Starting phenix.real_space_refine on Sat Jun 14 07:33:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bz3_45052/06_2025/9bz3_45052_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bz3_45052/06_2025/9bz3_45052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bz3_45052/06_2025/9bz3_45052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bz3_45052/06_2025/9bz3_45052.map" model { file = "/net/cci-nas-00/data/ceres_data/9bz3_45052/06_2025/9bz3_45052_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bz3_45052/06_2025/9bz3_45052_neut.cif" } resolution = 4.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 9.83, per 1000 atoms: 0.61 Number of scatterers: 16038 At special positions: 0 Unit cell: (96.615, 129.159, 132.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.24 Conformation dependent library (CDL) restraints added in 1.9 seconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.986A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.954A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.665A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.694A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.628A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.118A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.676A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.027A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.068A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.936A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.669A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.876A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.359A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.479A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.478A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.185A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.049A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.86 Time building geometry restraints manager: 4.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4851 1.34 - 1.46: 3061 1.46 - 1.58: 8293 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.25e-02 6.40e+03 2.39e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.039 1.20e-02 6.94e+03 1.04e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.032 1.08e-02 8.57e+03 8.87e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.569 -0.032 1.17e-02 7.31e+03 7.33e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.573 -0.033 1.25e-02 6.40e+03 6.81e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21581 2.09 - 4.18: 511 4.18 - 6.27: 36 6.27 - 8.36: 2 8.36 - 10.45: 4 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.63 -6.09 1.36e+00 5.41e-01 2.00e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.17 -4.46 1.15e+00 7.56e-01 1.50e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.25 -3.97 1.09e+00 8.42e-01 1.33e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.85 -4.35 1.23e+00 6.61e-01 1.25e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.71 -4.00 1.15e+00 7.56e-01 1.21e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 9468 35.80 - 71.59: 339 71.59 - 107.39: 37 107.39 - 143.19: 3 143.19 - 178.99: 3 Dihedral angle restraints: 9850 sinusoidal: 4092 harmonic: 5758 Sorted by residual: dihedral pdb=" C2 TTP A 803 " pdb=" C1' TTP A 803 " pdb=" N1 TTP A 803 " pdb=" O4' TTP A 803 " ideal model delta sinusoidal sigma weight residual -58.32 120.67 -178.99 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual 301.68 151.15 150.53 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" C5' TTP A 803 " pdb=" O5' TTP A 803 " pdb=" PA TTP A 803 " pdb=" O3A TTP A 803 " ideal model delta sinusoidal sigma weight residual 179.97 31.87 148.10 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 9847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2149 0.094 - 0.187: 178 0.187 - 0.281: 29 0.281 - 0.375: 2 0.375 - 0.469: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.49e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.56e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.13e-02 2.73e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " 0.017 2.00e-02 2.50e+03 1.12e-02 2.18e+00 pdb=" CG PHE D 92 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 179 " -0.017 2.00e-02 2.50e+03 9.83e-03 1.93e+00 pdb=" CG TYR D 179 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR D 179 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR D 179 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR D 179 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 179 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR D 179 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR D 179 " -0.005 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 129 2.51 - 3.11: 11559 3.11 - 3.70: 27043 3.70 - 4.30: 41517 4.30 - 4.90: 65377 Nonbonded interactions: 145625 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.012 3.040 ... (remaining 145620 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 36.480 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6486 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 0.061 16386 Z= 0.315 Angle : 0.740 10.455 22134 Z= 0.463 Chirality : 0.058 0.469 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.952 178.987 6154 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.34 % Allowed : 15.27 % Favored : 83.39 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.18), residues: 1932 helix: 0.58 (0.14), residues: 1151 sheet: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE C 227 TYR 0.020 0.002 TYR D 179 ARG 0.004 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.15421 ( 871) hydrogen bonds : angle 6.51731 ( 2571) covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74040 (22134) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 799 time to evaluate : 1.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8448 (t0) cc_final: 0.8233 (t70) REVERT: A 68 PHE cc_start: 0.8635 (p90) cc_final: 0.8321 (p90) REVERT: A 106 LEU cc_start: 0.9003 (tp) cc_final: 0.8678 (tp) REVERT: A 120 ASP cc_start: 0.7014 (m-30) cc_final: 0.6695 (m-30) REVERT: A 122 ILE cc_start: 0.9216 (mt) cc_final: 0.8938 (mt) REVERT: A 134 THR cc_start: 0.7929 (t) cc_final: 0.7572 (t) REVERT: A 186 ILE cc_start: 0.9310 (mt) cc_final: 0.9058 (mt) REVERT: A 200 SER cc_start: 0.9120 (t) cc_final: 0.8885 (p) REVERT: A 202 ASN cc_start: 0.9124 (t0) cc_final: 0.8608 (t0) REVERT: A 204 SER cc_start: 0.8970 (m) cc_final: 0.8633 (p) REVERT: A 227 MET cc_start: 0.8293 (mtp) cc_final: 0.7907 (mtp) REVERT: A 322 MET cc_start: 0.8217 (mmp) cc_final: 0.7943 (mmp) REVERT: A 362 ASP cc_start: 0.6331 (m-30) cc_final: 0.6082 (m-30) REVERT: A 367 VAL cc_start: 0.9095 (m) cc_final: 0.8753 (p) REVERT: A 417 LEU cc_start: 0.8510 (tt) cc_final: 0.7869 (tt) REVERT: A 425 ILE cc_start: 0.8978 (mt) cc_final: 0.8496 (mt) REVERT: A 436 LEU cc_start: 0.9194 (mt) cc_final: 0.8982 (mm) REVERT: A 447 ASN cc_start: 0.7972 (m-40) cc_final: 0.7770 (m-40) REVERT: A 458 MET cc_start: 0.8831 (mmm) cc_final: 0.8314 (mtm) REVERT: A 576 LEU cc_start: 0.8899 (mt) cc_final: 0.8676 (mt) REVERT: A 606 TYR cc_start: 0.6769 (m-80) cc_final: 0.6553 (m-80) REVERT: A 618 LEU cc_start: 0.9218 (tp) cc_final: 0.8982 (tp) REVERT: A 630 TYR cc_start: 0.7539 (m-80) cc_final: 0.6529 (m-80) REVERT: A 634 MET cc_start: 0.8587 (mmp) cc_final: 0.8324 (mmm) REVERT: A 640 MET cc_start: 0.7738 (tpp) cc_final: 0.7280 (tpp) REVERT: A 670 ILE cc_start: 0.9244 (mt) cc_final: 0.9021 (mt) REVERT: B 51 LEU cc_start: 0.8434 (tp) cc_final: 0.8203 (tp) REVERT: B 116 GLU cc_start: 0.7600 (mt-10) cc_final: 0.7299 (mt-10) REVERT: B 156 PHE cc_start: 0.8455 (t80) cc_final: 0.8206 (t80) REVERT: B 167 LEU cc_start: 0.8207 (mt) cc_final: 0.7977 (mt) REVERT: B 190 MET cc_start: 0.8381 (mtm) cc_final: 0.8117 (mtm) REVERT: B 322 MET cc_start: 0.8152 (mmm) cc_final: 0.7775 (tpp) REVERT: B 362 ASP cc_start: 0.6823 (m-30) cc_final: 0.6128 (m-30) REVERT: B 373 ILE cc_start: 0.8899 (mt) cc_final: 0.8608 (mt) REVERT: B 466 MET cc_start: 0.8431 (ptp) cc_final: 0.8108 (ptm) REVERT: B 467 ASN cc_start: 0.8888 (t0) cc_final: 0.8472 (t0) REVERT: B 471 TYR cc_start: 0.8362 (t80) cc_final: 0.8154 (t80) REVERT: B 500 ILE cc_start: 0.9270 (mt) cc_final: 0.9049 (mt) REVERT: B 522 TYR cc_start: 0.8492 (m-80) cc_final: 0.8089 (m-10) REVERT: B 550 MET cc_start: 0.8179 (mtm) cc_final: 0.7351 (mtp) REVERT: B 570 MET cc_start: 0.7240 (mtm) cc_final: 0.6749 (mtm) REVERT: B 576 LEU cc_start: 0.9116 (mt) cc_final: 0.8821 (mt) REVERT: B 590 SER cc_start: 0.8860 (p) cc_final: 0.8200 (t) REVERT: B 591 THR cc_start: 0.9291 (p) cc_final: 0.8607 (m) REVERT: B 597 ILE cc_start: 0.9135 (pt) cc_final: 0.8771 (pt) REVERT: C 31 LEU cc_start: 0.5709 (mt) cc_final: 0.5448 (mt) REVERT: C 155 LYS cc_start: 0.7170 (mttt) cc_final: 0.6918 (mttm) REVERT: D 136 GLN cc_start: 0.1070 (mm-40) cc_final: 0.0606 (tm-30) REVERT: D 137 MET cc_start: -0.0170 (mtp) cc_final: -0.0738 (mtp) REVERT: D 256 VAL cc_start: 0.5301 (t) cc_final: 0.4495 (t) outliers start: 23 outliers final: 7 residues processed: 810 average time/residue: 0.2981 time to fit residues: 348.0870 Evaluate side-chains 554 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 547 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 3.9990 chunk 145 optimal weight: 7.9990 chunk 80 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 150 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 174 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 242 GLN A 320 ASN A 370 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 410 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN B 668 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 80 HIS ** D 91 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 = 0.3987 r_free = 0.3987 target = 0.163350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.110810 restraints weight = 33115.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.114479 restraints weight = 16126.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.116852 restraints weight = 9653.950| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16386 Z= 0.217 Angle : 0.611 7.212 22134 Z= 0.329 Chirality : 0.043 0.281 2360 Planarity : 0.004 0.036 2818 Dihedral : 11.377 178.464 2242 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.12 % Allowed : 3.21 % Favored : 96.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.19), residues: 1932 helix: 1.45 (0.15), residues: 1128 sheet: -0.05 (0.41), residues: 146 loop : 0.53 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 623 HIS 0.009 0.001 HIS A 438 PHE 0.030 0.002 PHE C 227 TYR 0.026 0.002 TYR D 130 ARG 0.006 0.001 ARG B 90 Details of bonding type rmsd hydrogen bonds : bond 0.04648 ( 871) hydrogen bonds : angle 5.01974 ( 2571) covalent geometry : bond 0.00455 (16386) covalent geometry : angle 0.61077 (22134) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 620 time to evaluate : 1.664 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 122 ILE cc_start: 0.9340 (mt) cc_final: 0.9069 (mt) REVERT: A 150 GLN cc_start: 0.9036 (tm-30) cc_final: 0.8796 (tm-30) REVERT: A 188 ILE cc_start: 0.9607 (mt) cc_final: 0.9361 (mm) REVERT: A 202 ASN cc_start: 0.9292 (t0) cc_final: 0.9029 (t0) REVERT: A 204 SER cc_start: 0.9190 (m) cc_final: 0.8604 (t) REVERT: A 232 ASN cc_start: 0.8454 (m-40) cc_final: 0.8231 (m110) REVERT: A 286 ASP cc_start: 0.8091 (m-30) cc_final: 0.7740 (m-30) REVERT: A 308 LYS cc_start: 0.9580 (mtmt) cc_final: 0.9359 (mtmm) REVERT: A 362 ASP cc_start: 0.7267 (m-30) cc_final: 0.7062 (m-30) REVERT: A 367 VAL cc_start: 0.9703 (m) cc_final: 0.9476 (p) REVERT: A 447 ASN cc_start: 0.8408 (m-40) cc_final: 0.7312 (m-40) REVERT: A 458 MET cc_start: 0.9332 (mmm) cc_final: 0.8470 (mmm) REVERT: A 485 ARG cc_start: 0.8344 (mtm-85) cc_final: 0.7442 (mtm-85) REVERT: A 494 MET cc_start: 0.8714 (mtp) cc_final: 0.8369 (mtp) REVERT: A 576 LEU cc_start: 0.9035 (mt) cc_final: 0.8788 (mt) REVERT: A 583 SER cc_start: 0.9141 (m) cc_final: 0.8740 (t) REVERT: A 586 TYR cc_start: 0.8467 (m-80) cc_final: 0.8197 (m-10) REVERT: A 590 SER cc_start: 0.9259 (t) cc_final: 0.9005 (t) REVERT: A 602 GLU cc_start: 0.7267 (pt0) cc_final: 0.6579 (pt0) REVERT: A 606 TYR cc_start: 0.8026 (m-80) cc_final: 0.7736 (m-10) REVERT: A 630 TYR cc_start: 0.8576 (m-80) cc_final: 0.8368 (m-80) REVERT: A 640 MET cc_start: 0.9048 (tpp) cc_final: 0.8650 (tpp) REVERT: A 662 MET cc_start: 0.8431 (pmm) cc_final: 0.8182 (pmm) REVERT: A 667 LEU cc_start: 0.9031 (tt) cc_final: 0.8324 (tt) REVERT: A 668 ASN cc_start: 0.8900 (m110) cc_final: 0.8490 (m110) REVERT: B 51 LEU cc_start: 0.9103 (tp) cc_final: 0.8870 (tp) REVERT: B 108 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8496 (p) REVERT: B 147 GLN cc_start: 0.8766 (mt0) cc_final: 0.8486 (mt0) REVERT: B 156 PHE cc_start: 0.9205 (t80) cc_final: 0.8931 (t80) REVERT: B 190 MET cc_start: 0.9267 (mtm) cc_final: 0.9001 (mtm) REVERT: B 253 ILE cc_start: 0.9462 (tt) cc_final: 0.9233 (tt) REVERT: B 257 ASP cc_start: 0.8908 (m-30) cc_final: 0.8673 (m-30) REVERT: B 288 PHE cc_start: 0.9428 (t80) cc_final: 0.9180 (t80) REVERT: B 291 LEU cc_start: 0.9557 (mt) cc_final: 0.9355 (mt) REVERT: B 318 ASP cc_start: 0.8824 (t0) cc_final: 0.8547 (p0) REVERT: B 333 LYS cc_start: 0.8828 (tptp) cc_final: 0.7836 (tttp) REVERT: B 358 ILE cc_start: 0.9468 (mm) cc_final: 0.9182 (mm) REVERT: B 362 ASP cc_start: 0.8130 (m-30) cc_final: 0.7407 (m-30) REVERT: B 393 SER cc_start: 0.9543 (m) cc_final: 0.9259 (p) REVERT: B 396 ASP cc_start: 0.8082 (m-30) cc_final: 0.7853 (m-30) REVERT: B 471 TYR cc_start: 0.9002 (t80) cc_final: 0.8591 (t80) REVERT: B 493 MET cc_start: 0.9318 (tmm) cc_final: 0.9002 (tmm) REVERT: B 512 GLU cc_start: 0.8697 (pt0) cc_final: 0.8416 (pt0) REVERT: B 550 MET cc_start: 0.8410 (mtm) cc_final: 0.8153 (mtp) REVERT: B 561 LEU cc_start: 0.9391 (tp) cc_final: 0.9120 (tp) REVERT: B 597 ILE cc_start: 0.9345 (pt) cc_final: 0.9142 (pt) REVERT: B 610 LYS cc_start: 0.8808 (ptmt) cc_final: 0.8603 (ptpt) REVERT: B 615 MET cc_start: 0.9098 (mmp) cc_final: 0.8858 (mmm) REVERT: B 627 LYS cc_start: 0.9150 (tttt) cc_final: 0.8788 (tttp) REVERT: B 662 MET cc_start: 0.8291 (ptp) cc_final: 0.7963 (ptp) REVERT: C 74 MET cc_start: 0.7263 (mtt) cc_final: 0.6470 (mtt) REVERT: C 154 PHE cc_start: 0.8619 (t80) cc_final: 0.8278 (t80) REVERT: C 239 GLU cc_start: 0.9024 (tp30) cc_final: 0.8564 (tp30) REVERT: D 95 MET cc_start: 0.7166 (ttp) cc_final: 0.6836 (ttp) REVERT: D 208 LEU cc_start: 0.9295 (mm) cc_final: 0.9063 (mm) REVERT: D 242 TYR cc_start: 0.7826 (t80) cc_final: 0.7102 (t80) outliers start: 2 outliers final: 0 residues processed: 621 average time/residue: 0.2767 time to fit residues: 255.4535 Evaluate side-chains 479 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 478 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 175 optimal weight: 20.0000 chunk 34 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 191 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 171 optimal weight: 0.9990 chunk 189 optimal weight: 9.9990 chunk 141 optimal weight: 7.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS D 24 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.164069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.113528 restraints weight = 33512.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.117201 restraints weight = 16191.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.119396 restraints weight = 9607.612| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3269 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.4424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 16386 Z= 0.197 Angle : 0.585 8.605 22134 Z= 0.308 Chirality : 0.042 0.195 2360 Planarity : 0.003 0.039 2818 Dihedral : 11.175 178.241 2242 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.12 % Allowed : 2.39 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.19), residues: 1932 helix: 1.59 (0.15), residues: 1128 sheet: -0.20 (0.39), residues: 146 loop : 0.55 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 623 HIS 0.005 0.001 HIS A 438 PHE 0.032 0.002 PHE C 109 TYR 0.021 0.002 TYR D 130 ARG 0.006 0.001 ARG A 669 Details of bonding type rmsd hydrogen bonds : bond 0.04173 ( 871) hydrogen bonds : angle 4.81676 ( 2571) covalent geometry : bond 0.00435 (16386) covalent geometry : angle 0.58462 (22134) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 584 time to evaluate : 1.802 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: A 55 LEU cc_start: 0.9653 (mt) cc_final: 0.9263 (pp) REVERT: A 158 ASN cc_start: 0.9061 (m110) cc_final: 0.8837 (m110) REVERT: A 204 SER cc_start: 0.9246 (m) cc_final: 0.8697 (t) REVERT: A 232 ASN cc_start: 0.8440 (m-40) cc_final: 0.8160 (m110) REVERT: A 286 ASP cc_start: 0.8261 (m-30) cc_final: 0.7636 (m-30) REVERT: A 308 LYS cc_start: 0.9584 (mtmt) cc_final: 0.9343 (mtmm) REVERT: A 362 ASP cc_start: 0.7338 (m-30) cc_final: 0.7082 (m-30) REVERT: A 406 ASP cc_start: 0.8468 (m-30) cc_final: 0.8250 (m-30) REVERT: A 417 LEU cc_start: 0.9417 (tt) cc_final: 0.8484 (tt) REVERT: A 443 THR cc_start: 0.9135 (m) cc_final: 0.8915 (t) REVERT: A 447 ASN cc_start: 0.8165 (m-40) cc_final: 0.7717 (m-40) REVERT: A 458 MET cc_start: 0.9297 (mmm) cc_final: 0.8356 (mtm) REVERT: A 494 MET cc_start: 0.8766 (mtp) cc_final: 0.8532 (mtp) REVERT: A 557 ASP cc_start: 0.8861 (m-30) cc_final: 0.8660 (m-30) REVERT: A 576 LEU cc_start: 0.9104 (mt) cc_final: 0.8863 (mt) REVERT: A 583 SER cc_start: 0.9123 (m) cc_final: 0.8820 (t) REVERT: A 586 TYR cc_start: 0.8503 (m-80) cc_final: 0.8170 (m-10) REVERT: A 602 GLU cc_start: 0.7054 (pt0) cc_final: 0.6146 (pt0) REVERT: A 604 ARG cc_start: 0.8545 (tpp-160) cc_final: 0.8286 (tpp-160) REVERT: A 634 MET cc_start: 0.9036 (mmp) cc_final: 0.8793 (mmt) REVERT: A 645 GLN cc_start: 0.8899 (tp40) cc_final: 0.8636 (tp-100) REVERT: A 667 LEU cc_start: 0.9180 (tt) cc_final: 0.8583 (tt) REVERT: B 51 LEU cc_start: 0.9123 (tp) cc_final: 0.8732 (tp) REVERT: B 120 ASP cc_start: 0.8664 (m-30) cc_final: 0.8435 (m-30) REVERT: B 235 ARG cc_start: 0.8634 (ttm-80) cc_final: 0.8331 (ttm110) REVERT: B 276 LYS cc_start: 0.8836 (ptmt) cc_final: 0.8463 (ptpp) REVERT: B 288 PHE cc_start: 0.9501 (t80) cc_final: 0.9205 (t80) REVERT: B 291 LEU cc_start: 0.9532 (mt) cc_final: 0.9320 (mt) REVERT: B 333 LYS cc_start: 0.8842 (tptp) cc_final: 0.7826 (tptp) REVERT: B 348 MET cc_start: 0.7992 (tpp) cc_final: 0.7737 (tpp) REVERT: B 362 ASP cc_start: 0.8173 (m-30) cc_final: 0.7336 (m-30) REVERT: B 393 SER cc_start: 0.9489 (m) cc_final: 0.9222 (p) REVERT: B 471 TYR cc_start: 0.9111 (t80) cc_final: 0.8808 (t80) REVERT: B 493 MET cc_start: 0.9355 (tmm) cc_final: 0.9059 (tmm) REVERT: B 550 MET cc_start: 0.8416 (mtm) cc_final: 0.8027 (mtp) REVERT: B 561 LEU cc_start: 0.9487 (tp) cc_final: 0.9270 (tp) REVERT: B 615 MET cc_start: 0.9165 (mmp) cc_final: 0.8956 (mmm) REVERT: B 627 LYS cc_start: 0.9324 (tttt) cc_final: 0.8789 (tttp) REVERT: B 628 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8071 (mm-30) REVERT: B 640 MET cc_start: 0.8956 (tpp) cc_final: 0.8277 (tpp) REVERT: B 662 MET cc_start: 0.8581 (ptp) cc_final: 0.8238 (ptp) REVERT: C 74 MET cc_start: 0.7245 (mtt) cc_final: 0.6553 (mtt) REVERT: C 239 GLU cc_start: 0.8998 (tp30) cc_final: 0.8568 (tp30) REVERT: D 117 THR cc_start: 0.8562 (p) cc_final: 0.8251 (p) REVERT: D 173 TYR cc_start: 0.7258 (t80) cc_final: 0.6757 (t80) REVERT: D 242 TYR cc_start: 0.7721 (t80) cc_final: 0.7436 (t80) outliers start: 2 outliers final: 0 residues processed: 584 average time/residue: 0.2860 time to fit residues: 247.5714 Evaluate side-chains 472 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 472 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 180 optimal weight: 8.9990 chunk 99 optimal weight: 0.8980 chunk 1 optimal weight: 0.0670 chunk 39 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 71 optimal weight: 6.9990 chunk 74 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 overall best weight: 2.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 501 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.161069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.111417 restraints weight = 33750.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.114935 restraints weight = 16458.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.117085 restraints weight = 9781.369| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.4944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 16386 Z= 0.246 Angle : 0.620 7.890 22134 Z= 0.327 Chirality : 0.043 0.187 2360 Planarity : 0.003 0.033 2818 Dihedral : 11.095 176.392 2242 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.12 % Allowed : 2.91 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.19), residues: 1932 helix: 1.46 (0.15), residues: 1138 sheet: 0.26 (0.44), residues: 110 loop : 0.27 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 623 HIS 0.005 0.001 HIS A 438 PHE 0.033 0.002 PHE C 109 TYR 0.018 0.002 TYR D 130 ARG 0.006 0.001 ARG B 350 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 871) hydrogen bonds : angle 4.82350 ( 2571) covalent geometry : bond 0.00537 (16386) covalent geometry : angle 0.62006 (22134) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 538 time to evaluate : 1.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 GLU cc_start: 0.8299 (mp0) cc_final: 0.7935 (mp0) REVERT: A 144 MET cc_start: 0.8860 (mtm) cc_final: 0.8644 (mtm) REVERT: A 172 LEU cc_start: 0.9078 (mp) cc_final: 0.8733 (mp) REVERT: A 174 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7726 (mt-10) REVERT: A 188 ILE cc_start: 0.9504 (mm) cc_final: 0.9156 (mm) REVERT: A 204 SER cc_start: 0.9266 (m) cc_final: 0.8749 (t) REVERT: A 232 ASN cc_start: 0.8651 (m-40) cc_final: 0.8384 (m110) REVERT: A 286 ASP cc_start: 0.8077 (m-30) cc_final: 0.7795 (m-30) REVERT: A 290 GLU cc_start: 0.8690 (mm-30) cc_final: 0.8360 (mm-30) REVERT: A 308 LYS cc_start: 0.9594 (mtmt) cc_final: 0.9347 (mtmm) REVERT: A 362 ASP cc_start: 0.7334 (m-30) cc_final: 0.7011 (m-30) REVERT: A 383 SER cc_start: 0.8784 (p) cc_final: 0.8473 (t) REVERT: A 406 ASP cc_start: 0.8583 (m-30) cc_final: 0.8159 (m-30) REVERT: A 443 THR cc_start: 0.9210 (m) cc_final: 0.9009 (t) REVERT: A 447 ASN cc_start: 0.8041 (m-40) cc_final: 0.7463 (m-40) REVERT: A 456 LYS cc_start: 0.8892 (ptpp) cc_final: 0.8491 (ptpp) REVERT: A 458 MET cc_start: 0.9289 (mmm) cc_final: 0.8432 (mtm) REVERT: A 494 MET cc_start: 0.8771 (mtp) cc_final: 0.8421 (mtp) REVERT: A 557 ASP cc_start: 0.8809 (m-30) cc_final: 0.8594 (m-30) REVERT: A 576 LEU cc_start: 0.9112 (mt) cc_final: 0.8848 (mt) REVERT: A 583 SER cc_start: 0.9157 (m) cc_final: 0.8810 (t) REVERT: A 602 GLU cc_start: 0.7271 (pt0) cc_final: 0.6972 (pt0) REVERT: A 604 ARG cc_start: 0.8432 (tpp-160) cc_final: 0.7728 (ttm-80) REVERT: A 606 TYR cc_start: 0.7783 (m-10) cc_final: 0.7541 (m-10) REVERT: A 645 GLN cc_start: 0.8906 (tp40) cc_final: 0.8597 (tp-100) REVERT: A 667 LEU cc_start: 0.9252 (tt) cc_final: 0.8623 (tt) REVERT: B 51 LEU cc_start: 0.9138 (tp) cc_final: 0.8822 (tp) REVERT: B 102 ASN cc_start: 0.9278 (m110) cc_final: 0.8954 (m110) REVERT: B 120 ASP cc_start: 0.8718 (m-30) cc_final: 0.8493 (m-30) REVERT: B 150 GLN cc_start: 0.9203 (tp40) cc_final: 0.8923 (tp-100) REVERT: B 253 ILE cc_start: 0.9415 (tt) cc_final: 0.9208 (tt) REVERT: B 276 LYS cc_start: 0.8817 (ptmt) cc_final: 0.8440 (ptpp) REVERT: B 286 ASP cc_start: 0.8438 (m-30) cc_final: 0.8196 (m-30) REVERT: B 288 PHE cc_start: 0.9499 (t80) cc_final: 0.9210 (t80) REVERT: B 386 LEU cc_start: 0.9495 (mt) cc_final: 0.9252 (mp) REVERT: B 393 SER cc_start: 0.9509 (m) cc_final: 0.9191 (p) REVERT: B 458 MET cc_start: 0.9090 (mmp) cc_final: 0.8829 (mmm) REVERT: B 467 ASN cc_start: 0.9379 (t0) cc_final: 0.9002 (t0) REVERT: B 493 MET cc_start: 0.9343 (tmm) cc_final: 0.9049 (tmm) REVERT: B 601 ILE cc_start: 0.9211 (mm) cc_final: 0.8722 (mm) REVERT: B 604 ARG cc_start: 0.8745 (tpp80) cc_final: 0.8127 (tpp80) REVERT: B 615 MET cc_start: 0.9125 (mmp) cc_final: 0.8895 (mmm) REVERT: B 627 LYS cc_start: 0.9352 (tttt) cc_final: 0.8970 (tttp) REVERT: B 650 GLN cc_start: 0.7911 (mt0) cc_final: 0.7625 (mt0) REVERT: B 662 MET cc_start: 0.8564 (ptp) cc_final: 0.8273 (ptp) REVERT: C 74 MET cc_start: 0.7544 (mtt) cc_final: 0.7181 (mtt) REVERT: C 154 PHE cc_start: 0.8556 (t80) cc_final: 0.7751 (t80) REVERT: C 239 GLU cc_start: 0.9015 (tp30) cc_final: 0.8632 (tp30) REVERT: D 95 MET cc_start: 0.7069 (ttp) cc_final: 0.6699 (ttt) REVERT: D 173 TYR cc_start: 0.7102 (t80) cc_final: 0.6766 (t80) outliers start: 2 outliers final: 0 residues processed: 539 average time/residue: 0.2742 time to fit residues: 221.0634 Evaluate side-chains 446 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 446 time to evaluate : 1.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 67 optimal weight: 0.0870 chunk 41 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 175 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.167663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.118773 restraints weight = 33754.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.122414 restraints weight = 16032.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.124722 restraints weight = 9387.369| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16386 Z= 0.122 Angle : 0.562 8.041 22134 Z= 0.296 Chirality : 0.041 0.232 2360 Planarity : 0.003 0.034 2818 Dihedral : 10.695 174.055 2242 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.19), residues: 1932 helix: 1.51 (0.15), residues: 1126 sheet: -0.51 (0.39), residues: 146 loop : 0.36 (0.24), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 124 HIS 0.004 0.001 HIS A 438 PHE 0.039 0.002 PHE C 109 TYR 0.023 0.001 TYR A 683 ARG 0.006 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 871) hydrogen bonds : angle 4.69997 ( 2571) covalent geometry : bond 0.00266 (16386) covalent geometry : angle 0.56152 (22134) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 571 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7867 (mp0) REVERT: A 128 PHE cc_start: 0.8787 (t80) cc_final: 0.8583 (t80) REVERT: A 144 MET cc_start: 0.8703 (mtm) cc_final: 0.8470 (mtm) REVERT: A 158 ASN cc_start: 0.9032 (m110) cc_final: 0.8804 (m-40) REVERT: A 168 VAL cc_start: 0.8693 (t) cc_final: 0.8450 (m) REVERT: A 174 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7568 (mt-10) REVERT: A 188 ILE cc_start: 0.9458 (mm) cc_final: 0.9153 (mm) REVERT: A 204 SER cc_start: 0.9229 (m) cc_final: 0.8579 (t) REVERT: A 214 LYS cc_start: 0.7892 (tppt) cc_final: 0.7447 (mmtp) REVERT: A 257 ASP cc_start: 0.8855 (m-30) cc_final: 0.8549 (m-30) REVERT: A 286 ASP cc_start: 0.8053 (m-30) cc_final: 0.7825 (m-30) REVERT: A 301 PHE cc_start: 0.9087 (m-80) cc_final: 0.8861 (m-10) REVERT: A 308 LYS cc_start: 0.9575 (mtmt) cc_final: 0.9361 (mtmm) REVERT: A 406 ASP cc_start: 0.8595 (m-30) cc_final: 0.8339 (m-30) REVERT: A 417 LEU cc_start: 0.9318 (tt) cc_final: 0.8484 (tt) REVERT: A 456 LYS cc_start: 0.8878 (ptpp) cc_final: 0.8421 (ptpp) REVERT: A 458 MET cc_start: 0.9236 (mmm) cc_final: 0.8360 (mtm) REVERT: A 494 MET cc_start: 0.8666 (mtp) cc_final: 0.8465 (mtp) REVERT: A 576 LEU cc_start: 0.9137 (mt) cc_final: 0.8893 (mt) REVERT: A 602 GLU cc_start: 0.7113 (pt0) cc_final: 0.6478 (pt0) REVERT: A 604 ARG cc_start: 0.8308 (tpp-160) cc_final: 0.7571 (ttm-80) REVERT: A 615 MET cc_start: 0.9215 (mmt) cc_final: 0.8947 (mmp) REVERT: A 632 MET cc_start: 0.8827 (mtp) cc_final: 0.8481 (mtt) REVERT: A 640 MET cc_start: 0.9052 (tpp) cc_final: 0.8617 (tpp) REVERT: A 645 GLN cc_start: 0.8741 (tp40) cc_final: 0.8505 (tp-100) REVERT: A 667 LEU cc_start: 0.9132 (tt) cc_final: 0.8546 (tt) REVERT: A 686 ARG cc_start: 0.8401 (mtp-110) cc_final: 0.8178 (mtp-110) REVERT: B 16 ILE cc_start: 0.9368 (mm) cc_final: 0.9044 (mm) REVERT: B 51 LEU cc_start: 0.8952 (tp) cc_final: 0.8587 (tp) REVERT: B 102 ASN cc_start: 0.9279 (m110) cc_final: 0.8958 (m110) REVERT: B 276 LYS cc_start: 0.8654 (ptmt) cc_final: 0.8343 (ptpp) REVERT: B 286 ASP cc_start: 0.8440 (m-30) cc_final: 0.8218 (m-30) REVERT: B 288 PHE cc_start: 0.9438 (t80) cc_final: 0.9127 (t80) REVERT: B 291 LEU cc_start: 0.9522 (mt) cc_final: 0.9314 (mt) REVERT: B 333 LYS cc_start: 0.9049 (tttm) cc_final: 0.8490 (tttp) REVERT: B 386 LEU cc_start: 0.9445 (mt) cc_final: 0.9241 (mt) REVERT: B 393 SER cc_start: 0.9526 (m) cc_final: 0.9136 (p) REVERT: B 399 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8344 (mm-30) REVERT: B 427 LYS cc_start: 0.9448 (pttt) cc_final: 0.9239 (pttt) REVERT: B 467 ASN cc_start: 0.9224 (t0) cc_final: 0.8746 (t0) REVERT: B 493 MET cc_start: 0.9237 (tmm) cc_final: 0.8989 (tmm) REVERT: B 602 GLU cc_start: 0.7177 (pt0) cc_final: 0.6922 (pt0) REVERT: B 604 ARG cc_start: 0.8583 (tpp80) cc_final: 0.7967 (tpp80) REVERT: B 615 MET cc_start: 0.9044 (mmp) cc_final: 0.8775 (mmm) REVERT: B 627 LYS cc_start: 0.9216 (tttt) cc_final: 0.8873 (tttp) REVERT: B 640 MET cc_start: 0.8970 (tpp) cc_final: 0.8421 (tpp) REVERT: B 654 PHE cc_start: 0.9355 (t80) cc_final: 0.9141 (t80) REVERT: B 662 MET cc_start: 0.8490 (ptp) cc_final: 0.8093 (ptp) REVERT: C 74 MET cc_start: 0.8016 (mtt) cc_final: 0.7806 (mtt) REVERT: C 89 VAL cc_start: 0.4615 (m) cc_final: 0.4205 (m) REVERT: C 154 PHE cc_start: 0.8529 (t80) cc_final: 0.8029 (t80) REVERT: C 239 GLU cc_start: 0.8949 (tp30) cc_final: 0.8613 (tp30) REVERT: D 95 MET cc_start: 0.6939 (ttp) cc_final: 0.6525 (ttt) REVERT: D 173 TYR cc_start: 0.7230 (t80) cc_final: 0.6975 (t80) outliers start: 0 outliers final: 0 residues processed: 571 average time/residue: 0.2751 time to fit residues: 234.3362 Evaluate side-chains 444 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 444 time to evaluate : 1.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 31 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 69 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 115 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 169 optimal weight: 0.0270 chunk 113 optimal weight: 6.9990 chunk 177 optimal weight: 9.9990 overall best weight: 3.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.160570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.111644 restraints weight = 34022.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.115094 restraints weight = 16631.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.117238 restraints weight = 9880.343| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.5478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 16386 Z= 0.275 Angle : 0.647 10.134 22134 Z= 0.343 Chirality : 0.044 0.195 2360 Planarity : 0.004 0.048 2818 Dihedral : 10.913 173.053 2242 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.19), residues: 1932 helix: 1.51 (0.15), residues: 1104 sheet: -0.69 (0.39), residues: 146 loop : 0.30 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP D 124 HIS 0.006 0.001 HIS A 438 PHE 0.038 0.002 PHE C 109 TYR 0.024 0.002 TYR B 118 ARG 0.007 0.001 ARG B 90 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 871) hydrogen bonds : angle 4.89491 ( 2571) covalent geometry : bond 0.00598 (16386) covalent geometry : angle 0.64730 (22134) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 486 time to evaluate : 1.926 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: A 65 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8010 (mp0) REVERT: A 172 LEU cc_start: 0.9077 (mp) cc_final: 0.8716 (mp) REVERT: A 174 GLU cc_start: 0.7841 (mt-10) cc_final: 0.7550 (mt-10) REVERT: A 204 SER cc_start: 0.9279 (m) cc_final: 0.8784 (t) REVERT: A 308 LYS cc_start: 0.9597 (mtmt) cc_final: 0.9365 (mtmm) REVERT: A 362 ASP cc_start: 0.7529 (m-30) cc_final: 0.7144 (m-30) REVERT: A 406 ASP cc_start: 0.8616 (m-30) cc_final: 0.8272 (m-30) REVERT: A 447 ASN cc_start: 0.8234 (m-40) cc_final: 0.7921 (m-40) REVERT: A 458 MET cc_start: 0.9213 (mmm) cc_final: 0.8472 (mtm) REVERT: A 494 MET cc_start: 0.8660 (mtp) cc_final: 0.8363 (mtp) REVERT: A 576 LEU cc_start: 0.9110 (mt) cc_final: 0.8824 (mt) REVERT: A 584 ILE cc_start: 0.8979 (pt) cc_final: 0.8754 (pt) REVERT: A 645 GLN cc_start: 0.8887 (tp40) cc_final: 0.8549 (tp-100) REVERT: A 667 LEU cc_start: 0.9287 (tt) cc_final: 0.8679 (tt) REVERT: B 51 LEU cc_start: 0.9126 (tp) cc_final: 0.8839 (tp) REVERT: B 102 ASN cc_start: 0.9212 (m110) cc_final: 0.8896 (m110) REVERT: B 120 ASP cc_start: 0.8784 (m-30) cc_final: 0.8507 (m-30) REVERT: B 125 VAL cc_start: 0.9293 (t) cc_final: 0.9052 (p) REVERT: B 190 MET cc_start: 0.9196 (mtm) cc_final: 0.8785 (mtm) REVERT: B 213 ILE cc_start: 0.8702 (mp) cc_final: 0.8464 (mt) REVERT: B 258 ILE cc_start: 0.9512 (tp) cc_final: 0.9219 (tp) REVERT: B 276 LYS cc_start: 0.8881 (ptmt) cc_final: 0.8536 (ptpp) REVERT: B 322 MET cc_start: 0.8815 (mmt) cc_final: 0.8108 (mpp) REVERT: B 362 ASP cc_start: 0.8057 (m-30) cc_final: 0.7147 (m-30) REVERT: B 392 SER cc_start: 0.9285 (m) cc_final: 0.9051 (m) REVERT: B 393 SER cc_start: 0.9485 (m) cc_final: 0.9259 (p) REVERT: B 427 LYS cc_start: 0.9447 (pttt) cc_final: 0.9214 (pttt) REVERT: B 467 ASN cc_start: 0.9334 (t0) cc_final: 0.8866 (t0) REVERT: B 493 MET cc_start: 0.9342 (tmm) cc_final: 0.9015 (tmm) REVERT: B 604 ARG cc_start: 0.8605 (tpp80) cc_final: 0.8115 (tpp80) REVERT: B 615 MET cc_start: 0.9129 (mmp) cc_final: 0.8903 (mmm) REVERT: B 627 LYS cc_start: 0.9257 (tttt) cc_final: 0.8955 (tttp) REVERT: B 640 MET cc_start: 0.8926 (tpp) cc_final: 0.8189 (tpp) REVERT: B 662 MET cc_start: 0.8572 (ptp) cc_final: 0.8340 (ptp) REVERT: C 89 VAL cc_start: 0.5224 (m) cc_final: 0.4867 (m) REVERT: C 109 PHE cc_start: 0.6392 (m-80) cc_final: 0.5847 (m-80) REVERT: C 157 MET cc_start: 0.8814 (mpp) cc_final: 0.8105 (ptp) REVERT: D 56 MET cc_start: -0.0816 (mmm) cc_final: -0.1041 (mmm) REVERT: D 95 MET cc_start: 0.7874 (ttp) cc_final: 0.7392 (ttt) REVERT: D 108 ILE cc_start: 0.8259 (tp) cc_final: 0.7986 (pt) outliers start: 0 outliers final: 0 residues processed: 486 average time/residue: 0.2664 time to fit residues: 193.8622 Evaluate side-chains 404 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 404 time to evaluate : 1.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 39 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 146 optimal weight: 20.0000 chunk 184 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.159925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.110734 restraints weight = 33517.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.114116 restraints weight = 16257.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.116259 restraints weight = 9700.526| |-----------------------------------------------------------------------------| r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3279 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3279 r_free = 0.3279 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3279 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.5667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16386 Z= 0.163 Angle : 0.591 8.354 22134 Z= 0.313 Chirality : 0.042 0.161 2360 Planarity : 0.003 0.038 2818 Dihedral : 10.645 171.503 2242 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 1.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.19), residues: 1932 helix: 1.54 (0.15), residues: 1107 sheet: -0.38 (0.43), residues: 126 loop : 0.21 (0.23), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 124 HIS 0.004 0.001 HIS A 438 PHE 0.035 0.002 PHE C 109 TYR 0.022 0.002 TYR A 606 ARG 0.007 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.03935 ( 871) hydrogen bonds : angle 4.80262 ( 2571) covalent geometry : bond 0.00360 (16386) covalent geometry : angle 0.59073 (22134) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 529 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8481 (mm-30) cc_final: 0.7962 (mp0) REVERT: A 109 ASN cc_start: 0.8943 (m110) cc_final: 0.8631 (m-40) REVERT: A 174 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7567 (mt-10) REVERT: A 228 LYS cc_start: 0.9054 (mmmt) cc_final: 0.8692 (mmtt) REVERT: A 308 LYS cc_start: 0.9573 (mtmt) cc_final: 0.9336 (mtmm) REVERT: A 319 MET cc_start: 0.9283 (tpp) cc_final: 0.8824 (tpp) REVERT: A 344 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8321 (mt-10) REVERT: A 362 ASP cc_start: 0.7225 (m-30) cc_final: 0.6830 (m-30) REVERT: A 406 ASP cc_start: 0.8622 (m-30) cc_final: 0.8228 (m-30) REVERT: A 456 LYS cc_start: 0.8853 (ptpp) cc_final: 0.8510 (ptpp) REVERT: A 458 MET cc_start: 0.9199 (mmm) cc_final: 0.8508 (mtm) REVERT: A 576 LEU cc_start: 0.9082 (mt) cc_final: 0.8834 (mt) REVERT: A 606 TYR cc_start: 0.7885 (m-10) cc_final: 0.7424 (m-10) REVERT: A 615 MET cc_start: 0.9136 (mmt) cc_final: 0.8901 (mmt) REVERT: A 645 GLN cc_start: 0.8778 (tp40) cc_final: 0.8496 (tp-100) REVERT: A 667 LEU cc_start: 0.9223 (tt) cc_final: 0.8625 (tt) REVERT: A 686 ARG cc_start: 0.8523 (mtp-110) cc_final: 0.8084 (mtp-110) REVERT: B 102 ASN cc_start: 0.9265 (m110) cc_final: 0.8939 (m110) REVERT: B 120 ASP cc_start: 0.8718 (m-30) cc_final: 0.8447 (m-30) REVERT: B 147 GLN cc_start: 0.9188 (mt0) cc_final: 0.8872 (mt0) REVERT: B 172 LEU cc_start: 0.9211 (mp) cc_final: 0.8902 (mp) REVERT: B 173 LEU cc_start: 0.9379 (mt) cc_final: 0.9150 (mt) REVERT: B 190 MET cc_start: 0.9175 (mtm) cc_final: 0.8778 (mtm) REVERT: B 191 GLN cc_start: 0.8869 (mm-40) cc_final: 0.8153 (mm-40) REVERT: B 214 LYS cc_start: 0.7942 (mmtm) cc_final: 0.7732 (mmtm) REVERT: B 253 ILE cc_start: 0.9436 (tt) cc_final: 0.9223 (tt) REVERT: B 258 ILE cc_start: 0.9479 (tp) cc_final: 0.9209 (tp) REVERT: B 263 ASP cc_start: 0.8586 (m-30) cc_final: 0.8300 (m-30) REVERT: B 276 LYS cc_start: 0.8839 (ptmt) cc_final: 0.8502 (ptpp) REVERT: B 286 ASP cc_start: 0.8381 (m-30) cc_final: 0.8169 (m-30) REVERT: B 288 PHE cc_start: 0.9454 (t80) cc_final: 0.9131 (t80) REVERT: B 333 LYS cc_start: 0.9167 (tttm) cc_final: 0.8616 (tttp) REVERT: B 392 SER cc_start: 0.9246 (m) cc_final: 0.8994 (m) REVERT: B 427 LYS cc_start: 0.9455 (pttt) cc_final: 0.9234 (pttt) REVERT: B 467 ASN cc_start: 0.9284 (t0) cc_final: 0.8764 (t0) REVERT: B 493 MET cc_start: 0.9258 (tmm) cc_final: 0.8992 (tmm) REVERT: B 604 ARG cc_start: 0.8570 (tpp80) cc_final: 0.7675 (tpp80) REVERT: B 615 MET cc_start: 0.9126 (mmp) cc_final: 0.8880 (mmm) REVERT: B 627 LYS cc_start: 0.9241 (tttt) cc_final: 0.9019 (tttp) REVERT: B 640 MET cc_start: 0.8980 (tpp) cc_final: 0.8255 (tpp) REVERT: B 662 MET cc_start: 0.8564 (ptp) cc_final: 0.8290 (ptp) REVERT: C 89 VAL cc_start: 0.4880 (m) cc_final: 0.4430 (m) REVERT: C 109 PHE cc_start: 0.6462 (m-80) cc_final: 0.5811 (m-80) REVERT: C 157 MET cc_start: 0.8611 (mpp) cc_final: 0.8100 (ptp) REVERT: D 56 MET cc_start: -0.1100 (mmm) cc_final: -0.1372 (mmm) REVERT: D 95 MET cc_start: 0.8134 (ttp) cc_final: 0.7755 (ttt) REVERT: D 96 MET cc_start: 0.7636 (tpt) cc_final: 0.7278 (mmm) REVERT: D 108 ILE cc_start: 0.8238 (tp) cc_final: 0.7989 (pt) outliers start: 0 outliers final: 0 residues processed: 529 average time/residue: 0.2811 time to fit residues: 220.8838 Evaluate side-chains 439 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 439 time to evaluate : 1.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 51 optimal weight: 9.9990 chunk 159 optimal weight: 20.0000 chunk 72 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 180 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.162976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.114150 restraints weight = 33238.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.117623 restraints weight = 16108.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.119846 restraints weight = 9514.760| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.5866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16386 Z= 0.132 Angle : 0.602 13.012 22134 Z= 0.313 Chirality : 0.042 0.163 2360 Planarity : 0.003 0.036 2818 Dihedral : 10.357 171.970 2242 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.19), residues: 1932 helix: 1.48 (0.15), residues: 1115 sheet: 0.44 (0.47), residues: 106 loop : 0.09 (0.23), residues: 711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 124 HIS 0.005 0.001 HIS A 438 PHE 0.029 0.002 PHE C 109 TYR 0.026 0.002 TYR B 612 ARG 0.006 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.03799 ( 871) hydrogen bonds : angle 4.76496 ( 2571) covalent geometry : bond 0.00290 (16386) covalent geometry : angle 0.60169 (22134) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 535 time to evaluate : 2.547 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: A 9 TRP cc_start: 0.9250 (p90) cc_final: 0.8965 (p90) REVERT: A 174 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7555 (mt-10) REVERT: A 214 LYS cc_start: 0.7924 (tppt) cc_final: 0.7570 (mppt) REVERT: A 228 LYS cc_start: 0.8974 (mmmt) cc_final: 0.8625 (mmtt) REVERT: A 236 TYR cc_start: 0.9076 (t80) cc_final: 0.8684 (t80) REVERT: A 308 LYS cc_start: 0.9557 (mtmt) cc_final: 0.9340 (mtmm) REVERT: A 318 ASP cc_start: 0.8813 (t0) cc_final: 0.8576 (t0) REVERT: A 319 MET cc_start: 0.9274 (tpp) cc_final: 0.8787 (tpp) REVERT: A 344 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8348 (mt-10) REVERT: A 357 TYR cc_start: 0.8258 (m-80) cc_final: 0.7827 (m-80) REVERT: A 381 LEU cc_start: 0.8969 (tp) cc_final: 0.8264 (pt) REVERT: A 406 ASP cc_start: 0.8673 (m-30) cc_final: 0.8459 (m-30) REVERT: A 417 LEU cc_start: 0.9317 (tt) cc_final: 0.8612 (tt) REVERT: A 425 ILE cc_start: 0.9351 (mt) cc_final: 0.9060 (mt) REVERT: A 456 LYS cc_start: 0.8822 (ptpp) cc_final: 0.8443 (ptpp) REVERT: A 458 MET cc_start: 0.9160 (mmm) cc_final: 0.8478 (mtm) REVERT: A 576 LEU cc_start: 0.9174 (mt) cc_final: 0.8926 (mt) REVERT: A 584 ILE cc_start: 0.9032 (pt) cc_final: 0.8805 (pt) REVERT: A 615 MET cc_start: 0.9165 (mmt) cc_final: 0.8943 (mmt) REVERT: A 639 ASP cc_start: 0.8687 (m-30) cc_final: 0.8253 (m-30) REVERT: A 667 LEU cc_start: 0.9219 (tt) cc_final: 0.8608 (tt) REVERT: B 67 GLU cc_start: 0.8157 (mp0) cc_final: 0.7939 (mp0) REVERT: B 102 ASN cc_start: 0.9285 (m110) cc_final: 0.8955 (m110) REVERT: B 120 ASP cc_start: 0.8632 (m-30) cc_final: 0.8333 (m-30) REVERT: B 190 MET cc_start: 0.9108 (mtm) cc_final: 0.8746 (mtm) REVERT: B 191 GLN cc_start: 0.8816 (mm-40) cc_final: 0.8143 (mm-40) REVERT: B 214 LYS cc_start: 0.7876 (mmtm) cc_final: 0.7656 (mmtm) REVERT: B 235 ARG cc_start: 0.8521 (ttm110) cc_final: 0.7894 (mtm110) REVERT: B 253 ILE cc_start: 0.9395 (tt) cc_final: 0.9111 (tt) REVERT: B 258 ILE cc_start: 0.9460 (tp) cc_final: 0.9245 (tp) REVERT: B 276 LYS cc_start: 0.8830 (ptmt) cc_final: 0.8492 (ptpp) REVERT: B 282 VAL cc_start: 0.9594 (t) cc_final: 0.9363 (m) REVERT: B 288 PHE cc_start: 0.9399 (t80) cc_final: 0.9084 (t80) REVERT: B 320 ASN cc_start: 0.8691 (p0) cc_final: 0.8247 (p0) REVERT: B 333 LYS cc_start: 0.9129 (tttm) cc_final: 0.8605 (tttp) REVERT: B 362 ASP cc_start: 0.7941 (m-30) cc_final: 0.6983 (m-30) REVERT: B 392 SER cc_start: 0.9225 (m) cc_final: 0.8957 (m) REVERT: B 393 SER cc_start: 0.9428 (m) cc_final: 0.9196 (p) REVERT: B 410 ASN cc_start: 0.9039 (m-40) cc_final: 0.8606 (m-40) REVERT: B 427 LYS cc_start: 0.9437 (pttt) cc_final: 0.9211 (pttt) REVERT: B 467 ASN cc_start: 0.9240 (t0) cc_final: 0.8741 (t0) REVERT: B 493 MET cc_start: 0.9206 (tmm) cc_final: 0.8966 (tmm) REVERT: B 576 LEU cc_start: 0.9240 (mt) cc_final: 0.8940 (mt) REVERT: B 586 TYR cc_start: 0.8413 (m-80) cc_final: 0.8180 (m-10) REVERT: B 588 GLN cc_start: 0.9156 (mm-40) cc_final: 0.8726 (mm-40) REVERT: B 602 GLU cc_start: 0.7197 (pt0) cc_final: 0.6755 (pt0) REVERT: B 604 ARG cc_start: 0.8505 (tpp80) cc_final: 0.7755 (tpp80) REVERT: B 615 MET cc_start: 0.9107 (mmp) cc_final: 0.8897 (mmm) REVERT: B 627 LYS cc_start: 0.9311 (tttt) cc_final: 0.9089 (tttp) REVERT: B 640 MET cc_start: 0.8989 (tpp) cc_final: 0.8250 (tpp) REVERT: B 652 ILE cc_start: 0.9005 (mt) cc_final: 0.8782 (mt) REVERT: B 683 TYR cc_start: 0.8006 (t80) cc_final: 0.7786 (t80) REVERT: C 89 VAL cc_start: 0.4942 (m) cc_final: 0.4499 (m) REVERT: C 154 PHE cc_start: 0.8660 (t80) cc_final: 0.7697 (t80) REVERT: C 157 MET cc_start: 0.8678 (mpp) cc_final: 0.8101 (ptp) REVERT: D 56 MET cc_start: -0.1297 (mmm) cc_final: -0.1516 (mmm) REVERT: D 95 MET cc_start: 0.8042 (ttp) cc_final: 0.7726 (ttt) REVERT: D 108 ILE cc_start: 0.8256 (tp) cc_final: 0.7959 (pt) outliers start: 0 outliers final: 0 residues processed: 535 average time/residue: 0.2882 time to fit residues: 231.2551 Evaluate side-chains 427 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 427 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 111 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 182 optimal weight: 10.0000 chunk 107 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 188 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN A 645 GLN B 11 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.159215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.111076 restraints weight = 33683.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.114444 restraints weight = 16494.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.116674 restraints weight = 9848.836| |-----------------------------------------------------------------------------| r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3263 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3263 r_free = 0.3263 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3263 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.5977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 16386 Z= 0.222 Angle : 0.654 11.312 22134 Z= 0.344 Chirality : 0.044 0.163 2360 Planarity : 0.003 0.045 2818 Dihedral : 10.393 171.088 2242 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.19), residues: 1932 helix: 1.38 (0.15), residues: 1114 sheet: -0.34 (0.42), residues: 134 loop : 0.08 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP D 124 HIS 0.005 0.001 HIS A 438 PHE 0.050 0.002 PHE C 109 TYR 0.043 0.002 TYR D 130 ARG 0.008 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.03956 ( 871) hydrogen bonds : angle 4.88818 ( 2571) covalent geometry : bond 0.00493 (16386) covalent geometry : angle 0.65365 (22134) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 512 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 109 ASN cc_start: 0.8954 (m110) cc_final: 0.8716 (m-40) REVERT: A 174 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7579 (mt-10) REVERT: A 286 ASP cc_start: 0.8257 (m-30) cc_final: 0.7837 (m-30) REVERT: A 319 MET cc_start: 0.9299 (tpp) cc_final: 0.8879 (tpp) REVERT: A 344 GLU cc_start: 0.8815 (mt-10) cc_final: 0.8329 (mt-10) REVERT: A 406 ASP cc_start: 0.8630 (m-30) cc_final: 0.8387 (m-30) REVERT: A 447 ASN cc_start: 0.8061 (m110) cc_final: 0.7773 (m-40) REVERT: A 458 MET cc_start: 0.9192 (mmm) cc_final: 0.8451 (mtm) REVERT: A 576 LEU cc_start: 0.9102 (mt) cc_final: 0.8873 (mt) REVERT: A 584 ILE cc_start: 0.9022 (pt) cc_final: 0.8799 (pt) REVERT: A 602 GLU cc_start: 0.7161 (pt0) cc_final: 0.6636 (pt0) REVERT: A 667 LEU cc_start: 0.9257 (tt) cc_final: 0.8649 (tt) REVERT: B 102 ASN cc_start: 0.9257 (m110) cc_final: 0.8928 (m110) REVERT: B 120 ASP cc_start: 0.8656 (m-30) cc_final: 0.8369 (m-30) REVERT: B 190 MET cc_start: 0.9169 (mtm) cc_final: 0.8853 (mtm) REVERT: B 191 GLN cc_start: 0.8888 (mm-40) cc_final: 0.8204 (mm-40) REVERT: B 253 ILE cc_start: 0.9457 (tt) cc_final: 0.9192 (tt) REVERT: B 258 ILE cc_start: 0.9533 (tp) cc_final: 0.9323 (tp) REVERT: B 262 LEU cc_start: 0.9511 (mm) cc_final: 0.9308 (mm) REVERT: B 276 LYS cc_start: 0.8901 (ptmt) cc_final: 0.8553 (ptpp) REVERT: B 288 PHE cc_start: 0.9464 (t80) cc_final: 0.9157 (t80) REVERT: B 314 MET cc_start: 0.8423 (ttt) cc_final: 0.8197 (tmm) REVERT: B 333 LYS cc_start: 0.9125 (tttm) cc_final: 0.8643 (tttm) REVERT: B 362 ASP cc_start: 0.7955 (m-30) cc_final: 0.7151 (m-30) REVERT: B 392 SER cc_start: 0.9252 (m) cc_final: 0.9027 (m) REVERT: B 427 LYS cc_start: 0.9454 (pttt) cc_final: 0.9190 (pttt) REVERT: B 467 ASN cc_start: 0.9313 (t0) cc_final: 0.8846 (t0) REVERT: B 493 MET cc_start: 0.9283 (tmm) cc_final: 0.8991 (tmm) REVERT: B 602 GLU cc_start: 0.7174 (pt0) cc_final: 0.6955 (pt0) REVERT: B 604 ARG cc_start: 0.8556 (tpp80) cc_final: 0.7887 (tpp80) REVERT: B 627 LYS cc_start: 0.9320 (tttt) cc_final: 0.9008 (tttp) REVERT: B 640 MET cc_start: 0.8933 (tpp) cc_final: 0.8280 (tpp) REVERT: B 662 MET cc_start: 0.8526 (ptp) cc_final: 0.8180 (ptp) REVERT: C 90 LEU cc_start: 0.7157 (mt) cc_final: 0.6736 (tt) REVERT: C 95 MET cc_start: 0.6648 (tmm) cc_final: 0.6447 (tmm) REVERT: C 154 PHE cc_start: 0.8626 (t80) cc_final: 0.7464 (t80) REVERT: D 56 MET cc_start: -0.1126 (mmm) cc_final: -0.1333 (mmm) REVERT: D 95 MET cc_start: 0.8352 (ttp) cc_final: 0.7940 (ttt) REVERT: D 108 ILE cc_start: 0.8282 (tp) cc_final: 0.7995 (pt) REVERT: D 173 TYR cc_start: 0.5916 (t80) cc_final: 0.5585 (t80) REVERT: D 256 VAL cc_start: 0.3409 (t) cc_final: 0.3144 (t) outliers start: 0 outliers final: 0 residues processed: 512 average time/residue: 0.2703 time to fit residues: 207.9165 Evaluate side-chains 411 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 411 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 137 optimal weight: 0.1980 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 0.6980 chunk 160 optimal weight: 9.9990 chunk 106 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN A 645 GLN B 25 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.163667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.115422 restraints weight = 33405.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.118906 restraints weight = 15987.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.121125 restraints weight = 9475.935| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.113 | | 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) = 0.113 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.6162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16386 Z= 0.135 Angle : 0.636 9.444 22134 Z= 0.334 Chirality : 0.043 0.326 2360 Planarity : 0.003 0.039 2818 Dihedral : 10.116 168.625 2242 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.19), residues: 1932 helix: 1.36 (0.15), residues: 1115 sheet: 0.43 (0.48), residues: 96 loop : -0.03 (0.23), residues: 721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D 124 HIS 0.005 0.001 HIS A 438 PHE 0.049 0.002 PHE C 109 TYR 0.025 0.002 TYR C 174 ARG 0.009 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.03888 ( 871) hydrogen bonds : angle 4.88277 ( 2571) covalent geometry : bond 0.00298 (16386) covalent geometry : angle 0.63576 (22134) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 TRP cc_start: 0.9252 (p90) cc_final: 0.8964 (p90) REVERT: A 64 TYR cc_start: 0.8829 (m-10) cc_final: 0.8489 (m-10) REVERT: A 65 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8026 (mp0) REVERT: A 158 ASN cc_start: 0.8991 (m110) cc_final: 0.8755 (m-40) REVERT: A 174 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7653 (mt-10) REVERT: A 286 ASP cc_start: 0.8331 (m-30) cc_final: 0.7934 (m-30) REVERT: A 319 MET cc_start: 0.9306 (tpp) cc_final: 0.8868 (tpp) REVERT: A 344 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8459 (mt-10) REVERT: A 357 TYR cc_start: 0.8170 (m-80) cc_final: 0.7780 (m-80) REVERT: A 406 ASP cc_start: 0.8638 (m-30) cc_final: 0.8341 (m-30) REVERT: A 420 MET cc_start: 0.9360 (mmp) cc_final: 0.9132 (mmp) REVERT: A 447 ASN cc_start: 0.8193 (m-40) cc_final: 0.7526 (m-40) REVERT: A 458 MET cc_start: 0.9186 (mmm) cc_final: 0.8393 (mtm) REVERT: A 576 LEU cc_start: 0.9182 (mt) cc_final: 0.8949 (mt) REVERT: A 584 ILE cc_start: 0.8997 (pt) cc_final: 0.8795 (pt) REVERT: A 639 ASP cc_start: 0.8634 (m-30) cc_final: 0.8233 (m-30) REVERT: A 667 LEU cc_start: 0.9251 (tt) cc_final: 0.8632 (tt) REVERT: B 102 ASN cc_start: 0.9335 (m110) cc_final: 0.9025 (m110) REVERT: B 117 ARG cc_start: 0.8664 (mtt-85) cc_final: 0.8256 (mtt-85) REVERT: B 120 ASP cc_start: 0.8533 (m-30) cc_final: 0.8277 (m-30) REVERT: B 190 MET cc_start: 0.9145 (mtm) cc_final: 0.8777 (mtm) REVERT: B 191 GLN cc_start: 0.8712 (mm-40) cc_final: 0.8182 (mm-40) REVERT: B 214 LYS cc_start: 0.7760 (mmtm) cc_final: 0.7538 (mmtm) REVERT: B 235 ARG cc_start: 0.8524 (ttm110) cc_final: 0.7886 (mtm110) REVERT: B 253 ILE cc_start: 0.9388 (tt) cc_final: 0.9126 (tt) REVERT: B 258 ILE cc_start: 0.9497 (tp) cc_final: 0.9294 (tp) REVERT: B 262 LEU cc_start: 0.9476 (mm) cc_final: 0.9268 (mm) REVERT: B 276 LYS cc_start: 0.8883 (ptmt) cc_final: 0.8563 (ptpp) REVERT: B 288 PHE cc_start: 0.9395 (t80) cc_final: 0.9102 (t80) REVERT: B 333 LYS cc_start: 0.9122 (tttm) cc_final: 0.8613 (tttp) REVERT: B 362 ASP cc_start: 0.7996 (m-30) cc_final: 0.7214 (m-30) REVERT: B 389 SER cc_start: 0.8736 (p) cc_final: 0.8514 (p) REVERT: B 392 SER cc_start: 0.9231 (m) cc_final: 0.8939 (m) REVERT: B 393 SER cc_start: 0.9437 (m) cc_final: 0.9202 (p) REVERT: B 399 GLU cc_start: 0.8563 (mm-30) cc_final: 0.8347 (mm-30) REVERT: B 410 ASN cc_start: 0.9027 (m-40) cc_final: 0.8621 (m-40) REVERT: B 427 LYS cc_start: 0.9423 (pttt) cc_final: 0.9185 (pttt) REVERT: B 458 MET cc_start: 0.8914 (mmm) cc_final: 0.7970 (mmm) REVERT: B 467 ASN cc_start: 0.9260 (t0) cc_final: 0.8692 (t0) REVERT: B 576 LEU cc_start: 0.9270 (mt) cc_final: 0.9050 (mt) REVERT: B 604 ARG cc_start: 0.8497 (tpp80) cc_final: 0.7674 (tpp80) REVERT: B 627 LYS cc_start: 0.9295 (tttt) cc_final: 0.9070 (tttp) REVERT: B 640 MET cc_start: 0.8947 (tpp) cc_final: 0.8262 (tpp) REVERT: B 652 ILE cc_start: 0.8954 (mt) cc_final: 0.8736 (mt) REVERT: B 662 MET cc_start: 0.8394 (ptp) cc_final: 0.8033 (ptp) REVERT: C 90 LEU cc_start: 0.7300 (mt) cc_final: 0.6978 (tt) REVERT: C 95 MET cc_start: 0.6405 (tmm) cc_final: 0.6158 (tmm) REVERT: C 154 PHE cc_start: 0.8630 (t80) cc_final: 0.7697 (t80) REVERT: C 269 MET cc_start: 0.7490 (tmm) cc_final: 0.7101 (mmp) REVERT: D 56 MET cc_start: -0.1065 (mmm) cc_final: -0.1328 (mmm) REVERT: D 95 MET cc_start: 0.8205 (ttp) cc_final: 0.7795 (ttt) REVERT: D 108 ILE cc_start: 0.8312 (tp) cc_final: 0.8008 (pt) outliers start: 0 outliers final: 0 residues processed: 515 average time/residue: 0.2839 time to fit residues: 221.2731 Evaluate side-chains 437 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 437 time to evaluate : 1.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 81 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 chunk 2 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 179 optimal weight: 9.9990 chunk 190 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 180 optimal weight: 5.9990 chunk 108 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN A 646 GLN ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.162569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.114244 restraints weight = 33449.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.117720 restraints weight = 16164.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.119850 restraints weight = 9660.175| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3327 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3327 r_free = 0.3327 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3327 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.6293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 16386 Z= 0.144 Angle : 0.627 9.309 22134 Z= 0.329 Chirality : 0.043 0.271 2360 Planarity : 0.003 0.043 2818 Dihedral : 9.974 168.393 2242 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.19), residues: 1932 helix: 1.40 (0.15), residues: 1110 sheet: -0.41 (0.42), residues: 130 loop : 0.10 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP D 124 HIS 0.005 0.001 HIS A 438 PHE 0.048 0.002 PHE C 109 TYR 0.026 0.002 TYR B 683 ARG 0.009 0.001 ARG A 686 Details of bonding type rmsd hydrogen bonds : bond 0.03826 ( 871) hydrogen bonds : angle 4.85606 ( 2571) covalent geometry : bond 0.00321 (16386) covalent geometry : angle 0.62745 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6669.84 seconds wall clock time: 116 minutes 41.73 seconds (7001.73 seconds total)