 (tp) cc_final: 0.9167 (tp) REVERT: C 27 LYS cc_start: 0.9020 (mtmm) cc_final: 0.8761 (tptp) REVERT: C 49 LYS cc_start: 0.9110 (mttp) cc_final: 0.8868 (tmtt) REVERT: C 53 ASP cc_start: 0.8266 (t0) cc_final: 0.7847 (t0) REVERT: C 96 MET cc_start: 0.7355 (mmp) cc_final: 0.6740 (mmm) REVERT: C 243 THR cc_start: 0.7503 (p) cc_final: 0.6980 (t) REVERT: C 247 TYR cc_start: 0.8016 (m-80) cc_final: 0.7780 (m-80) REVERT: D 42 LEU cc_start: 0.5998 (pp) cc_final: 0.5635 (pp) REVERT: D 46 TYR cc_start: 0.8750 (m-80) cc_final: 0.8353 (m-80) REVERT: D 56 MET cc_start: 0.5565 (mpp) cc_final: 0.5106 (mpp) REVERT: D 93 MET cc_start: 0.8761 (mpp) cc_final: 0.8335 (tpt) REVERT: D 95 MET cc_start: 0.9207 (tmm) cc_final: 0.8797 (tmm) REVERT: D 96 MET cc_start: 0.8544 (mmm) cc_final: 0.7341 (mmm) REVERT: D 119 ASN cc_start: 0.9289 (m-40) cc_final: 0.8889 (t0) REVERT: D 138 ILE cc_start: 0.8867 (mm) cc_final: 0.8662 (mm) REVERT: D 142 TYR cc_start: 0.8528 (m-80) cc_final: 0.8193 (m-80) REVERT: D 149 ASP cc_start: 0.8566 (m-30) cc_final: 0.8292 (m-30) REVERT: D 185 MET cc_start: 0.8107 (mmm) cc_final: 0.6713 (pmm) REVERT: D 192 ASN cc_start: 0.8831 (t0) cc_final: 0.8333 (m-40) REVERT: D 196 ARG cc_start: 0.8412 (tpm170) cc_final: 0.8142 (tpm170) REVERT: D 224 LEU cc_start: 0.8938 (mt) cc_final: 0.8731 (mt) REVERT: D 233 ASN cc_start: 0.8688 (m110) cc_final: 0.8434 (m110) REVERT: D 259 PHE cc_start: 0.7696 (t80) cc_final: 0.7186 (t80) outliers start: 4 outliers final: 1 residues processed: 573 average time/residue: 0.1100 time to fit residues: 95.2640 Evaluate side-chains 469 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 466 time to evaluate : 0.605 ------------------------------------------------------------------------------- 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: 10.0000 chunk 51 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 186 optimal weight: 6.9990 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 232 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** D 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.128722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.094021 restraints weight = 38104.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.097366 restraints weight = 19200.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.099615 restraints weight = 11670.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.101125 restraints weight = 8012.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.102087 restraints weight = 6046.174| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.6577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16386 Z= 0.201 Angle : 0.645 12.189 22134 Z= 0.344 Chirality : 0.043 0.230 2360 Planarity : 0.004 0.043 2818 Dihedral : 8.691 137.484 2290 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.06 % Allowed : 1.22 % Favored : 98.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.19), residues: 1932 helix: 0.78 (0.15), residues: 1132 sheet: -0.64 (0.42), residues: 142 loop : 0.17 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 686 TYR 0.029 0.002 TYR C 46 PHE 0.039 0.002 PHE A 129 TRP 0.060 0.002 TRP D 124 HIS 0.009 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.20 (16386) covalent geometry : angle 0.64530 / 0.34 (22134) hydrogen bonds : bond 0.04037 / 2.53 ( 871) hydrogen bonds : angle 5.15232 / 3.74 ( 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 592 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 591 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.8905 (ttmt) cc_final: 0.8599 (ttpp) REVERT: A 40 TYR cc_start: 0.9008 (t80) cc_final: 0.8380 (t80) REVERT: A 131 ASN cc_start: 0.9181 (t0) cc_final: 0.8907 (t0) REVERT: A 147 GLN cc_start: 0.8834 (mt0) cc_final: 0.8508 (mt0) REVERT: A 150 GLN cc_start: 0.8892 (tp40) cc_final: 0.8038 (tm-30) REVERT: A 163 ARG cc_start: 0.8411 (tpt170) cc_final: 0.8123 (tpt170) REVERT: A 204 SER cc_start: 0.9334 (t) cc_final: 0.8945 (t) REVERT: A 263 ASP cc_start: 0.8391 (m-30) cc_final: 0.8130 (m-30) REVERT: A 348 MET cc_start: 0.8135 (tpt) cc_final: 0.7712 (tpt) REVERT: A 352 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7825 (mt-10) REVERT: A 493 MET cc_start: 0.8992 (tmm) cc_final: 0.8495 (tmm) REVERT: A 501 GLN cc_start: 0.9303 (tt0) cc_final: 0.9081 (tt0) REVERT: A 628 GLU cc_start: 0.8399 (mp0) cc_final: 0.8138 (mp0) REVERT: A 640 MET cc_start: 0.9133 (ttm) cc_final: 0.8807 (ttm) REVERT: B 71 LEU cc_start: 0.9536 (mm) cc_final: 0.9202 (mp) REVERT: B 119 GLU cc_start: 0.8927 (mp0) cc_final: 0.8542 (mp0) REVERT: B 140 TYR cc_start: 0.9258 (m-10) cc_final: 0.8897 (m-10) REVERT: B 147 GLN cc_start: 0.8923 (mt0) cc_final: 0.8065 (mt0) REVERT: B 157 LEU cc_start: 0.9138 (tp) cc_final: 0.8819 (tp) REVERT: B 211 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7409 (mm-30) REVERT: B 217 GLU cc_start: 0.8207 (tm-30) cc_final: 0.7760 (tm-30) REVERT: B 232 ASN cc_start: 0.7824 (t160) cc_final: 0.7558 (t0) REVERT: B 235 ARG cc_start: 0.8265 (mmm-85) cc_final: 0.8012 (mmm-85) REVERT: B 253 ILE cc_start: 0.9605 (tt) cc_final: 0.9317 (tt) REVERT: B 263 ASP cc_start: 0.9014 (m-30) cc_final: 0.8659 (m-30) REVERT: B 288 PHE cc_start: 0.9409 (t80) cc_final: 0.9065 (t80) REVERT: B 348 MET cc_start: 0.7953 (tpt) cc_final: 0.7261 (tpp) REVERT: B 373 ILE cc_start: 0.9587 (mt) cc_final: 0.9281 (mt) REVERT: B 379 SER cc_start: 0.8604 (t) cc_final: 0.8306 (t) REVERT: B 393 SER cc_start: 0.9417 (m) cc_final: 0.9033 (m) REVERT: B 394 TYR cc_start: 0.9110 (m-80) cc_final: 0.8427 (m-80) REVERT: B 425 ILE cc_start: 0.9591 (mt) cc_final: 0.9291 (mt) REVERT: B 436 LEU cc_start: 0.9356 (mt) cc_final: 0.9122 (mt) REVERT: B 467 ASN cc_start: 0.9156 (t0) cc_final: 0.8653 (t0) REVERT: B 493 MET cc_start: 0.9460 (tmm) cc_final: 0.9068 (tmm) REVERT: B 526 GLU cc_start: 0.8031 (tp30) cc_final: 0.7555 (tp30) REVERT: B 588 GLN cc_start: 0.9151 (mm-40) cc_final: 0.8356 (mm-40) REVERT: B 610 LYS cc_start: 0.9208 (ttpt) cc_final: 0.8896 (tmtt) REVERT: B 615 MET cc_start: 0.9493 (mmp) cc_final: 0.9044 (mmm) REVERT: B 667 LEU cc_start: 0.9448 (tp) cc_final: 0.9076 (tp) REVERT: C 27 LYS cc_start: 0.9014 (mtmm) cc_final: 0.8754 (tptp) REVERT: C 55 TYR cc_start: 0.7131 (t80) cc_final: 0.6407 (t80) REVERT: C 157 MET cc_start: 0.8952 (ptt) cc_final: 0.8734 (ptt) REVERT: C 243 THR cc_start: 0.7579 (p) cc_final: 0.7051 (t) REVERT: C 313 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8541 (mt-10) REVERT: D 42 LEU cc_start: 0.6039 (pp) cc_final: 0.5637 (pp) REVERT: D 46 TYR cc_start: 0.8837 (m-80) cc_final: 0.8370 (m-80) REVERT: D 95 MET cc_start: 0.9170 (tmm) cc_final: 0.8727 (tmm) REVERT: D 96 MET cc_start: 0.8699 (mmm) cc_final: 0.7545 (mmm) REVERT: D 149 ASP cc_start: 0.8500 (m-30) cc_final: 0.8214 (m-30) REVERT: D 185 MET cc_start: 0.8128 (mmm) cc_final: 0.6767 (pmm) REVERT: D 192 ASN cc_start: 0.8862 (t0) cc_final: 0.8392 (m-40) REVERT: D 198 GLU cc_start: 0.8416 (pt0) cc_final: 0.7459 (mm-30) REVERT: D 205 VAL cc_start: 0.9449 (t) cc_final: 0.9225 (t) REVERT: D 224 LEU cc_start: 0.8998 (mt) cc_final: 0.8781 (mt) REVERT: D 233 ASN cc_start: 0.8704 (m110) cc_final: 0.8426 (m110) REVERT: D 259 PHE cc_start: 0.7595 (t80) cc_final: 0.7160 (t80) outliers start: 1 outliers final: 0 residues processed: 591 average time/residue: 0.1112 time to fit residues: 99.3972 Evaluate side-chains 490 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 490 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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: 4.9990 chunk 99 optimal weight: 6.9990 chunk 61 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 134 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 151 optimal weight: 9.9990 chunk 81 optimal weight: 0.6980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN B 158 ASN B 218 ASN B 232 ASN B 361 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.130347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.095366 restraints weight = 38047.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.098773 restraints weight = 19309.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.100982 restraints weight = 11731.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.102536 restraints weight = 8059.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.103476 restraints weight = 6039.133| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (23 function evaluations) r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.6759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16386 Z= 0.162 Angle : 0.641 11.908 22134 Z= 0.338 Chirality : 0.043 0.170 2360 Planarity : 0.003 0.044 2818 Dihedral : 8.571 137.918 2290 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 13.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.06 % Allowed : 1.28 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.51 (0.19), residues: 1932 helix: 0.79 (0.15), residues: 1140 sheet: -0.71 (0.41), residues: 142 loop : 0.02 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 686 TYR 0.032 0.002 TYR A 118 PHE 0.042 0.002 PHE A 129 TRP 0.058 0.002 TRP D 124 HIS 0.009 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (16386) covalent geometry : angle 0.64129 / 0.34 (22134) hydrogen bonds : bond 0.04092 / 2.61 ( 871) hydrogen bonds : angle 5.06346 / 3.68 ( 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 593 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 592 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8980 (t80) cc_final: 0.8396 (t80) REVERT: A 131 ASN cc_start: 0.9175 (t0) cc_final: 0.8911 (t0) REVERT: A 147 GLN cc_start: 0.8773 (mt0) cc_final: 0.8433 (mt0) REVERT: A 150 GLN cc_start: 0.8842 (tp40) cc_final: 0.8083 (tm-30) REVERT: A 163 ARG cc_start: 0.8444 (tpt170) cc_final: 0.8195 (tpt170) REVERT: A 204 SER cc_start: 0.9323 (t) cc_final: 0.8899 (t) REVERT: A 221 LYS cc_start: 0.9070 (mmtm) cc_final: 0.8754 (mppt) REVERT: A 263 ASP cc_start: 0.8410 (m-30) cc_final: 0.7984 (m-30) REVERT: A 278 LEU cc_start: 0.9209 (tp) cc_final: 0.8943 (tp) REVERT: A 348 MET cc_start: 0.8111 (tpt) cc_final: 0.7645 (tpt) REVERT: A 352 GLU cc_start: 0.8403 (mt-10) cc_final: 0.7757 (mt-10) REVERT: A 479 TYR cc_start: 0.8898 (t80) cc_final: 0.8373 (t80) REVERT: A 493 MET cc_start: 0.8972 (tmm) cc_final: 0.8509 (tmm) REVERT: A 494 MET cc_start: 0.8636 (mtm) cc_final: 0.7784 (ptp) REVERT: A 501 GLN cc_start: 0.9304 (tt0) cc_final: 0.9095 (tt0) REVERT: A 628 GLU cc_start: 0.8281 (mp0) cc_final: 0.8060 (mp0) REVERT: A 634 MET cc_start: 0.8893 (mmm) cc_final: 0.8614 (mmm) REVERT: A 640 MET cc_start: 0.9106 (ttm) cc_final: 0.8774 (ttm) REVERT: B 71 LEU cc_start: 0.9531 (mm) cc_final: 0.9305 (mp) REVERT: B 119 GLU cc_start: 0.8918 (mp0) cc_final: 0.8559 (mp0) REVERT: B 140 TYR cc_start: 0.9210 (m-10) cc_final: 0.8853 (m-10) REVERT: B 157 LEU cc_start: 0.9099 (tp) cc_final: 0.8741 (tp) REVERT: B 211 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7434 (mm-30) REVERT: B 217 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7662 (tm-30) REVERT: B 218 ASN cc_start: 0.9086 (OUTLIER) cc_final: 0.8874 (t0) REVERT: B 232 ASN cc_start: 0.7830 (t160) cc_final: 0.7477 (t0) REVERT: B 235 ARG cc_start: 0.8215 (mmm-85) cc_final: 0.7754 (mmt90) REVERT: B 253 ILE cc_start: 0.9589 (tt) cc_final: 0.9316 (tt) REVERT: B 263 ASP cc_start: 0.8986 (m-30) cc_final: 0.8653 (m-30) REVERT: B 288 PHE cc_start: 0.9381 (t80) cc_final: 0.9006 (t80) REVERT: B 348 MET cc_start: 0.7878 (tpt) cc_final: 0.7252 (tpp) REVERT: B 373 ILE cc_start: 0.9572 (mt) cc_final: 0.9296 (mt) REVERT: B 393 SER cc_start: 0.9418 (m) cc_final: 0.9013 (m) REVERT: B 394 TYR cc_start: 0.9106 (m-80) cc_final: 0.8452 (m-80) REVERT: B 425 ILE cc_start: 0.9561 (mt) cc_final: 0.9273 (mt) REVERT: B 493 MET cc_start: 0.9439 (tmm) cc_final: 0.9033 (tmm) REVERT: B 526 GLU cc_start: 0.7910 (tp30) cc_final: 0.7357 (tp30) REVERT: B 595 MET cc_start: 0.8844 (mmm) cc_final: 0.8267 (mmm) REVERT: B 636 LYS cc_start: 0.9616 (mmtm) cc_final: 0.9371 (mmmm) REVERT: B 667 LEU cc_start: 0.9445 (tp) cc_final: 0.9082 (tp) REVERT: C 27 LYS cc_start: 0.9015 (mtmm) cc_final: 0.8761 (tptp) REVERT: C 55 TYR cc_start: 0.7093 (t80) cc_final: 0.6283 (t80) REVERT: C 243 THR cc_start: 0.7612 (p) cc_final: 0.7193 (t) REVERT: D 42 LEU cc_start: 0.6082 (pp) cc_final: 0.5629 (pp) REVERT: D 46 TYR cc_start: 0.8836 (m-80) cc_final: 0.8353 (m-80) REVERT: D 95 MET cc_start: 0.9061 (tmm) cc_final: 0.8620 (tmm) REVERT: D 96 MET cc_start: 0.8765 (mmm) cc_final: 0.7614 (mmm) REVERT: D 119 ASN cc_start: 0.9279 (m-40) cc_final: 0.9052 (t0) REVERT: D 149 ASP cc_start: 0.8464 (m-30) cc_final: 0.8178 (m-30) REVERT: D 185 MET cc_start: 0.8208 (mmm) cc_final: 0.7061 (pmm) REVERT: D 192 ASN cc_start: 0.8787 (t0) cc_final: 0.8292 (m-40) REVERT: D 198 GLU cc_start: 0.8783 (pt0) cc_final: 0.7631 (mm-30) REVERT: D 205 VAL cc_start: 0.9458 (t) cc_final: 0.9163 (t) REVERT: D 233 ASN cc_start: 0.8624 (m110) cc_final: 0.8319 (m110) REVERT: D 259 PHE cc_start: 0.7845 (t80) cc_final: 0.7486 (t80) outliers start: 1 outliers final: 0 residues processed: 592 average time/residue: 0.1089 time to fit residues: 97.7277 Evaluate side-chains 485 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 484 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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: 3.9990 chunk 133 optimal weight: 1.9990 chunk 149 optimal weight: 0.0670 chunk 16 optimal weight: 0.0770 chunk 114 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 0.2980 chunk 100 optimal weight: 0.0010 chunk 88 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.2482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 ASN A 361 GLN A 410 ASN A 447 ASN ** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 320 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN B 467 ASN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN C 238 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.136799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.101988 restraints weight = 37193.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.105340 restraints weight = 18786.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.107716 restraints weight = 11632.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.109342 restraints weight = 7902.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.110391 restraints weight = 5873.463| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.7043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16386 Z= 0.130 Angle : 0.649 12.804 22134 Z= 0.341 Chirality : 0.043 0.181 2360 Planarity : 0.004 0.071 2818 Dihedral : 8.355 136.757 2290 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.12 % Allowed : 0.70 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.54 (0.19), residues: 1932 helix: 0.78 (0.15), residues: 1133 sheet: 0.07 (0.47), residues: 100 loop : -0.13 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 225 TYR 0.030 0.001 TYR A 118 PHE 0.031 0.002 PHE A 129 TRP 0.064 0.002 TRP D 124 HIS 0.009 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (16386) covalent geometry : angle 0.64946 / 0.34 (22134) hydrogen bonds : bond 0.04052 / 2.59 ( 871) hydrogen bonds : angle 5.05376 / 3.67 ( 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 635 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 633 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8929 (t80) cc_final: 0.8383 (t80) REVERT: A 131 ASN cc_start: 0.9120 (t0) cc_final: 0.8787 (p0) REVERT: A 139 GLU cc_start: 0.8727 (mp0) cc_final: 0.8459 (mp0) REVERT: A 147 GLN cc_start: 0.8681 (mt0) cc_final: 0.8426 (mt0) REVERT: A 179 LEU cc_start: 0.9101 (tt) cc_final: 0.8896 (tt) REVERT: A 204 SER cc_start: 0.9267 (t) cc_final: 0.8901 (p) REVERT: A 221 LYS cc_start: 0.9018 (mmtm) cc_final: 0.8753 (mmtm) REVERT: A 278 LEU cc_start: 0.9195 (tp) cc_final: 0.8893 (tp) REVERT: A 290 GLU cc_start: 0.8509 (pm20) cc_final: 0.8283 (pm20) REVERT: A 348 MET cc_start: 0.8088 (tpt) cc_final: 0.7734 (tpt) REVERT: A 352 GLU cc_start: 0.8446 (mt-10) cc_final: 0.7702 (mt-10) REVERT: A 360 PHE cc_start: 0.8563 (m-80) cc_final: 0.8145 (m-80) REVERT: A 379 SER cc_start: 0.8404 (t) cc_final: 0.7707 (p) REVERT: A 474 GLN cc_start: 0.9115 (mt0) cc_final: 0.8779 (mm-40) REVERT: A 493 MET cc_start: 0.8989 (tmm) cc_final: 0.8556 (tmm) REVERT: A 494 MET cc_start: 0.8885 (mtm) cc_final: 0.8209 (mtt) REVERT: A 584 ILE cc_start: 0.9079 (pt) cc_final: 0.8833 (pt) REVERT: A 597 ILE cc_start: 0.9072 (pt) cc_final: 0.8850 (pt) REVERT: A 640 MET cc_start: 0.8841 (ttm) cc_final: 0.8591 (ttm) REVERT: B 12 LEU cc_start: 0.9526 (mt) cc_final: 0.9285 (mt) REVERT: B 98 PHE cc_start: 0.9378 (t80) cc_final: 0.8816 (t80) REVERT: B 119 GLU cc_start: 0.8813 (mp0) cc_final: 0.8469 (mp0) REVERT: B 140 TYR cc_start: 0.9155 (m-10) cc_final: 0.8745 (m-10) REVERT: B 157 LEU cc_start: 0.9027 (tp) cc_final: 0.8691 (tp) REVERT: B 211 GLU cc_start: 0.7674 (mm-30) cc_final: 0.7132 (mm-30) REVERT: B 218 ASN cc_start: 0.9191 (t0) cc_final: 0.8857 (t0) REVERT: B 235 ARG cc_start: 0.8233 (mmm-85) cc_final: 0.7934 (mmm-85) REVERT: B 253 ILE cc_start: 0.9630 (tt) cc_final: 0.9370 (tt) REVERT: B 259 ASN cc_start: 0.9118 (m-40) cc_final: 0.8632 (m-40) REVERT: B 263 ASP cc_start: 0.8951 (m-30) cc_final: 0.8460 (m-30) REVERT: B 266 LYS cc_start: 0.9256 (mtpp) cc_final: 0.8927 (mttp) REVERT: B 288 PHE cc_start: 0.9320 (t80) cc_final: 0.9065 (t80) REVERT: B 348 MET cc_start: 0.7817 (tpt) cc_final: 0.7380 (tpp) REVERT: B 381 LEU cc_start: 0.8736 (tp) cc_final: 0.8453 (tp) REVERT: B 393 SER cc_start: 0.9388 (m) cc_final: 0.9122 (m) REVERT: B 394 TYR cc_start: 0.9062 (m-80) cc_final: 0.8425 (m-80) REVERT: B 425 ILE cc_start: 0.9563 (mt) cc_final: 0.9315 (mt) REVERT: B 493 MET cc_start: 0.9398 (tmm) cc_final: 0.8993 (tmm) REVERT: B 526 GLU cc_start: 0.7792 (tp30) cc_final: 0.7202 (tp30) REVERT: B 585 SER cc_start: 0.9216 (p) cc_final: 0.9011 (t) REVERT: B 595 MET cc_start: 0.8851 (mmm) cc_final: 0.8136 (mmm) REVERT: B 599 GLU cc_start: 0.8235 (pt0) cc_final: 0.7736 (pt0) REVERT: B 601 ILE cc_start: 0.9107 (mm) cc_final: 0.8856 (mm) REVERT: B 602 GLU cc_start: 0.8113 (pt0) cc_final: 0.7443 (pt0) REVERT: B 604 ARG cc_start: 0.8717 (tpp80) cc_final: 0.7572 (mmp80) REVERT: B 610 LYS cc_start: 0.9265 (ttpt) cc_final: 0.9004 (tmtt) REVERT: B 615 MET cc_start: 0.9536 (mmp) cc_final: 0.9190 (mmm) REVERT: B 628 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8127 (mt-10) REVERT: B 667 LEU cc_start: 0.9460 (tp) cc_final: 0.9099 (tp) REVERT: B 683 TYR cc_start: 0.8157 (t80) cc_final: 0.7419 (t80) REVERT: C 27 LYS cc_start: 0.8953 (mtmm) cc_final: 0.8699 (tptp) REVERT: C 103 LYS cc_start: 0.6973 (tppt) cc_final: 0.6617 (tppt) REVERT: C 137 MET cc_start: 0.5265 (mpp) cc_final: 0.4720 (mpp) REVERT: C 243 THR cc_start: 0.7648 (p) cc_final: 0.7395 (t) REVERT: D 93 MET cc_start: 0.8569 (tmm) cc_final: 0.8086 (tpp) REVERT: D 95 MET cc_start: 0.9076 (tmm) cc_final: 0.8504 (tmm) REVERT: D 96 MET cc_start: 0.8419 (mmm) cc_final: 0.6807 (mmm) REVERT: D 101 HIS cc_start: 0.8156 (m90) cc_final: 0.7258 (m170) REVERT: D 119 ASN cc_start: 0.9237 (m-40) cc_final: 0.8977 (t0) REVERT: D 149 ASP cc_start: 0.8480 (m-30) cc_final: 0.8252 (m-30) REVERT: D 154 PHE cc_start: 0.8261 (t80) cc_final: 0.8009 (t80) REVERT: D 185 MET cc_start: 0.8386 (mmm) cc_final: 0.7423 (pmm) REVERT: D 192 ASN cc_start: 0.8802 (t0) cc_final: 0.8353 (m-40) REVERT: D 198 GLU cc_start: 0.8564 (pt0) cc_final: 0.7638 (mm-30) REVERT: D 205 VAL cc_start: 0.9338 (t) cc_final: 0.9073 (t) REVERT: D 224 LEU cc_start: 0.8922 (mt) cc_final: 0.8692 (mt) REVERT: D 232 LEU cc_start: 0.7910 (tp) cc_final: 0.7700 (tt) REVERT: D 233 ASN cc_start: 0.8550 (m110) cc_final: 0.8219 (m110) REVERT: D 259 PHE cc_start: 0.7807 (t80) cc_final: 0.7490 (t80) REVERT: D 269 MET cc_start: 0.8093 (ptp) cc_final: 0.7859 (ptp) outliers start: 2 outliers final: 0 residues processed: 635 average time/residue: 0.1079 time to fit residues: 103.5385 Evaluate side-chains 506 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 506 time to evaluate : 0.514 ------------------------------------------------------------------------------- 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: 4.9990 chunk 62 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 189 optimal weight: 8.9990 chunk 181 optimal weight: 8.9990 chunk 165 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 54 optimal weight: 0.0980 chunk 132 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 191 GLN A 361 GLN A 447 ASN ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN C 98 ASN D 28 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN ** D 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 238 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 = 0.3769 r_free = 0.3769 target = 0.136036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.101328 restraints weight = 37860.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.104815 restraints weight = 19098.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.107095 restraints weight = 11528.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.108526 restraints weight = 7965.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.109589 restraints weight = 6021.659| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3310 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3310 r_free = 0.3310 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.7171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16386 Z= 0.161 Angle : 0.691 12.670 22134 Z= 0.363 Chirality : 0.044 0.225 2360 Planarity : 0.004 0.042 2818 Dihedral : 8.455 140.890 2290 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.06 % Allowed : 0.47 % 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: 0.38 (0.19), residues: 1932 helix: 0.67 (0.15), residues: 1144 sheet: -0.42 (0.44), residues: 118 loop : -0.14 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 293 TYR 0.031 0.002 TYR A 522 PHE 0.031 0.002 PHE A 129 TRP 0.063 0.002 TRP D 124 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 (16386) covalent geometry : angle 0.69079 / 0.36 (22134) hydrogen bonds : bond 0.04025 / 2.54 ( 871) hydrogen bonds : angle 5.10806 / 3.70 ( 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 585 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 584 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 TYR cc_start: 0.8989 (t80) cc_final: 0.8368 (t80) REVERT: A 131 ASN cc_start: 0.9103 (t0) cc_final: 0.8834 (t0) REVERT: A 139 GLU cc_start: 0.8738 (mp0) cc_final: 0.8526 (mp0) REVERT: A 147 GLN cc_start: 0.8765 (mt0) cc_final: 0.8451 (mt0) REVERT: A 163 ARG cc_start: 0.8463 (tpt170) cc_final: 0.8213 (tpt170) REVERT: A 204 SER cc_start: 0.9317 (t) cc_final: 0.8799 (t) REVERT: A 217 GLU cc_start: 0.8771 (tp30) cc_final: 0.8544 (tp30) REVERT: A 263 ASP cc_start: 0.8416 (m-30) cc_final: 0.8179 (m-30) REVERT: A 290 GLU cc_start: 0.8439 (pm20) cc_final: 0.8187 (pm20) REVERT: A 348 MET cc_start: 0.8122 (tpt) cc_final: 0.6922 (tpt) REVERT: A 352 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8119 (mp0) REVERT: A 459 LYS cc_start: 0.8917 (mttp) cc_final: 0.8592 (ttmm) REVERT: A 493 MET cc_start: 0.9000 (tmm) cc_final: 0.8547 (tmm) REVERT: A 494 MET cc_start: 0.8802 (mtm) cc_final: 0.8177 (mtt) REVERT: A 640 MET cc_start: 0.9032 (ttm) cc_final: 0.8579 (ttm) REVERT: B 12 LEU cc_start: 0.9529 (mt) cc_final: 0.9150 (mt) REVERT: B 20 LYS cc_start: 0.9377 (pptt) cc_final: 0.9082 (ptmm) REVERT: B 95 MET cc_start: 0.9074 (tpp) cc_final: 0.8842 (mmm) REVERT: B 98 PHE cc_start: 0.9418 (t80) cc_final: 0.9191 (t80) REVERT: B 119 GLU cc_start: 0.8876 (mp0) cc_final: 0.8510 (mp0) REVERT: B 157 LEU cc_start: 0.9018 (tp) cc_final: 0.8726 (tp) REVERT: B 211 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7158 (mm-30) REVERT: B 253 ILE cc_start: 0.9564 (tt) cc_final: 0.9246 (tt) REVERT: B 259 ASN cc_start: 0.9116 (m-40) cc_final: 0.8625 (m-40) REVERT: B 263 ASP cc_start: 0.8986 (m-30) cc_final: 0.8636 (m-30) REVERT: B 348 MET cc_start: 0.7843 (tpt) cc_final: 0.7187 (tpp) REVERT: B 393 SER cc_start: 0.9431 (m) cc_final: 0.9028 (m) REVERT: B 394 TYR cc_start: 0.9115 (m-80) cc_final: 0.8474 (m-80) REVERT: B 425 ILE cc_start: 0.9618 (mt) cc_final: 0.9379 (mt) REVERT: B 526 GLU cc_start: 0.7829 (tp30) cc_final: 0.7255 (tp30) REVERT: B 585 SER cc_start: 0.9216 (p) cc_final: 0.8949 (t) REVERT: B 595 MET cc_start: 0.8829 (mmm) cc_final: 0.8175 (mmm) REVERT: B 599 GLU cc_start: 0.8287 (pt0) cc_final: 0.7821 (pt0) REVERT: B 601 ILE cc_start: 0.9136 (mm) cc_final: 0.8933 (mm) REVERT: B 615 MET cc_start: 0.9527 (mmp) cc_final: 0.9111 (mmm) REVERT: B 628 GLU cc_start: 0.8439 (mt-10) cc_final: 0.8203 (mt-10) REVERT: B 667 LEU cc_start: 0.9462 (tp) cc_final: 0.9106 (tp) REVERT: C 24 GLN cc_start: 0.8839 (pt0) cc_final: 0.8471 (pp30) REVERT: C 27 LYS cc_start: 0.8947 (mtmm) cc_final: 0.8706 (tptp) REVERT: C 243 THR cc_start: 0.7478 (p) cc_final: 0.7210 (p) REVERT: D 56 MET cc_start: 0.5747 (mpp) cc_final: 0.5334 (mpp) REVERT: D 95 MET cc_start: 0.9022 (tmm) cc_final: 0.8697 (tmm) REVERT: D 96 MET cc_start: 0.8479 (mmm) cc_final: 0.7739 (mmm) REVERT: D 101 HIS cc_start: 0.8083 (m90) cc_final: 0.7643 (m90) REVERT: D 119 ASN cc_start: 0.9188 (m-40) cc_final: 0.8871 (t0) REVERT: D 149 ASP cc_start: 0.8476 (m-30) cc_final: 0.8240 (m-30) REVERT: D 154 PHE cc_start: 0.8179 (t80) cc_final: 0.7955 (t80) REVERT: D 185 MET cc_start: 0.8431 (mmm) cc_final: 0.7475 (pmm) REVERT: D 192 ASN cc_start: 0.8803 (t0) cc_final: 0.8344 (m-40) REVERT: D 198 GLU cc_start: 0.8459 (pt0) cc_final: 0.7547 (mm-30) REVERT: D 205 VAL cc_start: 0.9256 (t) cc_final: 0.9013 (t) REVERT: D 224 LEU cc_start: 0.8984 (mt) cc_final: 0.8715 (mt) REVERT: D 233 ASN cc_start: 0.8576 (m110) cc_final: 0.8289 (m110) REVERT: D 259 PHE cc_start: 0.7817 (t80) cc_final: 0.7494 (t80) REVERT: D 263 ASN cc_start: 0.8043 (p0) cc_final: 0.7736 (p0) REVERT: D 269 MET cc_start: 0.8146 (ptp) cc_final: 0.7930 (ptt) outliers start: 1 outliers final: 0 residues processed: 585 average time/residue: 0.1044 time to fit residues: 91.9418 Evaluate side-chains 480 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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: 1.9990 chunk 1 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 39 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 148 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 438 HIS A 447 ASN ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 361 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN D 91 ASN D 214 ASN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.135004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.099947 restraints weight = 37929.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.103379 restraints weight = 19150.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.105633 restraints weight = 11557.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.107161 restraints weight = 7997.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.108050 restraints weight = 6020.066| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.7299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16386 Z= 0.172 Angle : 0.719 13.359 22134 Z= 0.376 Chirality : 0.045 0.206 2360 Planarity : 0.004 0.062 2818 Dihedral : 8.547 141.905 2290 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.06 % Allowed : 0.35 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.25 (0.19), residues: 1932 helix: 0.58 (0.15), residues: 1144 sheet: -0.43 (0.44), residues: 118 loop : -0.23 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 293 TYR 0.031 0.002 TYR A 522 PHE 0.028 0.002 PHE D 109 TRP 0.062 0.002 TRP D 124 HIS 0.011 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (16386) covalent geometry : angle 0.71883 / 0.38 (22134) hydrogen bonds : bond 0.04073 / 2.57 ( 871) hydrogen bonds : angle 5.17083 / 3.77 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2808.75 seconds wall clock time: 49 minutes 27.50 seconds (2967.50 seconds total)