Starting phenix.real_space_refine on Sun Aug 24 01:04:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzf_45066/08_2025/9bzf_45066_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzf_45066/08_2025/9bzf_45066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bzf_45066/08_2025/9bzf_45066_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzf_45066/08_2025/9bzf_45066_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bzf_45066/08_2025/9bzf_45066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzf_45066/08_2025/9bzf_45066.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 4.21, per 1000 atoms: 0.26 Number of scatterers: 16038 At special positions: 0 Unit cell: (100.386, 126.75, 130.806, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 719.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.985A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.953A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.664A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.695A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.393A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.628A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.676A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.646A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.027A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.067A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.934A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.669A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.876A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.360A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.478A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.185A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.049A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.20 Time building geometry restraints manager: 1.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4889 1.34 - 1.46: 3089 1.46 - 1.58: 8227 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.060 1.25e-02 6.40e+03 2.34e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.038 1.20e-02 6.94e+03 1.01e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.033 1.08e-02 8.57e+03 9.15e+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 7.42e+00 bond pdb=" CA ILE C 35 " pdb=" CB ILE C 35 " ideal model delta sigma weight residual 1.537 1.568 -0.031 1.21e-02 6.83e+03 6.76e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 21571 2.10 - 4.19: 521 4.19 - 6.29: 37 6.29 - 8.39: 1 8.39 - 10.49: 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 110.54 116.61 -6.07 1.36e+00 5.41e-01 1.99e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.09 -4.38 1.15e+00 7.56e-01 1.45e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.83 -4.33 1.23e+00 6.61e-01 1.24e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.67 -3.96 1.15e+00 7.56e-01 1.18e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.55 3.64 1.06e+00 8.90e-01 1.18e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 9469 35.80 - 71.59: 338 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 301.68 151.17 150.51 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" C5' TTP A 803 " pdb=" O5' TTP A 803 " pdb=" PA TTP A 803 " pdb=" O3A TTP A 803 " ideal model delta sinusoidal sigma weight residual 179.97 31.89 148.08 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 9847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2141 0.093 - 0.187: 187 0.187 - 0.280: 27 0.280 - 0.373: 3 0.373 - 0.466: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.44e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO D 75 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.018 2.00e-02 2.50e+03 1.13e-02 2.22e+00 pdb=" CG PHE D 92 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 177 " -0.017 2.00e-02 2.50e+03 9.84e-03 1.94e+00 pdb=" CG TYR C 177 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR C 177 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 177 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 177 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 177 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 177 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 177 " -0.010 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 132 2.51 - 3.11: 11553 3.11 - 3.70: 27046 3.70 - 4.30: 41515 4.30 - 4.90: 65404 Nonbonded interactions: 145650 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.012 3.040 ... (remaining 145645 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.810 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 16386 Z= 0.316 Angle : 0.740 10.486 22134 Z= 0.463 Chirality : 0.058 0.466 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.953 178.987 6154 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.34 % Allowed : 15.33 % Favored : 83.33 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.56 (0.18), residues: 1932 helix: 0.59 (0.14), residues: 1151 sheet: 0.47 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74027 (22134) hydrogen bonds : bond 0.15420 ( 871) hydrogen bonds : angle 6.51691 ( 2571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 901 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 878 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8173 (t0) cc_final: 0.7969 (t70) REVERT: A 37 PHE cc_start: 0.6567 (m-80) cc_final: 0.6213 (m-10) REVERT: A 41 ILE cc_start: 0.8350 (mm) cc_final: 0.8058 (mm) REVERT: A 101 TYR cc_start: 0.7570 (m-80) cc_final: 0.7216 (m-10) REVERT: A 119 GLU cc_start: 0.7561 (mp0) cc_final: 0.6800 (mp0) REVERT: A 143 LEU cc_start: 0.8762 (tp) cc_final: 0.8409 (tp) REVERT: A 168 VAL cc_start: 0.8904 (t) cc_final: 0.8646 (t) REVERT: A 181 ASP cc_start: 0.8597 (m-30) cc_final: 0.8145 (m-30) REVERT: A 191 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7519 (mm110) REVERT: A 258 ILE cc_start: 0.8700 (tp) cc_final: 0.8402 (tp) REVERT: A 264 THR cc_start: 0.8998 (p) cc_final: 0.8787 (m) REVERT: A 278 LEU cc_start: 0.8386 (tp) cc_final: 0.8154 (tp) REVERT: A 322 MET cc_start: 0.7510 (mmp) cc_final: 0.6584 (mmm) REVERT: A 362 ASP cc_start: 0.5877 (m-30) cc_final: 0.4814 (m-30) REVERT: A 425 ILE cc_start: 0.9125 (mt) cc_final: 0.8814 (mt) REVERT: A 431 LEU cc_start: 0.9210 (mt) cc_final: 0.8870 (mm) REVERT: A 436 LEU cc_start: 0.9165 (mt) cc_final: 0.8809 (mt) REVERT: A 447 ASN cc_start: 0.7619 (m-40) cc_final: 0.6723 (m110) REVERT: A 493 MET cc_start: 0.7567 (tmm) cc_final: 0.7061 (tmm) REVERT: A 494 MET cc_start: 0.7764 (mtp) cc_final: 0.7300 (mtp) REVERT: A 500 ILE cc_start: 0.9352 (mt) cc_final: 0.9024 (mt) REVERT: A 522 TYR cc_start: 0.7435 (m-80) cc_final: 0.6453 (m-10) REVERT: A 531 TYR cc_start: 0.6454 (m-80) cc_final: 0.6064 (m-80) REVERT: A 558 TRP cc_start: 0.8229 (m100) cc_final: 0.6925 (m100) REVERT: A 561 LEU cc_start: 0.8853 (tp) cc_final: 0.8601 (tp) REVERT: A 571 TYR cc_start: 0.6916 (t80) cc_final: 0.6597 (t80) REVERT: A 575 ARG cc_start: 0.8503 (mtm110) cc_final: 0.7973 (ptp90) REVERT: A 655 THR cc_start: 0.8855 (m) cc_final: 0.8483 (t) REVERT: A 684 TYR cc_start: 0.5726 (m-80) cc_final: 0.4259 (m-80) REVERT: B 41 ILE cc_start: 0.8888 (mm) cc_final: 0.8443 (mm) REVERT: B 51 LEU cc_start: 0.8225 (tp) cc_final: 0.7877 (tp) REVERT: B 78 LYS cc_start: 0.8360 (tttp) cc_final: 0.8114 (tttt) REVERT: B 95 MET cc_start: 0.6966 (tpp) cc_final: 0.6615 (tpp) REVERT: B 99 LYS cc_start: 0.8995 (mmtt) cc_final: 0.8748 (mmtt) REVERT: B 121 ARG cc_start: 0.8271 (tpm170) cc_final: 0.7560 (tpp-160) REVERT: B 122 ILE cc_start: 0.9011 (mt) cc_final: 0.8360 (mt) REVERT: B 147 GLN cc_start: 0.8114 (mt0) cc_final: 0.6125 (mt0) REVERT: B 157 LEU cc_start: 0.8161 (tp) cc_final: 0.7915 (tp) REVERT: B 172 LEU cc_start: 0.9041 (mp) cc_final: 0.8741 (mp) REVERT: B 181 ASP cc_start: 0.8259 (m-30) cc_final: 0.7809 (m-30) REVERT: B 191 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7853 (mm-40) REVERT: B 204 SER cc_start: 0.8945 (m) cc_final: 0.8457 (p) REVERT: B 258 ILE cc_start: 0.8950 (tp) cc_final: 0.8705 (tp) REVERT: B 291 LEU cc_start: 0.9105 (mt) cc_final: 0.8877 (mt) REVERT: B 319 MET cc_start: 0.7375 (tpp) cc_final: 0.7014 (mmp) REVERT: B 322 MET cc_start: 0.7547 (mmm) cc_final: 0.7007 (mmm) REVERT: B 467 ASN cc_start: 0.8417 (t0) cc_final: 0.8184 (m-40) REVERT: B 469 HIS cc_start: 0.8278 (t-170) cc_final: 0.7981 (t70) REVERT: B 515 ASP cc_start: 0.8433 (m-30) cc_final: 0.8185 (m-30) REVERT: B 522 TYR cc_start: 0.7414 (m-80) cc_final: 0.6997 (m-10) REVERT: B 570 MET cc_start: 0.6615 (mtm) cc_final: 0.5996 (mtm) REVERT: B 587 VAL cc_start: 0.8980 (t) cc_final: 0.8641 (t) REVERT: B 588 GLN cc_start: 0.7762 (mm-40) cc_final: 0.6652 (mm-40) REVERT: B 589 SER cc_start: 0.8503 (m) cc_final: 0.8043 (p) REVERT: B 627 LYS cc_start: 0.8225 (tttt) cc_final: 0.7889 (tttp) REVERT: B 631 ASP cc_start: 0.7629 (m-30) cc_final: 0.7177 (t0) REVERT: B 644 ILE cc_start: 0.8499 (mt) cc_final: 0.8200 (mt) REVERT: B 655 THR cc_start: 0.9341 (m) cc_final: 0.8555 (t) REVERT: C 56 MET cc_start: -0.0066 (mmm) cc_final: -0.0507 (ttp) REVERT: C 90 LEU cc_start: 0.5964 (mt) cc_final: 0.5475 (mt) REVERT: C 95 MET cc_start: 0.5795 (tmm) cc_final: 0.5485 (tmm) REVERT: D 185 MET cc_start: 0.2872 (mmm) cc_final: 0.0367 (mpp) outliers start: 23 outliers final: 6 residues processed: 887 average time/residue: 0.1568 time to fit residues: 198.3069 Evaluate side-chains 612 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 606 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 242 GLN A 320 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 218 ASN B 313 HIS B 645 GLN C 24 GLN C 28 GLN C 186 GLN C 238 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.143589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.096292 restraints weight = 43433.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.099772 restraints weight = 26300.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.102032 restraints weight = 17966.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.103560 restraints weight = 13477.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.104759 restraints weight = 10756.645| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3252 r_free = 0.3252 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3252 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.4328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16386 Z= 0.191 Angle : 0.647 9.169 22134 Z= 0.343 Chirality : 0.043 0.195 2360 Planarity : 0.004 0.058 2818 Dihedral : 11.466 179.379 2242 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.23 % Allowed : 2.91 % Favored : 96.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.19), residues: 1932 helix: 1.52 (0.15), residues: 1121 sheet: -0.34 (0.39), residues: 148 loop : 0.60 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 446 TYR 0.029 0.002 TYR A 498 PHE 0.036 0.002 PHE D 320 TRP 0.011 0.002 TRP C 30 HIS 0.009 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00399 (16386) covalent geometry : angle 0.64673 (22134) hydrogen bonds : bond 0.04558 ( 871) hydrogen bonds : angle 5.05275 ( 2571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 725 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9336 (t0) cc_final: 0.9021 (t70) REVERT: A 40 TYR cc_start: 0.9142 (t80) cc_final: 0.8861 (t80) REVERT: A 89 PHE cc_start: 0.8905 (t80) cc_final: 0.8263 (t80) REVERT: A 119 GLU cc_start: 0.9198 (mp0) cc_final: 0.8459 (tm-30) REVERT: A 120 ASP cc_start: 0.9248 (m-30) cc_final: 0.8814 (m-30) REVERT: A 143 LEU cc_start: 0.9390 (tp) cc_final: 0.8936 (tp) REVERT: A 148 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8394 (mt-10) REVERT: A 181 ASP cc_start: 0.9120 (m-30) cc_final: 0.8891 (m-30) REVERT: A 191 GLN cc_start: 0.9445 (mm-40) cc_final: 0.9156 (mm-40) REVERT: A 195 LEU cc_start: 0.9575 (mt) cc_final: 0.9315 (mt) REVERT: A 227 MET cc_start: 0.9257 (mtm) cc_final: 0.9042 (mtm) REVERT: A 235 ARG cc_start: 0.8720 (mtm110) cc_final: 0.8494 (mtm110) REVERT: A 239 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7403 (tt0) REVERT: A 252 ASN cc_start: 0.9380 (t0) cc_final: 0.8892 (t0) REVERT: A 307 TYR cc_start: 0.9560 (t80) cc_final: 0.9342 (t80) REVERT: A 322 MET cc_start: 0.9116 (mmp) cc_final: 0.8623 (mmm) REVERT: A 335 GLU cc_start: 0.8502 (mm-30) cc_final: 0.7752 (mm-30) REVERT: A 342 LEU cc_start: 0.9617 (tp) cc_final: 0.9309 (tp) REVERT: A 350 ARG cc_start: 0.8590 (mmm-85) cc_final: 0.8136 (mmm-85) REVERT: A 370 ASN cc_start: 0.9408 (m-40) cc_final: 0.9069 (m110) REVERT: A 402 GLU cc_start: 0.8552 (mp0) cc_final: 0.8262 (mp0) REVERT: A 447 ASN cc_start: 0.8937 (m-40) cc_final: 0.8690 (m-40) REVERT: A 459 LYS cc_start: 0.9166 (mttp) cc_final: 0.8658 (mtmt) REVERT: A 468 LEU cc_start: 0.9793 (tp) cc_final: 0.9497 (tp) REVERT: A 472 LEU cc_start: 0.9739 (mt) cc_final: 0.9455 (mt) REVERT: A 500 ILE cc_start: 0.9664 (mt) cc_final: 0.9220 (mt) REVERT: A 515 ASP cc_start: 0.9253 (m-30) cc_final: 0.8932 (m-30) REVERT: A 522 TYR cc_start: 0.9246 (m-80) cc_final: 0.8826 (m-10) REVERT: A 570 MET cc_start: 0.9099 (mtp) cc_final: 0.8208 (mtp) REVERT: A 575 ARG cc_start: 0.9144 (mtm110) cc_final: 0.8709 (mtm-85) REVERT: A 598 MET cc_start: 0.9239 (mtp) cc_final: 0.8597 (mmt) REVERT: A 615 MET cc_start: 0.8744 (mmp) cc_final: 0.8360 (mmp) REVERT: A 632 MET cc_start: 0.8907 (mtp) cc_final: 0.8511 (mtm) REVERT: A 645 GLN cc_start: 0.8775 (tp40) cc_final: 0.8548 (tp-100) REVERT: A 650 GLN cc_start: 0.8795 (mt0) cc_final: 0.8187 (mt0) REVERT: A 657 PHE cc_start: 0.8519 (m-80) cc_final: 0.7648 (m-80) REVERT: B 15 GLU cc_start: 0.9172 (tp30) cc_final: 0.8625 (tp30) REVERT: B 41 ILE cc_start: 0.9647 (mm) cc_final: 0.9430 (mm) REVERT: B 51 LEU cc_start: 0.9240 (tp) cc_final: 0.8942 (tp) REVERT: B 65 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8817 (mm-30) REVERT: B 95 MET cc_start: 0.9184 (tpp) cc_final: 0.8416 (mmm) REVERT: B 99 LYS cc_start: 0.9539 (mmmt) cc_final: 0.8913 (mmmt) REVERT: B 115 LEU cc_start: 0.9440 (mt) cc_final: 0.9202 (mt) REVERT: B 117 ARG cc_start: 0.9118 (ttm110) cc_final: 0.8770 (ttm110) REVERT: B 119 GLU cc_start: 0.9283 (mp0) cc_final: 0.8815 (mp0) REVERT: B 144 MET cc_start: 0.9279 (mtm) cc_final: 0.8925 (mtm) REVERT: B 147 GLN cc_start: 0.9267 (mt0) cc_final: 0.8148 (mt0) REVERT: B 205 LYS cc_start: 0.9433 (mmmt) cc_final: 0.9171 (mmmm) REVERT: B 211 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8291 (mm-30) REVERT: B 218 ASN cc_start: 0.9716 (t0) cc_final: 0.9422 (t0) REVERT: B 227 MET cc_start: 0.9426 (mtp) cc_final: 0.9184 (mtp) REVERT: B 251 LEU cc_start: 0.9521 (tp) cc_final: 0.9220 (tp) REVERT: B 286 ASP cc_start: 0.8735 (m-30) cc_final: 0.8188 (m-30) REVERT: B 288 PHE cc_start: 0.9422 (t80) cc_final: 0.9220 (t80) REVERT: B 290 GLU cc_start: 0.8826 (tm-30) cc_final: 0.8439 (pp20) REVERT: B 291 LEU cc_start: 0.9619 (mt) cc_final: 0.9333 (mt) REVERT: B 308 LYS cc_start: 0.9408 (mtmt) cc_final: 0.9139 (ptpp) REVERT: B 322 MET cc_start: 0.9291 (mmm) cc_final: 0.8689 (mmm) REVERT: B 342 LEU cc_start: 0.9710 (tp) cc_final: 0.9403 (tp) REVERT: B 345 LYS cc_start: 0.9514 (tttt) cc_final: 0.9257 (tttt) REVERT: B 348 MET cc_start: 0.9278 (tpp) cc_final: 0.8744 (tpp) REVERT: B 362 ASP cc_start: 0.9030 (m-30) cc_final: 0.8134 (m-30) REVERT: B 370 ASN cc_start: 0.9331 (m-40) cc_final: 0.8569 (m-40) REVERT: B 373 ILE cc_start: 0.9661 (mt) cc_final: 0.9439 (tp) REVERT: B 375 LYS cc_start: 0.9238 (mmtm) cc_final: 0.8805 (mmtm) REVERT: B 393 SER cc_start: 0.9697 (t) cc_final: 0.9067 (p) REVERT: B 398 ASP cc_start: 0.8794 (t70) cc_final: 0.8420 (t70) REVERT: B 403 ILE cc_start: 0.9370 (mp) cc_final: 0.9065 (tp) REVERT: B 430 LYS cc_start: 0.9148 (ptpp) cc_final: 0.8921 (mtmm) REVERT: B 458 MET cc_start: 0.9420 (mmm) cc_final: 0.8882 (mmm) REVERT: B 494 MET cc_start: 0.9470 (mtt) cc_final: 0.9194 (mtt) REVERT: B 500 ILE cc_start: 0.9756 (mt) cc_final: 0.9423 (mt) REVERT: B 501 GLN cc_start: 0.9701 (tt0) cc_final: 0.9131 (tp-100) REVERT: B 548 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8541 (mt-10) REVERT: B 570 MET cc_start: 0.9479 (mtp) cc_final: 0.8902 (mtp) REVERT: B 586 TYR cc_start: 0.9378 (m-80) cc_final: 0.9063 (m-80) REVERT: B 588 GLN cc_start: 0.9361 (mm-40) cc_final: 0.8998 (mm110) REVERT: B 603 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8293 (tm-30) REVERT: B 615 MET cc_start: 0.8787 (mmp) cc_final: 0.8406 (mmp) REVERT: B 631 ASP cc_start: 0.9408 (m-30) cc_final: 0.9099 (t0) REVERT: B 648 ILE cc_start: 0.9624 (mm) cc_final: 0.9378 (mm) REVERT: B 667 LEU cc_start: 0.9053 (tp) cc_final: 0.8705 (tp) REVERT: B 668 ASN cc_start: 0.9388 (m-40) cc_final: 0.8905 (m-40) REVERT: B 677 ARG cc_start: 0.9645 (mmm160) cc_final: 0.9295 (mmm-85) REVERT: C 95 MET cc_start: 0.8510 (tmm) cc_final: 0.8178 (tmm) REVERT: C 100 VAL cc_start: 0.8996 (t) cc_final: 0.8484 (t) REVERT: C 101 HIS cc_start: 0.8180 (m90) cc_final: 0.7888 (m90) REVERT: C 136 GLN cc_start: 0.0266 (mt0) cc_final: -0.0112 (tp40) REVERT: C 185 MET cc_start: 0.2127 (tmm) cc_final: 0.1544 (mmm) REVERT: D 96 MET cc_start: 0.9060 (mmm) cc_final: 0.8542 (mpp) REVERT: D 169 TYR cc_start: 0.8512 (m-80) cc_final: 0.8136 (m-80) REVERT: D 179 TYR cc_start: 0.6567 (t80) cc_final: 0.6112 (t80) REVERT: D 185 MET cc_start: 0.1418 (mmm) cc_final: 0.0826 (mpp) REVERT: D 197 ASP cc_start: 0.9388 (t70) cc_final: 0.9010 (t70) REVERT: D 201 HIS cc_start: 0.5328 (m170) cc_final: 0.4710 (m170) REVERT: D 212 ILE cc_start: 0.8849 (pt) cc_final: 0.8632 (pt) outliers start: 4 outliers final: 0 residues processed: 726 average time/residue: 0.1457 time to fit residues: 154.2230 Evaluate side-chains 592 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 591 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 167 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 182 optimal weight: 8.9990 chunk 159 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 chunk 150 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 147 GLN A 180 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 GLN A 675 HIS ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN B 475 ASN C 127 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.129227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.085686 restraints weight = 47805.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.088807 restraints weight = 28545.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.090791 restraints weight = 18999.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.092167 restraints weight = 14095.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.093089 restraints weight = 11217.209| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3196 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3196 r_free = 0.3196 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3196 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.5390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16386 Z= 0.242 Angle : 0.664 7.608 22134 Z= 0.351 Chirality : 0.042 0.151 2360 Planarity : 0.005 0.119 2818 Dihedral : 11.372 170.816 2242 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.19), residues: 1932 helix: 1.38 (0.15), residues: 1106 sheet: -0.49 (0.39), residues: 154 loop : 0.44 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 446 TYR 0.027 0.002 TYR B 574 PHE 0.020 0.002 PHE D 320 TRP 0.022 0.003 TRP C 124 HIS 0.007 0.002 HIS A 368 Details of bonding type rmsd covalent geometry : bond 0.00503 (16386) covalent geometry : angle 0.66373 (22134) hydrogen bonds : bond 0.04289 ( 871) hydrogen bonds : angle 5.03463 ( 2571) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 669 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9462 (t0) cc_final: 0.9232 (t70) REVERT: A 89 PHE cc_start: 0.9230 (t80) cc_final: 0.8795 (t80) REVERT: A 116 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8491 (tt0) REVERT: A 119 GLU cc_start: 0.9248 (mp0) cc_final: 0.8125 (tm-30) REVERT: A 143 LEU cc_start: 0.9408 (tp) cc_final: 0.8976 (tp) REVERT: A 148 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8351 (mt-10) REVERT: A 172 LEU cc_start: 0.9300 (mp) cc_final: 0.8914 (mp) REVERT: A 181 ASP cc_start: 0.9138 (m-30) cc_final: 0.8802 (m-30) REVERT: A 195 LEU cc_start: 0.9634 (mt) cc_final: 0.9414 (mt) REVERT: A 204 SER cc_start: 0.9380 (m) cc_final: 0.9148 (m) REVERT: A 227 MET cc_start: 0.9383 (mtm) cc_final: 0.9105 (mtm) REVERT: A 235 ARG cc_start: 0.8684 (mtm110) cc_final: 0.8341 (mtm110) REVERT: A 250 TYR cc_start: 0.8745 (m-80) cc_final: 0.8297 (m-80) REVERT: A 252 ASN cc_start: 0.9481 (t0) cc_final: 0.8946 (t0) REVERT: A 307 TYR cc_start: 0.9571 (t80) cc_final: 0.9150 (t80) REVERT: A 348 MET cc_start: 0.9328 (ptp) cc_final: 0.9099 (ptp) REVERT: A 350 ARG cc_start: 0.8673 (mmm-85) cc_final: 0.8127 (mmm-85) REVERT: A 370 ASN cc_start: 0.9586 (m-40) cc_final: 0.9307 (m110) REVERT: A 387 GLN cc_start: 0.9030 (mt0) cc_final: 0.8613 (mp10) REVERT: A 394 TYR cc_start: 0.9252 (m-80) cc_final: 0.9008 (m-80) REVERT: A 406 ASP cc_start: 0.8874 (m-30) cc_final: 0.8501 (m-30) REVERT: A 407 ILE cc_start: 0.9151 (mt) cc_final: 0.8807 (mt) REVERT: A 418 ASN cc_start: 0.9610 (m-40) cc_final: 0.9005 (m-40) REVERT: A 459 LYS cc_start: 0.9338 (mttp) cc_final: 0.8865 (mtmm) REVERT: A 468 LEU cc_start: 0.9778 (tp) cc_final: 0.9475 (tp) REVERT: A 472 LEU cc_start: 0.9700 (mt) cc_final: 0.9442 (mt) REVERT: A 493 MET cc_start: 0.9233 (tmm) cc_final: 0.9012 (tmm) REVERT: A 494 MET cc_start: 0.9473 (mtp) cc_final: 0.9040 (mtp) REVERT: A 500 ILE cc_start: 0.9651 (mt) cc_final: 0.9350 (mt) REVERT: A 515 ASP cc_start: 0.9336 (m-30) cc_final: 0.9074 (m-30) REVERT: A 522 TYR cc_start: 0.9364 (m-80) cc_final: 0.8875 (m-10) REVERT: A 558 TRP cc_start: 0.9253 (m100) cc_final: 0.8887 (m100) REVERT: A 570 MET cc_start: 0.9349 (mtp) cc_final: 0.8107 (mtp) REVERT: A 598 MET cc_start: 0.9214 (mtp) cc_final: 0.8612 (mmm) REVERT: A 610 LYS cc_start: 0.9467 (ptmm) cc_final: 0.9227 (ptmm) REVERT: A 612 TYR cc_start: 0.8847 (m-10) cc_final: 0.8244 (m-80) REVERT: A 615 MET cc_start: 0.8778 (mmp) cc_final: 0.8527 (mmp) REVERT: A 645 GLN cc_start: 0.8996 (tp40) cc_final: 0.8783 (tp-100) REVERT: A 650 GLN cc_start: 0.8816 (mt0) cc_final: 0.7612 (mt0) REVERT: A 657 PHE cc_start: 0.8602 (m-80) cc_final: 0.8245 (m-80) REVERT: A 686 ARG cc_start: 0.8825 (mmt180) cc_final: 0.8618 (mmt180) REVERT: B 15 GLU cc_start: 0.9145 (tp30) cc_final: 0.8740 (tp30) REVERT: B 54 LYS cc_start: 0.9516 (mttt) cc_final: 0.9245 (mtmm) REVERT: B 95 MET cc_start: 0.9280 (tpp) cc_final: 0.8865 (tpp) REVERT: B 99 LYS cc_start: 0.9600 (mmmt) cc_final: 0.9085 (mmmt) REVERT: B 115 LEU cc_start: 0.9581 (mt) cc_final: 0.9309 (mt) REVERT: B 136 LYS cc_start: 0.9633 (mmtp) cc_final: 0.9398 (mmmm) REVERT: B 144 MET cc_start: 0.9275 (mtm) cc_final: 0.8883 (mtm) REVERT: B 147 GLN cc_start: 0.9272 (mt0) cc_final: 0.8827 (mt0) REVERT: B 157 LEU cc_start: 0.9572 (tp) cc_final: 0.9134 (tp) REVERT: B 161 ARG cc_start: 0.8983 (ttm110) cc_final: 0.8350 (mtp85) REVERT: B 191 GLN cc_start: 0.9363 (mm-40) cc_final: 0.9158 (mm-40) REVERT: B 211 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8395 (mm-30) REVERT: B 218 ASN cc_start: 0.9662 (t0) cc_final: 0.9434 (t0) REVERT: B 227 MET cc_start: 0.9432 (mtp) cc_final: 0.9124 (mtp) REVERT: B 251 LEU cc_start: 0.9500 (tp) cc_final: 0.9225 (tp) REVERT: B 286 ASP cc_start: 0.8644 (m-30) cc_final: 0.7983 (m-30) REVERT: B 290 GLU cc_start: 0.9136 (tm-30) cc_final: 0.8663 (tm-30) REVERT: B 291 LEU cc_start: 0.9647 (mt) cc_final: 0.9378 (mt) REVERT: B 296 LYS cc_start: 0.8985 (mmpt) cc_final: 0.8554 (mtmm) REVERT: B 312 GLN cc_start: 0.9212 (pm20) cc_final: 0.8969 (pm20) REVERT: B 322 MET cc_start: 0.8749 (mmm) cc_final: 0.8434 (mmm) REVERT: B 342 LEU cc_start: 0.9774 (tp) cc_final: 0.9569 (tp) REVERT: B 345 LYS cc_start: 0.9571 (tttt) cc_final: 0.9238 (tttt) REVERT: B 350 ARG cc_start: 0.8688 (mtp85) cc_final: 0.8284 (mtp85) REVERT: B 362 ASP cc_start: 0.9056 (m-30) cc_final: 0.7990 (m-30) REVERT: B 370 ASN cc_start: 0.9602 (m-40) cc_final: 0.9243 (m-40) REVERT: B 373 ILE cc_start: 0.9694 (mt) cc_final: 0.9357 (mt) REVERT: B 393 SER cc_start: 0.9585 (t) cc_final: 0.9043 (t) REVERT: B 398 ASP cc_start: 0.8799 (t70) cc_final: 0.8587 (t70) REVERT: B 402 GLU cc_start: 0.8633 (mp0) cc_final: 0.8292 (mp0) REVERT: B 403 ILE cc_start: 0.9434 (mp) cc_final: 0.8969 (tp) REVERT: B 413 SER cc_start: 0.9449 (m) cc_final: 0.9047 (t) REVERT: B 427 LYS cc_start: 0.9587 (ptpp) cc_final: 0.9371 (ptpp) REVERT: B 458 MET cc_start: 0.9483 (mmm) cc_final: 0.9279 (mmm) REVERT: B 494 MET cc_start: 0.9546 (mtt) cc_final: 0.9126 (mtt) REVERT: B 500 ILE cc_start: 0.9653 (mt) cc_final: 0.9439 (mt) REVERT: B 506 ILE cc_start: 0.9558 (mm) cc_final: 0.9355 (mm) REVERT: B 547 PHE cc_start: 0.8828 (m-80) cc_final: 0.8349 (m-80) REVERT: B 571 TYR cc_start: 0.9351 (t80) cc_final: 0.9059 (t80) REVERT: B 615 MET cc_start: 0.8872 (mmp) cc_final: 0.8661 (mmp) REVERT: B 631 ASP cc_start: 0.9397 (m-30) cc_final: 0.9154 (m-30) REVERT: B 634 MET cc_start: 0.9372 (mmm) cc_final: 0.9112 (mmp) REVERT: B 648 ILE cc_start: 0.9618 (mm) cc_final: 0.9380 (mm) REVERT: B 668 ASN cc_start: 0.9366 (m-40) cc_final: 0.8941 (m-40) REVERT: B 677 ARG cc_start: 0.9673 (mmm160) cc_final: 0.9307 (mmm-85) REVERT: B 683 TYR cc_start: 0.9041 (t80) cc_final: 0.8810 (t80) REVERT: C 74 MET cc_start: 0.8622 (mtt) cc_final: 0.7765 (mtp) REVERT: C 93 MET cc_start: 0.9390 (mtm) cc_final: 0.8937 (tpt) REVERT: C 101 HIS cc_start: 0.7956 (m90) cc_final: 0.7018 (m90) REVERT: C 124 TRP cc_start: 0.7666 (t60) cc_final: 0.7124 (t60) REVERT: C 261 ARG cc_start: 0.7245 (mtp-110) cc_final: 0.7030 (ttp-170) REVERT: D 22 TYR cc_start: 0.5269 (t80) cc_final: 0.4887 (t80) REVERT: D 69 GLN cc_start: 0.9224 (tp40) cc_final: 0.8496 (tm-30) REVERT: D 146 GLN cc_start: 0.9239 (mt0) cc_final: 0.9017 (tm-30) REVERT: D 179 TYR cc_start: 0.7028 (t80) cc_final: 0.6808 (t80) REVERT: D 185 MET cc_start: 0.2174 (mmm) cc_final: 0.1636 (mpp) outliers start: 0 outliers final: 0 residues processed: 669 average time/residue: 0.1338 time to fit residues: 133.5746 Evaluate side-chains 564 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 564 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 7.9990 chunk 157 optimal weight: 20.0000 chunk 168 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 127 optimal weight: 0.9990 chunk 60 optimal weight: 7.9990 chunk 185 optimal weight: 9.9990 chunk 191 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 182 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 44 ASN A 150 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 410 ASN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN D 91 ASN D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.124522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.082073 restraints weight = 48518.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.084982 restraints weight = 28848.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.086964 restraints weight = 19373.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.088308 restraints weight = 14273.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.089306 restraints weight = 11350.805| |-----------------------------------------------------------------------------| r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.6317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 16386 Z= 0.285 Angle : 0.699 7.196 22134 Z= 0.372 Chirality : 0.043 0.148 2360 Planarity : 0.005 0.075 2818 Dihedral : 11.534 178.811 2242 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.06 % Allowed : 3.32 % Favored : 96.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.85 (0.18), residues: 1932 helix: 1.05 (0.15), residues: 1125 sheet: -0.40 (0.39), residues: 136 loop : 0.15 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 117 TYR 0.026 0.002 TYR C 174 PHE 0.023 0.002 PHE C 168 TRP 0.019 0.002 TRP C 124 HIS 0.008 0.002 HIS A 372 Details of bonding type rmsd covalent geometry : bond 0.00575 (16386) covalent geometry : angle 0.69939 (22134) hydrogen bonds : bond 0.04282 ( 871) hydrogen bonds : angle 5.20178 ( 2571) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 643 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9502 (t0) cc_final: 0.9172 (t70) REVERT: A 91 PHE cc_start: 0.9503 (m-80) cc_final: 0.8693 (m-80) REVERT: A 116 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8607 (tt0) REVERT: A 147 GLN cc_start: 0.9472 (mm-40) cc_final: 0.8937 (mm110) REVERT: A 164 ARG cc_start: 0.8346 (ptm-80) cc_final: 0.7487 (ptm-80) REVERT: A 172 LEU cc_start: 0.9370 (mp) cc_final: 0.9088 (mp) REVERT: A 195 LEU cc_start: 0.9667 (mt) cc_final: 0.9401 (mt) REVERT: A 204 SER cc_start: 0.9417 (m) cc_final: 0.9195 (m) REVERT: A 227 MET cc_start: 0.9344 (mtm) cc_final: 0.9041 (mtm) REVERT: A 251 LEU cc_start: 0.9572 (tp) cc_final: 0.9245 (tp) REVERT: A 252 ASN cc_start: 0.9533 (t0) cc_final: 0.9019 (t0) REVERT: A 255 HIS cc_start: 0.8898 (t-90) cc_final: 0.8462 (t-90) REVERT: A 307 TYR cc_start: 0.9616 (t80) cc_final: 0.9186 (t80) REVERT: A 320 ASN cc_start: 0.9471 (m-40) cc_final: 0.9159 (m-40) REVERT: A 337 ILE cc_start: 0.9490 (mp) cc_final: 0.9153 (mp) REVERT: A 348 MET cc_start: 0.9340 (ptp) cc_final: 0.9092 (ptp) REVERT: A 350 ARG cc_start: 0.8813 (mmm-85) cc_final: 0.8373 (mmm-85) REVERT: A 361 GLN cc_start: 0.9570 (tt0) cc_final: 0.9203 (tp40) REVERT: A 377 LYS cc_start: 0.8957 (mttt) cc_final: 0.8674 (mtmt) REVERT: A 387 GLN cc_start: 0.9036 (mt0) cc_final: 0.8504 (mp10) REVERT: A 394 TYR cc_start: 0.9304 (m-80) cc_final: 0.8573 (m-80) REVERT: A 406 ASP cc_start: 0.8968 (m-30) cc_final: 0.8716 (m-30) REVERT: A 415 ASN cc_start: 0.9413 (t0) cc_final: 0.8715 (t0) REVERT: A 418 ASN cc_start: 0.9494 (m-40) cc_final: 0.8873 (m-40) REVERT: A 421 GLU cc_start: 0.9319 (tm-30) cc_final: 0.9082 (tm-30) REVERT: A 425 ILE cc_start: 0.9599 (mp) cc_final: 0.9391 (mp) REVERT: A 459 LYS cc_start: 0.9452 (mttp) cc_final: 0.9093 (mtmm) REVERT: A 468 LEU cc_start: 0.9766 (tp) cc_final: 0.9535 (tp) REVERT: A 472 LEU cc_start: 0.9726 (mt) cc_final: 0.9471 (mt) REVERT: A 493 MET cc_start: 0.9154 (tmm) cc_final: 0.8891 (tmm) REVERT: A 494 MET cc_start: 0.9388 (mtp) cc_final: 0.8984 (mtp) REVERT: A 496 ASN cc_start: 0.9561 (t0) cc_final: 0.8256 (t0) REVERT: A 500 ILE cc_start: 0.9699 (mt) cc_final: 0.8715 (mt) REVERT: A 515 ASP cc_start: 0.9346 (m-30) cc_final: 0.9094 (m-30) REVERT: A 522 TYR cc_start: 0.9270 (m-80) cc_final: 0.9032 (m-10) REVERT: A 570 MET cc_start: 0.9326 (mtp) cc_final: 0.8206 (mtp) REVERT: A 575 ARG cc_start: 0.9325 (mtm-85) cc_final: 0.8945 (mpp80) REVERT: A 586 TYR cc_start: 0.9006 (m-10) cc_final: 0.8768 (m-10) REVERT: A 598 MET cc_start: 0.9209 (mtp) cc_final: 0.8691 (mmm) REVERT: A 602 GLU cc_start: 0.8411 (pt0) cc_final: 0.6705 (pt0) REVERT: A 612 TYR cc_start: 0.8961 (m-10) cc_final: 0.8215 (m-80) REVERT: A 613 TYR cc_start: 0.8952 (t80) cc_final: 0.8298 (t80) REVERT: A 615 MET cc_start: 0.8879 (mmp) cc_final: 0.8265 (mmp) REVERT: A 645 GLN cc_start: 0.9087 (tp40) cc_final: 0.8869 (tp-100) REVERT: A 650 GLN cc_start: 0.8862 (mt0) cc_final: 0.7497 (mt0) REVERT: A 657 PHE cc_start: 0.8620 (m-80) cc_final: 0.8166 (m-80) REVERT: A 686 ARG cc_start: 0.8983 (mmt180) cc_final: 0.8640 (mmt180) REVERT: B 15 GLU cc_start: 0.9170 (tp30) cc_final: 0.8939 (tp30) REVERT: B 51 LEU cc_start: 0.9361 (tp) cc_final: 0.9156 (tp) REVERT: B 99 LYS cc_start: 0.9566 (mmmt) cc_final: 0.9301 (mmmm) REVERT: B 107 LYS cc_start: 0.9598 (mptt) cc_final: 0.9296 (mmtt) REVERT: B 115 LEU cc_start: 0.9610 (mt) cc_final: 0.9383 (mt) REVERT: B 136 LYS cc_start: 0.9643 (mmtp) cc_final: 0.9431 (mmmm) REVERT: B 144 MET cc_start: 0.9255 (mtm) cc_final: 0.8926 (mtm) REVERT: B 147 GLN cc_start: 0.9184 (mt0) cc_final: 0.8831 (mt0) REVERT: B 157 LEU cc_start: 0.9603 (tp) cc_final: 0.9118 (tp) REVERT: B 158 ASN cc_start: 0.9651 (m110) cc_final: 0.9084 (p0) REVERT: B 161 ARG cc_start: 0.9188 (ttm110) cc_final: 0.8478 (mtt180) REVERT: B 164 ARG cc_start: 0.9306 (ttp80) cc_final: 0.8687 (ttp80) REVERT: B 211 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8195 (mm-30) REVERT: B 251 LEU cc_start: 0.9449 (tp) cc_final: 0.9151 (tp) REVERT: B 286 ASP cc_start: 0.8818 (m-30) cc_final: 0.8038 (m-30) REVERT: B 290 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8968 (tm-30) REVERT: B 291 LEU cc_start: 0.9633 (mt) cc_final: 0.9275 (mt) REVERT: B 345 LYS cc_start: 0.9633 (tttt) cc_final: 0.9315 (tttt) REVERT: B 350 ARG cc_start: 0.8863 (mtp85) cc_final: 0.8157 (mtp85) REVERT: B 362 ASP cc_start: 0.9185 (m-30) cc_final: 0.8075 (m-30) REVERT: B 373 ILE cc_start: 0.9667 (mt) cc_final: 0.9403 (mt) REVERT: B 375 LYS cc_start: 0.9286 (mmtm) cc_final: 0.8997 (mmtm) REVERT: B 387 GLN cc_start: 0.7738 (mp10) cc_final: 0.7455 (mp10) REVERT: B 390 GLN cc_start: 0.9352 (mt0) cc_final: 0.9080 (mm110) REVERT: B 393 SER cc_start: 0.9557 (t) cc_final: 0.9323 (t) REVERT: B 398 ASP cc_start: 0.8974 (t70) cc_final: 0.8743 (t70) REVERT: B 403 ILE cc_start: 0.9392 (mp) cc_final: 0.8897 (tp) REVERT: B 413 SER cc_start: 0.9432 (m) cc_final: 0.8977 (t) REVERT: B 494 MET cc_start: 0.9560 (mtt) cc_final: 0.8903 (mtt) REVERT: B 571 TYR cc_start: 0.9331 (t80) cc_final: 0.8976 (t80) REVERT: B 615 MET cc_start: 0.8905 (mmp) cc_final: 0.8626 (mmp) REVERT: B 626 TYR cc_start: 0.9291 (m-80) cc_final: 0.9070 (m-80) REVERT: B 632 MET cc_start: 0.8271 (mmp) cc_final: 0.7914 (mmp) REVERT: B 636 LYS cc_start: 0.9688 (mptt) cc_final: 0.9476 (mmmt) REVERT: B 645 GLN cc_start: 0.9385 (tp-100) cc_final: 0.9168 (tp-100) REVERT: B 646 GLN cc_start: 0.9313 (pm20) cc_final: 0.9077 (pm20) REVERT: B 648 ILE cc_start: 0.9578 (mm) cc_final: 0.9376 (mm) REVERT: B 667 LEU cc_start: 0.9383 (tp) cc_final: 0.9153 (tt) REVERT: B 668 ASN cc_start: 0.9399 (m-40) cc_final: 0.8826 (m110) REVERT: B 677 ARG cc_start: 0.9668 (mmm160) cc_final: 0.9275 (mmm-85) REVERT: C 95 MET cc_start: 0.9072 (tmm) cc_final: 0.8779 (tmm) REVERT: C 98 ASN cc_start: 0.7663 (p0) cc_final: 0.7329 (p0) REVERT: C 101 HIS cc_start: 0.8535 (m90) cc_final: 0.7916 (m90) REVERT: D 25 ASN cc_start: 0.8292 (m-40) cc_final: 0.7921 (m-40) REVERT: D 69 GLN cc_start: 0.9402 (tp-100) cc_final: 0.9151 (tp40) REVERT: D 100 VAL cc_start: 0.5096 (t) cc_final: 0.4680 (t) REVERT: D 179 TYR cc_start: 0.7053 (t80) cc_final: 0.6814 (t80) REVERT: D 185 MET cc_start: 0.2420 (mmm) cc_final: 0.1796 (mpp) outliers start: 1 outliers final: 1 residues processed: 643 average time/residue: 0.1363 time to fit residues: 130.0099 Evaluate side-chains 566 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 565 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 99 optimal weight: 4.9990 chunk 46 optimal weight: 5.9990 chunk 120 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 126 optimal weight: 0.6980 chunk 129 optimal weight: 0.0980 chunk 32 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 115 optimal weight: 0.8980 chunk 168 optimal weight: 20.0000 chunk 157 optimal weight: 10.0000 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 313 HIS A 338 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN C 24 GLN C 186 GLN D 69 GLN D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.132830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.088582 restraints weight = 46045.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.091713 restraints weight = 27186.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.093854 restraints weight = 18101.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.095279 restraints weight = 13245.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.096289 restraints weight = 10430.962| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.6508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16386 Z= 0.126 Angle : 0.592 6.484 22134 Z= 0.313 Chirality : 0.042 0.250 2360 Planarity : 0.004 0.048 2818 Dihedral : 10.945 178.281 2242 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.06 % Allowed : 1.40 % Favored : 98.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.18), residues: 1932 helix: 1.24 (0.15), residues: 1132 sheet: -0.24 (0.41), residues: 128 loop : 0.15 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 235 TYR 0.048 0.002 TYR B 683 PHE 0.027 0.002 PHE B 487 TRP 0.025 0.001 TRP C 124 HIS 0.006 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00271 (16386) covalent geometry : angle 0.59151 (22134) hydrogen bonds : bond 0.03849 ( 871) hydrogen bonds : angle 4.90279 ( 2571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 667 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9524 (t0) cc_final: 0.9104 (t70) REVERT: A 62 GLN cc_start: 0.9196 (mp10) cc_final: 0.8565 (mp10) REVERT: A 95 MET cc_start: 0.9123 (tpt) cc_final: 0.8858 (tpt) REVERT: A 116 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8432 (tt0) REVERT: A 119 GLU cc_start: 0.9139 (mp0) cc_final: 0.8236 (tm-30) REVERT: A 143 LEU cc_start: 0.9626 (tp) cc_final: 0.9288 (tp) REVERT: A 147 GLN cc_start: 0.9280 (mm-40) cc_final: 0.8698 (mm110) REVERT: A 164 ARG cc_start: 0.8503 (ptm-80) cc_final: 0.7657 (ptm-80) REVERT: A 172 LEU cc_start: 0.9193 (mp) cc_final: 0.8868 (mp) REVERT: A 173 LEU cc_start: 0.9352 (mt) cc_final: 0.9119 (mt) REVERT: A 195 LEU cc_start: 0.9610 (mt) cc_final: 0.9390 (mt) REVERT: A 204 SER cc_start: 0.9428 (m) cc_final: 0.9146 (m) REVERT: A 227 MET cc_start: 0.9348 (mtm) cc_final: 0.9123 (mtm) REVERT: A 252 ASN cc_start: 0.9398 (t0) cc_final: 0.8713 (t0) REVERT: A 255 HIS cc_start: 0.8779 (t-90) cc_final: 0.8526 (t-90) REVERT: A 307 TYR cc_start: 0.9675 (t80) cc_final: 0.9221 (t80) REVERT: A 322 MET cc_start: 0.9126 (tpt) cc_final: 0.8798 (mmm) REVERT: A 342 LEU cc_start: 0.9617 (tp) cc_final: 0.9407 (tp) REVERT: A 348 MET cc_start: 0.9324 (ptp) cc_final: 0.9023 (ptp) REVERT: A 350 ARG cc_start: 0.8873 (mmm-85) cc_final: 0.8338 (mmm-85) REVERT: A 370 ASN cc_start: 0.9597 (m-40) cc_final: 0.9325 (m-40) REVERT: A 373 ILE cc_start: 0.9416 (mt) cc_final: 0.9145 (mt) REVERT: A 387 GLN cc_start: 0.8935 (mt0) cc_final: 0.8553 (mp10) REVERT: A 394 TYR cc_start: 0.9309 (m-80) cc_final: 0.8574 (m-80) REVERT: A 406 ASP cc_start: 0.8972 (m-30) cc_final: 0.8491 (m-30) REVERT: A 407 ILE cc_start: 0.9074 (mt) cc_final: 0.8649 (mt) REVERT: A 415 ASN cc_start: 0.9407 (t0) cc_final: 0.8705 (t0) REVERT: A 418 ASN cc_start: 0.9513 (m-40) cc_final: 0.8804 (m-40) REVERT: A 421 GLU cc_start: 0.9251 (tm-30) cc_final: 0.8963 (tm-30) REVERT: A 459 LYS cc_start: 0.9337 (mttp) cc_final: 0.8439 (mtmm) REVERT: A 466 MET cc_start: 0.9608 (ptt) cc_final: 0.9220 (ptt) REVERT: A 468 LEU cc_start: 0.9688 (tp) cc_final: 0.9410 (tp) REVERT: A 472 LEU cc_start: 0.9706 (mt) cc_final: 0.9496 (mt) REVERT: A 493 MET cc_start: 0.9148 (tmm) cc_final: 0.8780 (tmm) REVERT: A 494 MET cc_start: 0.9403 (mtp) cc_final: 0.9090 (mtp) REVERT: A 496 ASN cc_start: 0.9523 (t0) cc_final: 0.8275 (t0) REVERT: A 500 ILE cc_start: 0.9667 (mt) cc_final: 0.8609 (mt) REVERT: A 501 GLN cc_start: 0.9174 (tp-100) cc_final: 0.8848 (tp-100) REVERT: A 515 ASP cc_start: 0.9290 (m-30) cc_final: 0.9018 (m-30) REVERT: A 522 TYR cc_start: 0.9194 (m-80) cc_final: 0.8927 (m-10) REVERT: A 570 MET cc_start: 0.9448 (mtp) cc_final: 0.8065 (mtp) REVERT: A 575 ARG cc_start: 0.9244 (mtm-85) cc_final: 0.8882 (mpp80) REVERT: A 612 TYR cc_start: 0.9062 (m-80) cc_final: 0.8233 (m-80) REVERT: A 639 ASP cc_start: 0.9233 (m-30) cc_final: 0.9025 (m-30) REVERT: A 645 GLN cc_start: 0.9108 (tp40) cc_final: 0.8857 (tp-100) REVERT: A 646 GLN cc_start: 0.9522 (pt0) cc_final: 0.9276 (pt0) REVERT: A 650 GLN cc_start: 0.8812 (mt0) cc_final: 0.7628 (mt0) REVERT: B 15 GLU cc_start: 0.9167 (tp30) cc_final: 0.8535 (tp30) REVERT: B 51 LEU cc_start: 0.9210 (tp) cc_final: 0.8992 (tp) REVERT: B 99 LYS cc_start: 0.9583 (mmmt) cc_final: 0.8938 (mmmt) REVERT: B 107 LYS cc_start: 0.9642 (mptt) cc_final: 0.9348 (mmtt) REVERT: B 115 LEU cc_start: 0.9598 (mt) cc_final: 0.9397 (mt) REVERT: B 119 GLU cc_start: 0.9214 (mp0) cc_final: 0.8799 (tm-30) REVERT: B 120 ASP cc_start: 0.9246 (m-30) cc_final: 0.8910 (m-30) REVERT: B 136 LYS cc_start: 0.9661 (mmtp) cc_final: 0.9373 (mmmm) REVERT: B 139 GLU cc_start: 0.9478 (mp0) cc_final: 0.9235 (mp0) REVERT: B 144 MET cc_start: 0.9033 (mtm) cc_final: 0.8713 (mtm) REVERT: B 145 ILE cc_start: 0.9699 (tp) cc_final: 0.9435 (tp) REVERT: B 147 GLN cc_start: 0.9119 (mt0) cc_final: 0.8387 (mt0) REVERT: B 157 LEU cc_start: 0.9587 (tp) cc_final: 0.9178 (tp) REVERT: B 158 ASN cc_start: 0.9594 (m110) cc_final: 0.9008 (p0) REVERT: B 161 ARG cc_start: 0.8906 (ttm110) cc_final: 0.8331 (mtt180) REVERT: B 164 ARG cc_start: 0.9232 (ttp80) cc_final: 0.8683 (ttp80) REVERT: B 211 GLU cc_start: 0.8309 (mm-30) cc_final: 0.7624 (mm-30) REVERT: B 251 LEU cc_start: 0.9409 (tp) cc_final: 0.9120 (tp) REVERT: B 283 VAL cc_start: 0.9373 (t) cc_final: 0.9020 (t) REVERT: B 286 ASP cc_start: 0.8713 (m-30) cc_final: 0.8008 (m-30) REVERT: B 290 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8449 (tm-30) REVERT: B 296 LYS cc_start: 0.8935 (mmpt) cc_final: 0.8638 (mtmm) REVERT: B 301 PHE cc_start: 0.8916 (m-80) cc_final: 0.8573 (m-10) REVERT: B 312 GLN cc_start: 0.9258 (pm20) cc_final: 0.8755 (pm20) REVERT: B 322 MET cc_start: 0.8791 (mmm) cc_final: 0.8590 (mmm) REVERT: B 345 LYS cc_start: 0.9685 (tttt) cc_final: 0.9398 (tttt) REVERT: B 350 ARG cc_start: 0.8697 (mtp85) cc_final: 0.8281 (mtp85) REVERT: B 355 TYR cc_start: 0.9243 (m-10) cc_final: 0.8777 (m-10) REVERT: B 362 ASP cc_start: 0.9179 (m-30) cc_final: 0.8079 (m-30) REVERT: B 370 ASN cc_start: 0.9613 (m110) cc_final: 0.9358 (m110) REVERT: B 373 ILE cc_start: 0.9646 (mt) cc_final: 0.9355 (mt) REVERT: B 375 LYS cc_start: 0.9208 (mmtm) cc_final: 0.9002 (mmtm) REVERT: B 386 LEU cc_start: 0.8943 (mt) cc_final: 0.8461 (mt) REVERT: B 390 GLN cc_start: 0.9431 (mt0) cc_final: 0.9072 (mm-40) REVERT: B 398 ASP cc_start: 0.8805 (t70) cc_final: 0.8581 (t70) REVERT: B 399 GLU cc_start: 0.8919 (mp0) cc_final: 0.8554 (mp0) REVERT: B 403 ILE cc_start: 0.9328 (mp) cc_final: 0.8874 (tp) REVERT: B 425 ILE cc_start: 0.9628 (mp) cc_final: 0.9415 (mp) REVERT: B 440 SER cc_start: 0.9747 (t) cc_final: 0.9302 (p) REVERT: B 443 THR cc_start: 0.9386 (m) cc_final: 0.9090 (t) REVERT: B 494 MET cc_start: 0.9494 (mtt) cc_final: 0.8745 (mtt) REVERT: B 501 GLN cc_start: 0.9667 (tt0) cc_final: 0.9323 (mt0) REVERT: B 585 SER cc_start: 0.9061 (p) cc_final: 0.8630 (t) REVERT: B 588 GLN cc_start: 0.9493 (mm-40) cc_final: 0.9281 (mm110) REVERT: B 591 THR cc_start: 0.9185 (p) cc_final: 0.8825 (p) REVERT: B 606 TYR cc_start: 0.8664 (m-80) cc_final: 0.8118 (m-10) REVERT: B 615 MET cc_start: 0.8984 (mmp) cc_final: 0.8598 (mmp) REVERT: B 632 MET cc_start: 0.8408 (mmp) cc_final: 0.8150 (mmm) REVERT: B 636 LYS cc_start: 0.9704 (mptt) cc_final: 0.9448 (mmmt) REVERT: B 639 ASP cc_start: 0.9338 (m-30) cc_final: 0.8962 (m-30) REVERT: B 646 GLN cc_start: 0.9236 (pm20) cc_final: 0.8958 (pm20) REVERT: B 650 GLN cc_start: 0.6934 (mp10) cc_final: 0.6563 (mm-40) REVERT: B 667 LEU cc_start: 0.9384 (tp) cc_final: 0.9057 (tp) REVERT: B 668 ASN cc_start: 0.9365 (m-40) cc_final: 0.8806 (m110) REVERT: B 677 ARG cc_start: 0.9618 (mmm160) cc_final: 0.9296 (mmm-85) REVERT: B 684 TYR cc_start: 0.7601 (m-80) cc_final: 0.7292 (m-80) REVERT: D 69 GLN cc_start: 0.9312 (tp40) cc_final: 0.8977 (tm-30) REVERT: D 100 VAL cc_start: 0.5209 (t) cc_final: 0.4986 (t) REVERT: D 201 HIS cc_start: 0.7476 (m170) cc_final: 0.7218 (m90) outliers start: 1 outliers final: 0 residues processed: 667 average time/residue: 0.1363 time to fit residues: 134.9224 Evaluate side-chains 564 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 564 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 115 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 172 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 136 optimal weight: 7.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 HIS ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.129185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.085943 restraints weight = 46917.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.088937 restraints weight = 27942.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.090965 restraints weight = 18637.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.092280 restraints weight = 13818.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.093201 restraints weight = 10967.898| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.6876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16386 Z= 0.193 Angle : 0.634 9.468 22134 Z= 0.335 Chirality : 0.043 0.262 2360 Planarity : 0.004 0.047 2818 Dihedral : 10.886 170.256 2242 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (0.19), residues: 1932 helix: 1.11 (0.15), residues: 1136 sheet: -0.52 (0.40), residues: 140 loop : 0.17 (0.24), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 161 TYR 0.033 0.002 TYR B 683 PHE 0.022 0.002 PHE A 378 TRP 0.009 0.001 TRP A 623 HIS 0.010 0.002 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00406 (16386) covalent geometry : angle 0.63400 (22134) hydrogen bonds : bond 0.03919 ( 871) hydrogen bonds : angle 4.90666 ( 2571) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 648 time to evaluate : 0.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9464 (t0) cc_final: 0.9055 (t70) REVERT: A 62 GLN cc_start: 0.9173 (mp10) cc_final: 0.8739 (mp10) REVERT: A 116 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8543 (tt0) REVERT: A 119 GLU cc_start: 0.9236 (mp0) cc_final: 0.8309 (tm-30) REVERT: A 124 ILE cc_start: 0.9802 (mm) cc_final: 0.9590 (mm) REVERT: A 143 LEU cc_start: 0.9615 (tp) cc_final: 0.9262 (tp) REVERT: A 147 GLN cc_start: 0.9382 (mm-40) cc_final: 0.8687 (mm110) REVERT: A 148 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8695 (mt-10) REVERT: A 172 LEU cc_start: 0.9349 (mp) cc_final: 0.8897 (mp) REVERT: A 173 LEU cc_start: 0.9368 (mt) cc_final: 0.9099 (mt) REVERT: A 180 ASN cc_start: 0.9137 (m-40) cc_final: 0.8928 (t0) REVERT: A 195 LEU cc_start: 0.9614 (mt) cc_final: 0.9397 (mt) REVERT: A 204 SER cc_start: 0.9375 (m) cc_final: 0.8844 (p) REVERT: A 206 LEU cc_start: 0.9129 (mt) cc_final: 0.8923 (mt) REVERT: A 227 MET cc_start: 0.9282 (mtm) cc_final: 0.9049 (mtm) REVERT: A 251 LEU cc_start: 0.9618 (tp) cc_final: 0.9379 (tp) REVERT: A 252 ASN cc_start: 0.9463 (t0) cc_final: 0.8872 (t0) REVERT: A 255 HIS cc_start: 0.8828 (t-90) cc_final: 0.8523 (t-90) REVERT: A 307 TYR cc_start: 0.9655 (t80) cc_final: 0.9231 (t80) REVERT: A 312 GLN cc_start: 0.9368 (pt0) cc_final: 0.8906 (pt0) REVERT: A 345 LYS cc_start: 0.9691 (tttt) cc_final: 0.9481 (mttt) REVERT: A 348 MET cc_start: 0.9326 (ptp) cc_final: 0.9058 (ptp) REVERT: A 350 ARG cc_start: 0.8842 (mmm-85) cc_final: 0.8364 (mmm-85) REVERT: A 370 ASN cc_start: 0.9678 (m-40) cc_final: 0.9328 (m110) REVERT: A 387 GLN cc_start: 0.9076 (mt0) cc_final: 0.8577 (mp10) REVERT: A 394 TYR cc_start: 0.9236 (m-80) cc_final: 0.8423 (m-80) REVERT: A 406 ASP cc_start: 0.8984 (m-30) cc_final: 0.8570 (m-30) REVERT: A 415 ASN cc_start: 0.9625 (t0) cc_final: 0.8931 (t0) REVERT: A 418 ASN cc_start: 0.9515 (m-40) cc_final: 0.8964 (m-40) REVERT: A 421 GLU cc_start: 0.9211 (tm-30) cc_final: 0.8918 (tm-30) REVERT: A 468 LEU cc_start: 0.9728 (tp) cc_final: 0.9430 (tp) REVERT: A 472 LEU cc_start: 0.9731 (mt) cc_final: 0.9511 (mt) REVERT: A 493 MET cc_start: 0.9149 (tmm) cc_final: 0.8763 (tmm) REVERT: A 494 MET cc_start: 0.9407 (mtp) cc_final: 0.9104 (mtp) REVERT: A 500 ILE cc_start: 0.9686 (mt) cc_final: 0.8889 (mt) REVERT: A 501 GLN cc_start: 0.9223 (tp-100) cc_final: 0.8919 (tp-100) REVERT: A 515 ASP cc_start: 0.9385 (m-30) cc_final: 0.9014 (m-30) REVERT: A 522 TYR cc_start: 0.9204 (m-80) cc_final: 0.8923 (m-10) REVERT: A 570 MET cc_start: 0.9332 (mtp) cc_final: 0.7990 (mtp) REVERT: A 575 ARG cc_start: 0.9254 (mtm-85) cc_final: 0.8740 (mpp80) REVERT: A 588 GLN cc_start: 0.9286 (tp40) cc_final: 0.8927 (tp40) REVERT: A 612 TYR cc_start: 0.9007 (m-80) cc_final: 0.8460 (m-80) REVERT: A 615 MET cc_start: 0.8972 (mmp) cc_final: 0.8750 (mmp) REVERT: A 645 GLN cc_start: 0.9119 (tp40) cc_final: 0.8874 (tp-100) REVERT: A 646 GLN cc_start: 0.9562 (pt0) cc_final: 0.9325 (pt0) REVERT: A 650 GLN cc_start: 0.8890 (mt0) cc_final: 0.7502 (mt0) REVERT: A 655 THR cc_start: 0.8930 (m) cc_final: 0.8666 (m) REVERT: B 15 GLU cc_start: 0.9143 (tp30) cc_final: 0.8738 (tp30) REVERT: B 95 MET cc_start: 0.9199 (tpp) cc_final: 0.8614 (tpp) REVERT: B 99 LYS cc_start: 0.9595 (mmmt) cc_final: 0.9110 (mmmt) REVERT: B 115 LEU cc_start: 0.9618 (mt) cc_final: 0.9402 (mt) REVERT: B 119 GLU cc_start: 0.9270 (mp0) cc_final: 0.8826 (tm-30) REVERT: B 136 LYS cc_start: 0.9682 (mmtp) cc_final: 0.9342 (mmmm) REVERT: B 144 MET cc_start: 0.9112 (mtm) cc_final: 0.8814 (mtm) REVERT: B 147 GLN cc_start: 0.9166 (mt0) cc_final: 0.8572 (mt0) REVERT: B 157 LEU cc_start: 0.9531 (tp) cc_final: 0.9141 (tp) REVERT: B 158 ASN cc_start: 0.9613 (m110) cc_final: 0.8966 (p0) REVERT: B 161 ARG cc_start: 0.8933 (ttm110) cc_final: 0.8302 (mtt180) REVERT: B 164 ARG cc_start: 0.9233 (ttp80) cc_final: 0.8633 (ttp80) REVERT: B 211 GLU cc_start: 0.8360 (mm-30) cc_final: 0.7544 (mm-30) REVERT: B 227 MET cc_start: 0.9332 (mtm) cc_final: 0.9131 (mtm) REVERT: B 251 LEU cc_start: 0.9435 (tp) cc_final: 0.9158 (tp) REVERT: B 283 VAL cc_start: 0.9290 (t) cc_final: 0.9023 (t) REVERT: B 286 ASP cc_start: 0.8669 (m-30) cc_final: 0.7788 (m-30) REVERT: B 290 GLU cc_start: 0.9070 (tm-30) cc_final: 0.8130 (tm-30) REVERT: B 291 LEU cc_start: 0.9625 (mt) cc_final: 0.9284 (mt) REVERT: B 294 GLU cc_start: 0.9236 (mp0) cc_final: 0.8917 (mp0) REVERT: B 296 LYS cc_start: 0.9012 (mmpt) cc_final: 0.8692 (mtmm) REVERT: B 301 PHE cc_start: 0.8817 (m-80) cc_final: 0.8547 (m-10) REVERT: B 322 MET cc_start: 0.8822 (mmm) cc_final: 0.8580 (mmm) REVERT: B 333 LYS cc_start: 0.9508 (ttmm) cc_final: 0.9202 (ttmm) REVERT: B 344 GLU cc_start: 0.9272 (mm-30) cc_final: 0.9050 (mm-30) REVERT: B 345 LYS cc_start: 0.9690 (tttt) cc_final: 0.9424 (tttt) REVERT: B 350 ARG cc_start: 0.8781 (mtp85) cc_final: 0.8101 (mtp85) REVERT: B 362 ASP cc_start: 0.9089 (m-30) cc_final: 0.7869 (m-30) REVERT: B 370 ASN cc_start: 0.9599 (m110) cc_final: 0.9222 (m110) REVERT: B 375 LYS cc_start: 0.9175 (mmtm) cc_final: 0.8822 (mmtm) REVERT: B 386 LEU cc_start: 0.8971 (mt) cc_final: 0.8290 (mt) REVERT: B 398 ASP cc_start: 0.8860 (t70) cc_final: 0.8658 (t70) REVERT: B 399 GLU cc_start: 0.8972 (mp0) cc_final: 0.8663 (mp0) REVERT: B 403 ILE cc_start: 0.9334 (mp) cc_final: 0.8861 (tp) REVERT: B 413 SER cc_start: 0.9491 (m) cc_final: 0.9035 (t) REVERT: B 440 SER cc_start: 0.9763 (t) cc_final: 0.9553 (t) REVERT: B 494 MET cc_start: 0.9494 (mtt) cc_final: 0.8880 (mtt) REVERT: B 501 GLN cc_start: 0.9675 (tt0) cc_final: 0.9341 (mt0) REVERT: B 574 TYR cc_start: 0.8720 (m-10) cc_final: 0.8143 (m-10) REVERT: B 606 TYR cc_start: 0.8465 (m-80) cc_final: 0.7954 (m-10) REVERT: B 615 MET cc_start: 0.9056 (mmp) cc_final: 0.8684 (mmp) REVERT: B 627 LYS cc_start: 0.9374 (ttpt) cc_final: 0.9120 (ttpp) REVERT: B 632 MET cc_start: 0.8394 (mmp) cc_final: 0.7692 (mmp) REVERT: B 636 LYS cc_start: 0.9702 (mptt) cc_final: 0.9459 (mmmt) REVERT: B 639 ASP cc_start: 0.9343 (m-30) cc_final: 0.9014 (m-30) REVERT: B 650 GLN cc_start: 0.7227 (mp10) cc_final: 0.7024 (mm-40) REVERT: B 667 LEU cc_start: 0.9440 (tp) cc_final: 0.9165 (tt) REVERT: B 668 ASN cc_start: 0.9417 (m-40) cc_final: 0.8996 (m-40) REVERT: B 677 ARG cc_start: 0.9605 (mmm160) cc_final: 0.9369 (mmm-85) REVERT: C 98 ASN cc_start: 0.7220 (p0) cc_final: 0.6976 (p0) REVERT: C 100 VAL cc_start: 0.8647 (t) cc_final: 0.8191 (p) REVERT: D 69 GLN cc_start: 0.9405 (tp40) cc_final: 0.9077 (tm-30) REVERT: D 91 ASN cc_start: 0.8435 (m110) cc_final: 0.7926 (m110) REVERT: D 100 VAL cc_start: 0.5252 (t) cc_final: 0.5012 (t) REVERT: D 185 MET cc_start: 0.1398 (mmp) cc_final: 0.1172 (mpp) REVERT: D 201 HIS cc_start: 0.7179 (m170) cc_final: 0.6479 (m90) REVERT: D 312 VAL cc_start: 0.9782 (p) cc_final: 0.9485 (p) outliers start: 0 outliers final: 0 residues processed: 648 average time/residue: 0.1351 time to fit residues: 130.9423 Evaluate side-chains 551 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 551 time to evaluate : 0.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 10 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 74 optimal weight: 9.9990 chunk 105 optimal weight: 0.0970 chunk 56 optimal weight: 2.9990 chunk 186 optimal weight: 0.9980 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 9.9990 overall best weight: 1.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.134040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.090920 restraints weight = 45601.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.094146 restraints weight = 26838.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.096263 restraints weight = 17745.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.097658 restraints weight = 13033.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.098551 restraints weight = 10260.091| |-----------------------------------------------------------------------------| r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.7054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16386 Z= 0.139 Angle : 0.619 13.269 22134 Z= 0.323 Chirality : 0.042 0.190 2360 Planarity : 0.004 0.048 2818 Dihedral : 10.721 170.005 2242 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.90 (0.19), residues: 1932 helix: 1.11 (0.15), residues: 1139 sheet: -0.30 (0.42), residues: 128 loop : 0.06 (0.23), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 161 TYR 0.051 0.002 TYR B 683 PHE 0.036 0.002 PHE B 360 TRP 0.013 0.001 TRP C 124 HIS 0.019 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00307 (16386) covalent geometry : angle 0.61909 (22134) hydrogen bonds : bond 0.03726 ( 871) hydrogen bonds : angle 4.82797 ( 2571) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 638 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 638 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9450 (t0) cc_final: 0.9106 (t70) REVERT: A 124 ILE cc_start: 0.9797 (mm) cc_final: 0.9547 (mm) REVERT: A 143 LEU cc_start: 0.9621 (tp) cc_final: 0.9315 (tp) REVERT: A 172 LEU cc_start: 0.9304 (mp) cc_final: 0.8884 (mp) REVERT: A 173 LEU cc_start: 0.9342 (mt) cc_final: 0.9100 (mt) REVERT: A 176 ASN cc_start: 0.9059 (t0) cc_final: 0.8564 (m-40) REVERT: A 195 LEU cc_start: 0.9578 (mt) cc_final: 0.9361 (mt) REVERT: A 204 SER cc_start: 0.9360 (m) cc_final: 0.8824 (p) REVERT: A 206 LEU cc_start: 0.9116 (mt) cc_final: 0.8911 (mt) REVERT: A 252 ASN cc_start: 0.9431 (t0) cc_final: 0.8786 (t0) REVERT: A 255 HIS cc_start: 0.8768 (t-90) cc_final: 0.8488 (t-90) REVERT: A 307 TYR cc_start: 0.9646 (t80) cc_final: 0.9196 (t80) REVERT: A 322 MET cc_start: 0.8894 (tpp) cc_final: 0.8599 (mmm) REVERT: A 344 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8977 (mt-10) REVERT: A 350 ARG cc_start: 0.8901 (mmm-85) cc_final: 0.8445 (mmm-85) REVERT: A 370 ASN cc_start: 0.9649 (m-40) cc_final: 0.9280 (m110) REVERT: A 387 GLN cc_start: 0.9005 (mt0) cc_final: 0.8526 (mp10) REVERT: A 394 TYR cc_start: 0.9149 (m-80) cc_final: 0.8858 (m-80) REVERT: A 406 ASP cc_start: 0.8912 (m-30) cc_final: 0.8490 (m-30) REVERT: A 415 ASN cc_start: 0.9625 (t0) cc_final: 0.8923 (t0) REVERT: A 418 ASN cc_start: 0.9555 (m-40) cc_final: 0.8985 (m-40) REVERT: A 421 GLU cc_start: 0.9221 (tm-30) cc_final: 0.8939 (tm-30) REVERT: A 459 LYS cc_start: 0.9318 (mttp) cc_final: 0.8392 (mtmm) REVERT: A 468 LEU cc_start: 0.9686 (tp) cc_final: 0.9395 (tp) REVERT: A 472 LEU cc_start: 0.9717 (mt) cc_final: 0.9474 (mt) REVERT: A 493 MET cc_start: 0.9140 (tmm) cc_final: 0.8776 (tmm) REVERT: A 494 MET cc_start: 0.9421 (mtp) cc_final: 0.9110 (mtp) REVERT: A 500 ILE cc_start: 0.9682 (mt) cc_final: 0.8882 (mt) REVERT: A 515 ASP cc_start: 0.9236 (m-30) cc_final: 0.8950 (m-30) REVERT: A 570 MET cc_start: 0.9341 (mtp) cc_final: 0.8428 (mtp) REVERT: A 575 ARG cc_start: 0.9219 (mtm-85) cc_final: 0.8781 (mpp80) REVERT: A 602 GLU cc_start: 0.8520 (pp20) cc_final: 0.8098 (tm-30) REVERT: A 615 MET cc_start: 0.8952 (mmp) cc_final: 0.8748 (mmp) REVERT: A 640 MET cc_start: 0.9073 (tpp) cc_final: 0.8757 (tpp) REVERT: A 645 GLN cc_start: 0.9068 (tp40) cc_final: 0.8825 (tp-100) REVERT: A 650 GLN cc_start: 0.8837 (mt0) cc_final: 0.7467 (mt0) REVERT: B 15 GLU cc_start: 0.9096 (tp30) cc_final: 0.8472 (tp30) REVERT: B 95 MET cc_start: 0.9043 (tpp) cc_final: 0.8446 (tpp) REVERT: B 99 LYS cc_start: 0.9586 (mmmt) cc_final: 0.9152 (mmmt) REVERT: B 119 GLU cc_start: 0.9252 (mp0) cc_final: 0.8735 (tm-30) REVERT: B 120 ASP cc_start: 0.9287 (m-30) cc_final: 0.9032 (m-30) REVERT: B 136 LYS cc_start: 0.9661 (mmtp) cc_final: 0.9300 (mmmm) REVERT: B 144 MET cc_start: 0.8967 (mtm) cc_final: 0.8724 (mtm) REVERT: B 147 GLN cc_start: 0.9159 (mt0) cc_final: 0.8732 (mt0) REVERT: B 157 LEU cc_start: 0.9549 (tp) cc_final: 0.8559 (tp) REVERT: B 161 ARG cc_start: 0.8852 (ttm110) cc_final: 0.8208 (mtt180) REVERT: B 164 ARG cc_start: 0.9224 (ttp80) cc_final: 0.8980 (ttp80) REVERT: B 200 SER cc_start: 0.9071 (t) cc_final: 0.8829 (t) REVERT: B 211 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7693 (mm-30) REVERT: B 227 MET cc_start: 0.9369 (mtm) cc_final: 0.9116 (mtm) REVERT: B 251 LEU cc_start: 0.9450 (tp) cc_final: 0.9185 (tp) REVERT: B 286 ASP cc_start: 0.8639 (m-30) cc_final: 0.7950 (m-30) REVERT: B 290 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8413 (tm-30) REVERT: B 291 LEU cc_start: 0.9634 (mt) cc_final: 0.9366 (mt) REVERT: B 296 LYS cc_start: 0.8970 (mmpt) cc_final: 0.8639 (mtmm) REVERT: B 301 PHE cc_start: 0.8792 (m-80) cc_final: 0.8507 (m-10) REVERT: B 322 MET cc_start: 0.8913 (mmm) cc_final: 0.8685 (mmm) REVERT: B 333 LYS cc_start: 0.9481 (ttmm) cc_final: 0.9154 (ttmm) REVERT: B 344 GLU cc_start: 0.9273 (mm-30) cc_final: 0.9024 (mm-30) REVERT: B 345 LYS cc_start: 0.9729 (tttt) cc_final: 0.9429 (tttt) REVERT: B 350 ARG cc_start: 0.8663 (mtp85) cc_final: 0.8086 (mtp85) REVERT: B 362 ASP cc_start: 0.9058 (m-30) cc_final: 0.7928 (m-30) REVERT: B 370 ASN cc_start: 0.9507 (m110) cc_final: 0.9022 (m110) REVERT: B 398 ASP cc_start: 0.8817 (t70) cc_final: 0.8609 (t70) REVERT: B 399 GLU cc_start: 0.8979 (mp0) cc_final: 0.8670 (mp0) REVERT: B 441 GLU cc_start: 0.9035 (pm20) cc_final: 0.8767 (pm20) REVERT: B 494 MET cc_start: 0.9455 (mtt) cc_final: 0.8847 (mtt) REVERT: B 501 GLN cc_start: 0.9659 (tt0) cc_final: 0.9308 (mt0) REVERT: B 561 LEU cc_start: 0.9645 (tp) cc_final: 0.9441 (tp) REVERT: B 588 GLN cc_start: 0.9460 (mm110) cc_final: 0.9196 (mm110) REVERT: B 606 TYR cc_start: 0.8465 (m-80) cc_final: 0.8018 (m-10) REVERT: B 631 ASP cc_start: 0.9469 (m-30) cc_final: 0.9214 (m-30) REVERT: B 636 LYS cc_start: 0.9728 (mptt) cc_final: 0.9459 (mmmt) REVERT: B 639 ASP cc_start: 0.9327 (m-30) cc_final: 0.8986 (m-30) REVERT: B 650 GLN cc_start: 0.7267 (mp10) cc_final: 0.6956 (mp10) REVERT: B 667 LEU cc_start: 0.9456 (tp) cc_final: 0.9210 (tt) REVERT: B 668 ASN cc_start: 0.9434 (m-40) cc_final: 0.8993 (m-40) REVERT: B 675 HIS cc_start: 0.9418 (t-90) cc_final: 0.9211 (t-90) REVERT: C 101 HIS cc_start: 0.8323 (m90) cc_final: 0.8031 (m90) REVERT: D 69 GLN cc_start: 0.9382 (tp40) cc_final: 0.9066 (tm-30) REVERT: D 185 MET cc_start: 0.1891 (mmp) cc_final: 0.1488 (mpp) outliers start: 0 outliers final: 0 residues processed: 638 average time/residue: 0.1369 time to fit residues: 129.7915 Evaluate side-chains 562 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 562 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 7.9990 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 158 optimal weight: 10.0000 chunk 97 optimal weight: 2.9990 chunk 151 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN B 447 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 HIS ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.136193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.092540 restraints weight = 46764.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.095654 restraints weight = 27418.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.097772 restraints weight = 18280.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.099251 restraints weight = 13446.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.100245 restraints weight = 10546.966| |-----------------------------------------------------------------------------| r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.7345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16386 Z= 0.149 Angle : 0.623 9.656 22134 Z= 0.328 Chirality : 0.043 0.189 2360 Planarity : 0.004 0.049 2818 Dihedral : 10.730 168.249 2242 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.06 % Allowed : 0.82 % Favored : 99.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.79 (0.19), residues: 1932 helix: 1.06 (0.15), residues: 1126 sheet: -0.38 (0.43), residues: 128 loop : -0.01 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 161 TYR 0.048 0.002 TYR C 142 PHE 0.025 0.002 PHE B 487 TRP 0.011 0.001 TRP C 124 HIS 0.012 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00327 (16386) covalent geometry : angle 0.62261 (22134) hydrogen bonds : bond 0.03697 ( 871) hydrogen bonds : angle 4.90617 ( 2571) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 618 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 617 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9459 (t0) cc_final: 0.9116 (t70) REVERT: A 91 PHE cc_start: 0.9501 (m-80) cc_final: 0.8864 (m-80) REVERT: A 95 MET cc_start: 0.9160 (tpt) cc_final: 0.8369 (tpp) REVERT: A 101 TYR cc_start: 0.9385 (m-80) cc_final: 0.9149 (m-10) REVERT: A 116 GLU cc_start: 0.8802 (tt0) cc_final: 0.8471 (tt0) REVERT: A 119 GLU cc_start: 0.9089 (mp0) cc_final: 0.8763 (mt-10) REVERT: A 143 LEU cc_start: 0.9621 (tp) cc_final: 0.9273 (tp) REVERT: A 148 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8667 (mt-10) REVERT: A 172 LEU cc_start: 0.9310 (mp) cc_final: 0.8917 (mp) REVERT: A 173 LEU cc_start: 0.9360 (mt) cc_final: 0.9058 (mt) REVERT: A 176 ASN cc_start: 0.9023 (t0) cc_final: 0.8550 (m-40) REVERT: A 188 ILE cc_start: 0.9618 (mt) cc_final: 0.9410 (mt) REVERT: A 195 LEU cc_start: 0.9550 (mt) cc_final: 0.9346 (mt) REVERT: A 204 SER cc_start: 0.9394 (m) cc_final: 0.8850 (p) REVERT: A 251 LEU cc_start: 0.9614 (tp) cc_final: 0.9368 (tp) REVERT: A 252 ASN cc_start: 0.9361 (t0) cc_final: 0.8915 (t0) REVERT: A 255 HIS cc_start: 0.8761 (t-90) cc_final: 0.8524 (t-90) REVERT: A 301 PHE cc_start: 0.9261 (m-10) cc_final: 0.8802 (m-10) REVERT: A 307 TYR cc_start: 0.9656 (t80) cc_final: 0.9209 (t80) REVERT: A 322 MET cc_start: 0.8833 (tpp) cc_final: 0.8525 (mmm) REVERT: A 342 LEU cc_start: 0.9690 (tp) cc_final: 0.9487 (tp) REVERT: A 350 ARG cc_start: 0.8915 (mmm-85) cc_final: 0.8452 (mmm-85) REVERT: A 370 ASN cc_start: 0.9615 (m-40) cc_final: 0.9234 (m110) REVERT: A 387 GLN cc_start: 0.9209 (mt0) cc_final: 0.8631 (mp10) REVERT: A 394 TYR cc_start: 0.9170 (m-80) cc_final: 0.8905 (m-80) REVERT: A 406 ASP cc_start: 0.8981 (m-30) cc_final: 0.8564 (m-30) REVERT: A 415 ASN cc_start: 0.9630 (t0) cc_final: 0.8860 (t0) REVERT: A 418 ASN cc_start: 0.9532 (m-40) cc_final: 0.8975 (m-40) REVERT: A 421 GLU cc_start: 0.9219 (tm-30) cc_final: 0.8944 (tm-30) REVERT: A 459 LYS cc_start: 0.9322 (mttp) cc_final: 0.8384 (mtmm) REVERT: A 468 LEU cc_start: 0.9708 (tp) cc_final: 0.9416 (tp) REVERT: A 472 LEU cc_start: 0.9734 (mt) cc_final: 0.9488 (mt) REVERT: A 493 MET cc_start: 0.9142 (tmm) cc_final: 0.8766 (tmm) REVERT: A 494 MET cc_start: 0.9422 (mtp) cc_final: 0.9106 (mtp) REVERT: A 500 ILE cc_start: 0.9689 (mt) cc_final: 0.8930 (mt) REVERT: A 515 ASP cc_start: 0.9259 (m-30) cc_final: 0.9004 (m-30) REVERT: A 522 TYR cc_start: 0.9160 (m-10) cc_final: 0.8770 (m-10) REVERT: A 570 MET cc_start: 0.9333 (mtp) cc_final: 0.8141 (mtp) REVERT: A 575 ARG cc_start: 0.9286 (mtm-85) cc_final: 0.8646 (mpp80) REVERT: A 615 MET cc_start: 0.8953 (mmp) cc_final: 0.8726 (mmp) REVERT: A 640 MET cc_start: 0.9035 (tpp) cc_final: 0.8763 (tpp) REVERT: A 645 GLN cc_start: 0.9038 (tp40) cc_final: 0.8398 (tp-100) REVERT: A 650 GLN cc_start: 0.8770 (mt0) cc_final: 0.7345 (mt0) REVERT: A 655 THR cc_start: 0.8810 (m) cc_final: 0.8569 (m) REVERT: A 657 PHE cc_start: 0.8511 (m-80) cc_final: 0.8276 (m-80) REVERT: A 680 LYS cc_start: 0.8718 (mttt) cc_final: 0.8187 (mttt) REVERT: B 15 GLU cc_start: 0.9112 (tp30) cc_final: 0.8660 (tp30) REVERT: B 62 GLN cc_start: 0.9360 (mp10) cc_final: 0.9058 (mp10) REVERT: B 95 MET cc_start: 0.9091 (tpp) cc_final: 0.8489 (tpp) REVERT: B 99 LYS cc_start: 0.9581 (mmmt) cc_final: 0.9156 (mmmt) REVERT: B 119 GLU cc_start: 0.9283 (mp0) cc_final: 0.8749 (tm-30) REVERT: B 120 ASP cc_start: 0.9237 (m-30) cc_final: 0.9037 (m-30) REVERT: B 136 LYS cc_start: 0.9684 (mmtp) cc_final: 0.9315 (mmmm) REVERT: B 211 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7582 (mm-30) REVERT: B 218 ASN cc_start: 0.9506 (t0) cc_final: 0.9248 (t0) REVERT: B 227 MET cc_start: 0.9315 (mtm) cc_final: 0.9092 (mtm) REVERT: B 251 LEU cc_start: 0.9460 (tp) cc_final: 0.9231 (tp) REVERT: B 286 ASP cc_start: 0.8584 (m-30) cc_final: 0.7718 (m-30) REVERT: B 290 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8355 (tm-30) REVERT: B 291 LEU cc_start: 0.9597 (mt) cc_final: 0.9294 (mt) REVERT: B 296 LYS cc_start: 0.8958 (mmpt) cc_final: 0.8612 (mtmm) REVERT: B 301 PHE cc_start: 0.8766 (m-80) cc_final: 0.8531 (m-10) REVERT: B 312 GLN cc_start: 0.9283 (pm20) cc_final: 0.8783 (pm20) REVERT: B 314 MET cc_start: 0.9028 (ttt) cc_final: 0.8271 (tmm) REVERT: B 319 MET cc_start: 0.9003 (mmp) cc_final: 0.8427 (mmp) REVERT: B 322 MET cc_start: 0.8789 (mmm) cc_final: 0.8555 (mmm) REVERT: B 333 LYS cc_start: 0.9474 (ttmm) cc_final: 0.9163 (ttmm) REVERT: B 344 GLU cc_start: 0.9273 (mm-30) cc_final: 0.9016 (mm-30) REVERT: B 345 LYS cc_start: 0.9714 (tttt) cc_final: 0.9427 (tttt) REVERT: B 350 ARG cc_start: 0.8738 (mtp85) cc_final: 0.8120 (mtp85) REVERT: B 362 ASP cc_start: 0.9041 (m-30) cc_final: 0.7954 (m-30) REVERT: B 370 ASN cc_start: 0.9590 (m110) cc_final: 0.9250 (m110) REVERT: B 373 ILE cc_start: 0.9477 (mt) cc_final: 0.9244 (mt) REVERT: B 398 ASP cc_start: 0.8822 (t70) cc_final: 0.8497 (t70) REVERT: B 399 GLU cc_start: 0.8878 (mp0) cc_final: 0.8675 (mp0) REVERT: B 403 ILE cc_start: 0.9213 (mm) cc_final: 0.8817 (tp) REVERT: B 413 SER cc_start: 0.9504 (m) cc_final: 0.9035 (t) REVERT: B 447 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.7893 (m110) REVERT: B 494 MET cc_start: 0.9474 (mtt) cc_final: 0.8853 (mtt) REVERT: B 501 GLN cc_start: 0.9654 (tt0) cc_final: 0.9300 (mt0) REVERT: B 561 LEU cc_start: 0.9639 (tp) cc_final: 0.9425 (tp) REVERT: B 576 LEU cc_start: 0.9318 (mt) cc_final: 0.9061 (mt) REVERT: B 588 GLN cc_start: 0.9425 (mm110) cc_final: 0.9214 (mm-40) REVERT: B 606 TYR cc_start: 0.8520 (m-80) cc_final: 0.8039 (m-10) REVERT: B 631 ASP cc_start: 0.9450 (m-30) cc_final: 0.9062 (m-30) REVERT: B 636 LYS cc_start: 0.9712 (mptt) cc_final: 0.9399 (mmmt) REVERT: B 639 ASP cc_start: 0.9221 (m-30) cc_final: 0.8859 (m-30) REVERT: B 646 GLN cc_start: 0.9269 (pm20) cc_final: 0.9063 (pm20) REVERT: B 650 GLN cc_start: 0.7279 (mp10) cc_final: 0.6841 (mp10) REVERT: B 667 LEU cc_start: 0.9474 (tp) cc_final: 0.9251 (tt) REVERT: B 668 ASN cc_start: 0.9354 (m-40) cc_final: 0.8965 (m-40) REVERT: C 100 VAL cc_start: 0.8679 (t) cc_final: 0.8272 (p) REVERT: C 311 THR cc_start: 0.8274 (t) cc_final: 0.7944 (t) REVERT: D 69 GLN cc_start: 0.9390 (tp40) cc_final: 0.9143 (tm-30) REVERT: D 185 MET cc_start: 0.1976 (mmp) cc_final: 0.1513 (mpp) outliers start: 1 outliers final: 0 residues processed: 617 average time/residue: 0.1351 time to fit residues: 124.7184 Evaluate side-chains 552 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 551 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 20.0000 chunk 133 optimal weight: 0.8980 chunk 149 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 100 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 77 optimal weight: 0.6980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN B 474 GLN C 132 GLN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.135814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.092881 restraints weight = 46865.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.096164 restraints weight = 27464.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.098333 restraints weight = 18056.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.099814 restraints weight = 13063.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.100795 restraints weight = 10096.593| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3242 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3242 r_free = 0.3242 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3242 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.7552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16386 Z= 0.158 Angle : 0.666 13.598 22134 Z= 0.347 Chirality : 0.044 0.238 2360 Planarity : 0.004 0.053 2818 Dihedral : 10.678 163.719 2242 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 16.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.06 % Allowed : 0.17 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.19), residues: 1932 helix: 1.01 (0.15), residues: 1125 sheet: -0.32 (0.44), residues: 128 loop : -0.11 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 161 TYR 0.045 0.002 TYR C 142 PHE 0.026 0.002 PHE B 360 TRP 0.012 0.001 TRP C 124 HIS 0.011 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00344 (16386) covalent geometry : angle 0.66626 (22134) hydrogen bonds : bond 0.03823 ( 871) hydrogen bonds : angle 5.00467 ( 2571) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 617 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 616 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9484 (t0) cc_final: 0.9139 (t70) REVERT: A 91 PHE cc_start: 0.9477 (m-80) cc_final: 0.8959 (m-80) REVERT: A 116 GLU cc_start: 0.8662 (tt0) cc_final: 0.7824 (tt0) REVERT: A 119 GLU cc_start: 0.9069 (mp0) cc_final: 0.8740 (mt-10) REVERT: A 143 LEU cc_start: 0.9615 (tp) cc_final: 0.9271 (tp) REVERT: A 147 GLN cc_start: 0.9326 (mm110) cc_final: 0.9038 (mm110) REVERT: A 172 LEU cc_start: 0.9298 (mp) cc_final: 0.8932 (mp) REVERT: A 173 LEU cc_start: 0.9419 (mt) cc_final: 0.9181 (mt) REVERT: A 176 ASN cc_start: 0.9056 (t0) cc_final: 0.8624 (m-40) REVERT: A 180 ASN cc_start: 0.9067 (m-40) cc_final: 0.8513 (m-40) REVERT: A 187 ASP cc_start: 0.9372 (t70) cc_final: 0.9081 (t0) REVERT: A 190 MET cc_start: 0.9656 (mmm) cc_final: 0.9287 (mmm) REVERT: A 204 SER cc_start: 0.9409 (m) cc_final: 0.8901 (p) REVERT: A 235 ARG cc_start: 0.9050 (ptp90) cc_final: 0.8592 (mtm110) REVERT: A 252 ASN cc_start: 0.9403 (t0) cc_final: 0.8992 (t0) REVERT: A 255 HIS cc_start: 0.8780 (t-90) cc_final: 0.8517 (t-90) REVERT: A 301 PHE cc_start: 0.9260 (m-10) cc_final: 0.8717 (m-10) REVERT: A 307 TYR cc_start: 0.9645 (t80) cc_final: 0.9176 (t80) REVERT: A 322 MET cc_start: 0.8844 (tpp) cc_final: 0.8544 (mmm) REVERT: A 350 ARG cc_start: 0.8978 (mmm-85) cc_final: 0.8467 (mmm-85) REVERT: A 370 ASN cc_start: 0.9617 (m-40) cc_final: 0.9245 (m110) REVERT: A 387 GLN cc_start: 0.9252 (mt0) cc_final: 0.8631 (mp10) REVERT: A 394 TYR cc_start: 0.9194 (m-80) cc_final: 0.8903 (m-80) REVERT: A 406 ASP cc_start: 0.8942 (m-30) cc_final: 0.8553 (m-30) REVERT: A 415 ASN cc_start: 0.9635 (t0) cc_final: 0.8703 (t0) REVERT: A 418 ASN cc_start: 0.9525 (m-40) cc_final: 0.8954 (m-40) REVERT: A 421 GLU cc_start: 0.9105 (tm-30) cc_final: 0.8806 (tm-30) REVERT: A 466 MET cc_start: 0.9653 (ptt) cc_final: 0.9298 (ptt) REVERT: A 468 LEU cc_start: 0.9729 (tp) cc_final: 0.9427 (tp) REVERT: A 472 LEU cc_start: 0.9739 (mt) cc_final: 0.9483 (mt) REVERT: A 493 MET cc_start: 0.9132 (tmm) cc_final: 0.8737 (tmm) REVERT: A 494 MET cc_start: 0.9415 (mtp) cc_final: 0.9055 (mtp) REVERT: A 500 ILE cc_start: 0.9699 (mt) cc_final: 0.9469 (mt) REVERT: A 515 ASP cc_start: 0.9261 (m-30) cc_final: 0.8990 (m-30) REVERT: A 522 TYR cc_start: 0.9087 (m-10) cc_final: 0.8452 (m-10) REVERT: A 570 MET cc_start: 0.9308 (mtp) cc_final: 0.8043 (mtp) REVERT: A 615 MET cc_start: 0.9016 (mmp) cc_final: 0.8777 (mmp) REVERT: A 640 MET cc_start: 0.9008 (tpp) cc_final: 0.8778 (tpp) REVERT: A 645 GLN cc_start: 0.9153 (tp40) cc_final: 0.8493 (tp-100) REVERT: A 650 GLN cc_start: 0.8838 (mt0) cc_final: 0.7407 (mt0) REVERT: A 655 THR cc_start: 0.8728 (m) cc_final: 0.8457 (m) REVERT: A 680 LYS cc_start: 0.8741 (mttt) cc_final: 0.8540 (mttt) REVERT: B 15 GLU cc_start: 0.9092 (tp30) cc_final: 0.8650 (tp30) REVERT: B 95 MET cc_start: 0.9127 (tpp) cc_final: 0.8546 (tpp) REVERT: B 99 LYS cc_start: 0.9582 (mmmt) cc_final: 0.9167 (mmmt) REVERT: B 119 GLU cc_start: 0.9275 (mp0) cc_final: 0.8752 (tm-30) REVERT: B 120 ASP cc_start: 0.9260 (m-30) cc_final: 0.9039 (m-30) REVERT: B 136 LYS cc_start: 0.9687 (mmtp) cc_final: 0.9309 (mmmm) REVERT: B 157 LEU cc_start: 0.9548 (tp) cc_final: 0.9201 (tp) REVERT: B 161 ARG cc_start: 0.8769 (ttm110) cc_final: 0.8234 (mtp85) REVERT: B 211 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7585 (mm-30) REVERT: B 227 MET cc_start: 0.9399 (mtm) cc_final: 0.9081 (mtm) REVERT: B 251 LEU cc_start: 0.9463 (tp) cc_final: 0.9246 (tp) REVERT: B 283 VAL cc_start: 0.9415 (t) cc_final: 0.9000 (t) REVERT: B 286 ASP cc_start: 0.8638 (m-30) cc_final: 0.7892 (m-30) REVERT: B 290 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8367 (tm-30) REVERT: B 291 LEU cc_start: 0.9592 (mt) cc_final: 0.9278 (mt) REVERT: B 296 LYS cc_start: 0.8939 (mmpt) cc_final: 0.8608 (mtmm) REVERT: B 301 PHE cc_start: 0.8754 (m-80) cc_final: 0.8460 (m-10) REVERT: B 322 MET cc_start: 0.8786 (mmm) cc_final: 0.8566 (mmm) REVERT: B 333 LYS cc_start: 0.9480 (ttmm) cc_final: 0.9167 (ttmm) REVERT: B 342 LEU cc_start: 0.9751 (tp) cc_final: 0.9492 (tp) REVERT: B 344 GLU cc_start: 0.9278 (mm-30) cc_final: 0.8976 (mm-30) REVERT: B 345 LYS cc_start: 0.9719 (tttt) cc_final: 0.9440 (tttt) REVERT: B 346 LEU cc_start: 0.9689 (mt) cc_final: 0.9458 (mt) REVERT: B 359 MET cc_start: 0.9143 (ttm) cc_final: 0.8891 (ttm) REVERT: B 362 ASP cc_start: 0.9061 (m-30) cc_final: 0.7939 (m-30) REVERT: B 370 ASN cc_start: 0.9607 (m110) cc_final: 0.9206 (m110) REVERT: B 390 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8501 (mm-40) REVERT: B 398 ASP cc_start: 0.8762 (t70) cc_final: 0.8440 (t70) REVERT: B 399 GLU cc_start: 0.8888 (mp0) cc_final: 0.8657 (mp0) REVERT: B 403 ILE cc_start: 0.9197 (mm) cc_final: 0.8792 (tp) REVERT: B 441 GLU cc_start: 0.9109 (pm20) cc_final: 0.8906 (pm20) REVERT: B 447 ASN cc_start: 0.8811 (m110) cc_final: 0.8196 (m-40) REVERT: B 477 ILE cc_start: 0.9615 (mp) cc_final: 0.9087 (tp) REVERT: B 501 GLN cc_start: 0.9646 (tt0) cc_final: 0.9318 (mt0) REVERT: B 588 GLN cc_start: 0.9460 (mm110) cc_final: 0.9113 (mm-40) REVERT: B 606 TYR cc_start: 0.8523 (m-80) cc_final: 0.8028 (m-10) REVERT: B 631 ASP cc_start: 0.9448 (m-30) cc_final: 0.9060 (m-30) REVERT: B 634 MET cc_start: 0.9499 (mmt) cc_final: 0.9288 (mmp) REVERT: B 636 LYS cc_start: 0.9687 (mptt) cc_final: 0.9370 (mmmt) REVERT: B 639 ASP cc_start: 0.9264 (m-30) cc_final: 0.8960 (m-30) REVERT: B 667 LEU cc_start: 0.9476 (tp) cc_final: 0.9241 (tt) REVERT: B 668 ASN cc_start: 0.9388 (m-40) cc_final: 0.8962 (m-40) REVERT: B 683 TYR cc_start: 0.8362 (t80) cc_final: 0.7745 (t80) REVERT: C 100 VAL cc_start: 0.8590 (t) cc_final: 0.8261 (p) REVERT: C 101 HIS cc_start: 0.8075 (m90) cc_final: 0.7816 (m90) REVERT: C 261 ARG cc_start: 0.4811 (mtm-85) cc_final: 0.4271 (ptp-170) REVERT: C 318 ASP cc_start: 0.9453 (p0) cc_final: 0.9202 (p0) REVERT: D 69 GLN cc_start: 0.9474 (tp40) cc_final: 0.9021 (tm-30) REVERT: D 74 MET cc_start: 0.6544 (mtm) cc_final: 0.6179 (mtm) REVERT: D 185 MET cc_start: 0.2170 (mmp) cc_final: 0.1741 (mpp) REVERT: D 205 VAL cc_start: 0.9259 (t) cc_final: 0.8932 (t) outliers start: 1 outliers final: 0 residues processed: 616 average time/residue: 0.1342 time to fit residues: 123.4145 Evaluate side-chains 545 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 545 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 189 optimal weight: 0.0980 chunk 181 optimal weight: 10.0000 chunk 165 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 132 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 186 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.139870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.097222 restraints weight = 45847.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.100317 restraints weight = 26715.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.102413 restraints weight = 17817.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.103981 restraints weight = 13088.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.105079 restraints weight = 10281.602| |-----------------------------------------------------------------------------| r_work (final): 0.3278 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3278 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.7738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16386 Z= 0.132 Angle : 0.656 10.923 22134 Z= 0.342 Chirality : 0.044 0.259 2360 Planarity : 0.004 0.057 2818 Dihedral : 10.494 163.486 2242 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.06 % Allowed : 0.35 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.63 (0.19), residues: 1932 helix: 0.95 (0.15), residues: 1125 sheet: -0.31 (0.45), residues: 128 loop : -0.15 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 161 TYR 0.047 0.002 TYR C 142 PHE 0.026 0.002 PHE B 360 TRP 0.013 0.001 TRP C 124 HIS 0.010 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00293 (16386) covalent geometry : angle 0.65570 (22134) hydrogen bonds : bond 0.03774 ( 871) hydrogen bonds : angle 4.91821 ( 2571) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 620 time to evaluate : 0.647 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.9464 (mp0) cc_final: 0.9240 (mp0) REVERT: A 91 PHE cc_start: 0.9448 (m-80) cc_final: 0.8964 (m-80) REVERT: A 95 MET cc_start: 0.8182 (tpt) cc_final: 0.7462 (tpp) REVERT: A 119 GLU cc_start: 0.9078 (mp0) cc_final: 0.8724 (mt-10) REVERT: A 143 LEU cc_start: 0.9630 (tp) cc_final: 0.9300 (tp) REVERT: A 147 GLN cc_start: 0.9289 (mm110) cc_final: 0.8986 (mm110) REVERT: A 172 LEU cc_start: 0.9281 (mp) cc_final: 0.8933 (mp) REVERT: A 173 LEU cc_start: 0.9417 (mt) cc_final: 0.9132 (mt) REVERT: A 176 ASN cc_start: 0.9043 (t0) cc_final: 0.8622 (m-40) REVERT: A 180 ASN cc_start: 0.8984 (m-40) cc_final: 0.8526 (m-40) REVERT: A 190 MET cc_start: 0.9536 (mmm) cc_final: 0.9009 (mmm) REVERT: A 204 SER cc_start: 0.9408 (m) cc_final: 0.8883 (p) REVERT: A 251 LEU cc_start: 0.9613 (tp) cc_final: 0.9346 (tp) REVERT: A 252 ASN cc_start: 0.9274 (t0) cc_final: 0.8956 (t0) REVERT: A 266 LYS cc_start: 0.9175 (mttp) cc_final: 0.8795 (mttp) REVERT: A 301 PHE cc_start: 0.9175 (m-10) cc_final: 0.8667 (m-10) REVERT: A 307 TYR cc_start: 0.9653 (t80) cc_final: 0.9156 (t80) REVERT: A 322 MET cc_start: 0.8855 (tpp) cc_final: 0.8548 (mmm) REVERT: A 342 LEU cc_start: 0.9710 (tp) cc_final: 0.9476 (tp) REVERT: A 350 ARG cc_start: 0.9019 (mmm-85) cc_final: 0.8509 (mmm-85) REVERT: A 370 ASN cc_start: 0.9545 (m-40) cc_final: 0.9121 (m110) REVERT: A 387 GLN cc_start: 0.9219 (mt0) cc_final: 0.8736 (mp10) REVERT: A 394 TYR cc_start: 0.9131 (m-80) cc_final: 0.8874 (m-80) REVERT: A 406 ASP cc_start: 0.8989 (m-30) cc_final: 0.8614 (m-30) REVERT: A 415 ASN cc_start: 0.9606 (t0) cc_final: 0.8822 (t0) REVERT: A 418 ASN cc_start: 0.9508 (m-40) cc_final: 0.8915 (m-40) REVERT: A 421 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8795 (tm-30) REVERT: A 459 LYS cc_start: 0.9331 (mttp) cc_final: 0.8862 (mtmm) REVERT: A 466 MET cc_start: 0.9577 (ptt) cc_final: 0.9192 (ptt) REVERT: A 468 LEU cc_start: 0.9708 (tp) cc_final: 0.9435 (tp) REVERT: A 479 TYR cc_start: 0.9009 (t80) cc_final: 0.8808 (t80) REVERT: A 493 MET cc_start: 0.9131 (tmm) cc_final: 0.8755 (tmm) REVERT: A 494 MET cc_start: 0.9404 (mtp) cc_final: 0.9065 (mtp) REVERT: A 500 ILE cc_start: 0.9698 (mt) cc_final: 0.9377 (mt) REVERT: A 515 ASP cc_start: 0.9262 (m-30) cc_final: 0.9021 (m-30) REVERT: A 522 TYR cc_start: 0.9042 (m-10) cc_final: 0.8674 (m-10) REVERT: A 570 MET cc_start: 0.9272 (mtp) cc_final: 0.7943 (mtp) REVERT: A 586 TYR cc_start: 0.8978 (m-10) cc_final: 0.8590 (m-10) REVERT: A 612 TYR cc_start: 0.8630 (m-80) cc_final: 0.8330 (m-80) REVERT: A 615 MET cc_start: 0.9120 (mmp) cc_final: 0.8858 (mmp) REVERT: A 639 ASP cc_start: 0.9171 (m-30) cc_final: 0.8953 (m-30) REVERT: A 640 MET cc_start: 0.9011 (tpp) cc_final: 0.8808 (tpp) REVERT: A 645 GLN cc_start: 0.9091 (tp40) cc_final: 0.8420 (tp-100) REVERT: A 650 GLN cc_start: 0.8754 (mt0) cc_final: 0.7379 (mt0) REVERT: A 668 ASN cc_start: 0.9570 (m110) cc_final: 0.9309 (m-40) REVERT: A 680 LYS cc_start: 0.8737 (mttt) cc_final: 0.8218 (mttt) REVERT: B 15 GLU cc_start: 0.9075 (tp30) cc_final: 0.8469 (tp30) REVERT: B 29 ASP cc_start: 0.9433 (t70) cc_final: 0.9165 (t70) REVERT: B 95 MET cc_start: 0.9071 (tpp) cc_final: 0.8514 (tpp) REVERT: B 99 LYS cc_start: 0.9534 (mmmt) cc_final: 0.9144 (mmmt) REVERT: B 136 LYS cc_start: 0.9687 (mmtp) cc_final: 0.9304 (mmmm) REVERT: B 157 LEU cc_start: 0.9539 (tp) cc_final: 0.9190 (tp) REVERT: B 161 ARG cc_start: 0.8734 (ttm110) cc_final: 0.8194 (mtp85) REVERT: B 211 GLU cc_start: 0.8370 (mm-30) cc_final: 0.7710 (mm-30) REVERT: B 227 MET cc_start: 0.9271 (mtm) cc_final: 0.9064 (mtm) REVERT: B 251 LEU cc_start: 0.9486 (tp) cc_final: 0.9283 (tp) REVERT: B 258 ILE cc_start: 0.9525 (tp) cc_final: 0.9318 (tp) REVERT: B 283 VAL cc_start: 0.9362 (t) cc_final: 0.9078 (t) REVERT: B 286 ASP cc_start: 0.8581 (m-30) cc_final: 0.7802 (m-30) REVERT: B 290 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8358 (tm-30) REVERT: B 291 LEU cc_start: 0.9584 (mt) cc_final: 0.9238 (mt) REVERT: B 296 LYS cc_start: 0.8908 (mmpt) cc_final: 0.8579 (mtmm) REVERT: B 301 PHE cc_start: 0.8735 (m-80) cc_final: 0.8476 (m-10) REVERT: B 322 MET cc_start: 0.8811 (mmm) cc_final: 0.8607 (mmm) REVERT: B 333 LYS cc_start: 0.9508 (ttmm) cc_final: 0.9242 (ttmm) REVERT: B 345 LYS cc_start: 0.9736 (tttt) cc_final: 0.9481 (tttt) REVERT: B 350 ARG cc_start: 0.9407 (tpp80) cc_final: 0.9001 (tpp80) REVERT: B 362 ASP cc_start: 0.8992 (m-30) cc_final: 0.7849 (m-30) REVERT: B 370 ASN cc_start: 0.9514 (m110) cc_final: 0.8944 (m110) REVERT: B 390 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8397 (mm-40) REVERT: B 398 ASP cc_start: 0.8746 (t70) cc_final: 0.8393 (t70) REVERT: B 399 GLU cc_start: 0.8900 (mp0) cc_final: 0.8667 (mp0) REVERT: B 403 ILE cc_start: 0.9149 (mm) cc_final: 0.8800 (tp) REVERT: B 441 GLU cc_start: 0.9025 (pm20) cc_final: 0.8813 (pm20) REVERT: B 447 ASN cc_start: 0.8666 (m110) cc_final: 0.8115 (m-40) REVERT: B 477 ILE cc_start: 0.9624 (mp) cc_final: 0.9133 (tp) REVERT: B 494 MET cc_start: 0.9462 (mtt) cc_final: 0.8846 (mtt) REVERT: B 501 GLN cc_start: 0.9661 (tt0) cc_final: 0.9280 (mt0) REVERT: B 576 LEU cc_start: 0.9349 (mt) cc_final: 0.8893 (mt) REVERT: B 606 TYR cc_start: 0.8466 (m-80) cc_final: 0.8068 (m-10) REVERT: B 631 ASP cc_start: 0.9436 (m-30) cc_final: 0.9053 (m-30) REVERT: B 636 LYS cc_start: 0.9681 (mptt) cc_final: 0.9388 (mmmt) REVERT: B 639 ASP cc_start: 0.9279 (m-30) cc_final: 0.8973 (m-30) REVERT: B 650 GLN cc_start: 0.7380 (mp10) cc_final: 0.7032 (mp10) REVERT: B 658 LEU cc_start: 0.9539 (mm) cc_final: 0.9303 (mm) REVERT: B 667 LEU cc_start: 0.9523 (tp) cc_final: 0.9289 (tt) REVERT: B 668 ASN cc_start: 0.9383 (m-40) cc_final: 0.8888 (m-40) REVERT: B 684 TYR cc_start: 0.8185 (m-80) cc_final: 0.7690 (m-10) REVERT: C 100 VAL cc_start: 0.8515 (t) cc_final: 0.8176 (p) REVERT: C 101 HIS cc_start: 0.7967 (m90) cc_final: 0.7634 (m90) REVERT: D 69 GLN cc_start: 0.9388 (tp40) cc_final: 0.8875 (tm-30) REVERT: D 74 MET cc_start: 0.6362 (mtm) cc_final: 0.6155 (mtm) REVERT: D 185 MET cc_start: 0.2315 (mmp) cc_final: 0.1869 (mpp) REVERT: D 205 VAL cc_start: 0.9278 (t) cc_final: 0.8980 (t) outliers start: 1 outliers final: 1 residues processed: 621 average time/residue: 0.1288 time to fit residues: 119.9975 Evaluate side-chains 543 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 542 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 93 optimal weight: 1.9990 chunk 1 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 39 optimal weight: 0.4980 chunk 25 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 125 optimal weight: 0.0270 chunk 28 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 201 HIS D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.140038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.096692 restraints weight = 45760.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.099838 restraints weight = 26750.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.101946 restraints weight = 17784.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.103512 restraints weight = 12994.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.104570 restraints weight = 10049.871| |-----------------------------------------------------------------------------| r_work (final): 0.3296 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.7918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 16386 Z= 0.133 Angle : 0.648 10.227 22134 Z= 0.344 Chirality : 0.043 0.216 2360 Planarity : 0.004 0.058 2818 Dihedral : 10.394 163.103 2242 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.19), residues: 1932 helix: 0.95 (0.15), residues: 1125 sheet: -0.25 (0.45), residues: 128 loop : -0.12 (0.23), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 161 TYR 0.044 0.002 TYR C 142 PHE 0.024 0.002 PHE B 261 TRP 0.017 0.001 TRP C 44 HIS 0.010 0.001 HIS D 201 Details of bonding type rmsd covalent geometry : bond 0.00295 (16386) covalent geometry : angle 0.64774 (22134) hydrogen bonds : bond 0.03761 ( 871) hydrogen bonds : angle 4.94959 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3749.87 seconds wall clock time: 65 minutes 54.83 seconds (3954.83 seconds total)