Starting phenix.real_space_refine on Sat Sep 12 12:42:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzm_45071/09_2026/9bzm_45071_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzm_45071/09_2026/9bzm_45071.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bzm_45071/09_2026/9bzm_45071.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzm_45071/09_2026/9bzm_45071.map" model { file = "/net/cci-nas-00/data/ceres_data/9bzm_45071/09_2026/9bzm_45071_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzm_45071/09_2026/9bzm_45071_neut.cif" } resolution = 4.19 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-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.52, per 1000 atoms: 0.22 Number of scatterers: 16038 At special positions: 0 Unit cell: (93.288, 127.764, 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: 1.15 Conformation dependent library (CDL) restraints added in 671.2 milliseconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 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: 4.095A 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: 3.694A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.628A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A 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: 6.026A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.068A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.567A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.669A 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: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.359A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A 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: 6.605A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.717A 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: 5.661A 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: 7.228A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.064A 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: 7.906A 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: 8.346A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 1.55 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: 4888 1.34 - 1.46: 3062 1.46 - 1.58: 8255 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.80e+01 bond pdb=" O3B TTP A 803 " pdb=" PG TTP A 803 " ideal model delta sigma weight residual 1.748 1.610 0.138 2.00e-02 2.50e+03 4.76e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.060 1.25e-02 6.40e+03 2.34e+01 bond pdb=" O3A TTP A 803 " pdb=" PB TTP A 803 " ideal model delta sigma weight residual 1.675 1.606 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21524 2.09 - 4.18: 528 4.18 - 6.27: 64 6.27 - 8.36: 9 8.36 - 10.45: 9 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.59 -6.05 1.36e+00 5.41e-01 1.98e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.13 -4.42 1.15e+00 7.56e-01 1.48e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.22 -3.94 1.09e+00 8.42e-01 1.30e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.88 -4.38 1.23e+00 6.61e-01 1.27e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.68 -3.97 1.15e+00 7.56e-01 1.19e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.06: 9088 25.06 - 50.11: 657 50.11 - 75.17: 125 75.17 - 100.22: 26 100.22 - 125.28: 2 Dihedral angle restraints: 9898 sinusoidal: 4140 harmonic: 5758 Sorted by residual: dihedral pdb=" O4' GDP A 802 " pdb=" C1' GDP A 802 " pdb=" N9 GDP A 802 " pdb=" C8 GDP A 802 " ideal model delta sinusoidal sigma weight residual 27.02 -98.26 125.28 1 2.00e+01 2.50e-03 3.79e+01 dihedral pdb=" O4' GDP B 804 " pdb=" C1' GDP B 804 " pdb=" N9 GDP B 804 " pdb=" C8 GDP B 804 " ideal model delta sinusoidal sigma weight residual 27.02 -95.56 122.59 1 2.00e+01 2.50e-03 3.69e+01 dihedral pdb=" C VAL C 125 " pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta harmonic sigma weight residual -122.00 -134.34 12.34 0 2.50e+00 1.60e-01 2.44e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2134 0.093 - 0.186: 192 0.186 - 0.278: 29 0.278 - 0.371: 3 0.371 - 0.464: 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 2.05 0.46 2.00e-01 2.50e+01 5.38e+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 4.54e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+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 4.12e-02 2.72e+00 pdb=" N PRO D 75 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.017 2.00e-02 2.50e+03 1.11e-02 2.15e+00 pdb=" CG PHE D 92 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 169 " 0.017 2.00e-02 2.50e+03 9.83e-03 1.93e+00 pdb=" CG TYR C 169 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 169 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 169 " 0.008 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 131 2.51 - 3.11: 11557 3.11 - 3.70: 27051 3.70 - 4.30: 41544 4.30 - 4.90: 65430 Nonbonded interactions: 145713 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 1.961 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 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 2.013 3.040 ... (remaining 145708 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: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.980 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6305 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.139 16386 Z= 0.334 Angle : 0.788 10.446 22134 Z= 0.472 Chirality : 0.058 0.464 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.681 125.280 6202 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.28 % Allowed : 15.38 % Favored : 83.33 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.18), residues: 1932 helix: 0.58 (0.14), residues: 1151 sheet: 0.46 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.33 (16386) covalent geometry : angle 0.78750 / 0.47 (22134) hydrogen bonds : bond 0.15420 / 9.51 ( 871) hydrogen bonds : angle 6.51745 / 4.65 ( 2571) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 976 time to evaluate : 0.552 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 41 ILE cc_start: 0.8814 (mm) cc_final: 0.8405 (mm) REVERT: A 69 LEU cc_start: 0.8277 (mt) cc_final: 0.8074 (mt) REVERT: A 147 GLN cc_start: 0.8267 (mt0) cc_final: 0.7402 (mt0) REVERT: A 171 PHE cc_start: 0.8520 (m-80) cc_final: 0.8260 (m-10) REVERT: A 172 LEU cc_start: 0.9471 (mp) cc_final: 0.9232 (mp) REVERT: A 179 LEU cc_start: 0.8863 (tp) cc_final: 0.8584 (tp) REVERT: A 181 ASP cc_start: 0.8375 (m-30) cc_final: 0.7893 (m-30) REVERT: A 188 ILE cc_start: 0.9195 (mt) cc_final: 0.8963 (mt) REVERT: A 192 LEU cc_start: 0.9448 (mt) cc_final: 0.9076 (mt) REVERT: A 204 SER cc_start: 0.9104 (m) cc_final: 0.8827 (p) REVERT: A 211 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6462 (mm-30) REVERT: A 224 VAL cc_start: 0.8632 (t) cc_final: 0.8365 (p) REVERT: A 258 ILE cc_start: 0.9037 (tp) cc_final: 0.8639 (tp) REVERT: A 278 LEU cc_start: 0.8477 (tp) cc_final: 0.8204 (tp) REVERT: A 294 GLU cc_start: 0.7178 (mt-10) cc_final: 0.6505 (mt-10) REVERT: A 322 MET cc_start: 0.8113 (mmp) cc_final: 0.7470 (mmm) REVERT: A 345 LYS cc_start: 0.8603 (tttt) cc_final: 0.8208 (tttt) REVERT: A 349 LEU cc_start: 0.7856 (mt) cc_final: 0.7544 (mt) REVERT: A 362 ASP cc_start: 0.6167 (m-30) cc_final: 0.5640 (m-30) REVERT: A 407 ILE cc_start: 0.9091 (mt) cc_final: 0.8447 (mt) REVERT: A 417 LEU cc_start: 0.8546 (tt) cc_final: 0.8165 (tt) REVERT: A 420 MET cc_start: 0.8019 (mmm) cc_final: 0.7724 (mmm) REVERT: A 430 LYS cc_start: 0.8978 (mttt) cc_final: 0.8732 (mtpp) REVERT: A 436 LEU cc_start: 0.9196 (mt) cc_final: 0.8961 (mt) REVERT: A 442 THR cc_start: 0.8962 (p) cc_final: 0.8749 (m) REVERT: A 474 GLN cc_start: 0.8573 (mt0) cc_final: 0.8186 (mt0) REVERT: A 494 MET cc_start: 0.8146 (mtp) cc_final: 0.7793 (mtm) REVERT: A 500 ILE cc_start: 0.9349 (mt) cc_final: 0.9129 (mt) REVERT: A 556 GLU cc_start: 0.6880 (tp30) cc_final: 0.6411 (tp30) REVERT: A 558 TRP cc_start: 0.8988 (m100) cc_final: 0.8763 (m100) REVERT: A 573 SER cc_start: 0.9425 (p) cc_final: 0.8954 (p) REVERT: A 587 VAL cc_start: 0.9000 (t) cc_final: 0.8695 (t) REVERT: A 594 VAL cc_start: 0.9180 (m) cc_final: 0.8950 (m) REVERT: A 597 ILE cc_start: 0.9037 (pt) cc_final: 0.8811 (pt) REVERT: A 612 TYR cc_start: 0.7431 (m-80) cc_final: 0.6557 (m-10) REVERT: A 618 LEU cc_start: 0.9165 (tp) cc_final: 0.8895 (tp) REVERT: A 634 MET cc_start: 0.8112 (mmp) cc_final: 0.7738 (mmm) REVERT: A 644 ILE cc_start: 0.8686 (mt) cc_final: 0.7854 (mt) REVERT: A 653 SER cc_start: 0.8990 (OUTLIER) cc_final: 0.8740 (p) REVERT: A 655 THR cc_start: 0.9153 (m) cc_final: 0.8901 (t) REVERT: A 657 PHE cc_start: 0.7945 (m-80) cc_final: 0.7493 (m-80) REVERT: A 667 LEU cc_start: 0.8211 (tt) cc_final: 0.7969 (tt) REVERT: B 11 GLN cc_start: 0.7854 (mt0) cc_final: 0.6857 (mt0) REVERT: B 12 LEU cc_start: 0.9071 (mt) cc_final: 0.8785 (mt) REVERT: B 25 GLN cc_start: 0.7229 (mt0) cc_final: 0.6496 (mt0) REVERT: B 51 LEU cc_start: 0.8138 (tp) cc_final: 0.7823 (tp) REVERT: B 89 PHE cc_start: 0.7544 (t80) cc_final: 0.6837 (t80) REVERT: B 122 ILE cc_start: 0.9370 (mt) cc_final: 0.8919 (mt) REVERT: B 149 TYR cc_start: 0.8400 (t80) cc_final: 0.8037 (t80) REVERT: B 171 PHE cc_start: 0.8786 (m-80) cc_final: 0.8517 (m-80) REVERT: B 181 ASP cc_start: 0.8563 (m-30) cc_final: 0.8331 (m-30) REVERT: B 186 ILE cc_start: 0.9054 (mt) cc_final: 0.8797 (mt) REVERT: B 192 LEU cc_start: 0.9264 (mt) cc_final: 0.8633 (mt) REVERT: B 202 ASN cc_start: 0.8817 (t0) cc_final: 0.8042 (p0) REVERT: B 211 GLU cc_start: 0.7192 (mt-10) cc_final: 0.6002 (mm-30) REVERT: B 232 ASN cc_start: 0.8315 (OUTLIER) cc_final: 0.7374 (t0) REVERT: B 256 ARG cc_start: 0.7723 (ttp80) cc_final: 0.7514 (tmt-80) REVERT: B 258 ILE cc_start: 0.8586 (tp) cc_final: 0.8378 (tp) REVERT: B 278 LEU cc_start: 0.8728 (tp) cc_final: 0.8237 (tp) REVERT: B 322 MET cc_start: 0.8012 (mmm) cc_final: 0.6336 (mmt) REVERT: B 332 VAL cc_start: 0.8875 (t) cc_final: 0.8649 (t) REVERT: B 345 LYS cc_start: 0.8630 (tttt) cc_final: 0.8111 (tttt) REVERT: B 362 ASP cc_start: 0.6716 (m-30) cc_final: 0.5834 (m-30) REVERT: B 364 VAL cc_start: 0.8922 (t) cc_final: 0.8520 (t) REVERT: B 381 LEU cc_start: 0.9084 (tp) cc_final: 0.8824 (tp) REVERT: B 384 GLU cc_start: 0.8761 (pm20) cc_final: 0.8504 (pm20) REVERT: B 403 ILE cc_start: 0.9387 (mm) cc_final: 0.8916 (mp) REVERT: B 446 ARG cc_start: 0.7142 (mmm160) cc_final: 0.6902 (mtp85) REVERT: B 453 ARG cc_start: 0.8968 (ttt90) cc_final: 0.8080 (ttp80) REVERT: B 505 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6725 (mt-10) REVERT: B 550 MET cc_start: 0.7401 (mtm) cc_final: 0.5930 (mtp) REVERT: B 558 TRP cc_start: 0.8293 (m100) cc_final: 0.7920 (m100) REVERT: B 570 MET cc_start: 0.7401 (mtm) cc_final: 0.6952 (mtm) REVERT: B 587 VAL cc_start: 0.8816 (t) cc_final: 0.8555 (t) REVERT: B 656 LEU cc_start: 0.8446 (mt) cc_final: 0.8218 (mt) REVERT: C 42 LEU cc_start: 0.6344 (mt) cc_final: 0.5897 (mt) REVERT: C 90 LEU cc_start: 0.5256 (mt) cc_final: 0.4763 (mt) REVERT: C 153 LEU cc_start: 0.5389 (tp) cc_final: 0.5079 (tt) REVERT: D 96 MET cc_start: 0.2343 (mmm) cc_final: 0.2078 (mmt) REVERT: D 178 PHE cc_start: 0.5464 (m-80) cc_final: 0.4360 (m-80) REVERT: D 286 VAL cc_start: 0.7829 (t) cc_final: 0.7046 (p) REVERT: D 321 TYR cc_start: 0.6487 (m-80) cc_final: 0.5325 (m-10) outliers start: 22 outliers final: 7 residues processed: 988 average time/residue: 0.1329 time to fit residues: 190.6254 Evaluate side-chains 682 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 673 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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: 1.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN A 43 GLN A 180 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN B 11 GLN B 19 GLN B 61 ASN B 218 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN B 387 GLN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN B 645 GLN B 676 HIS ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN D 71 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.138034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.094008 restraints weight = 37576.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.097419 restraints weight = 20101.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.099748 restraints weight = 13003.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.101327 restraints weight = 9348.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.102328 restraints weight = 7331.350| |-----------------------------------------------------------------------------| r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (14 function evaluations) r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16386 Z= 0.197 Angle : 0.638 7.394 22134 Z= 0.346 Chirality : 0.043 0.294 2360 Planarity : 0.004 0.031 2818 Dihedral : 9.890 132.999 2290 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.17 % Allowed : 2.62 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.18), residues: 1932 helix: 1.19 (0.15), residues: 1128 sheet: 0.35 (0.44), residues: 126 loop : 0.42 (0.23), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 196 TYR 0.052 0.002 TYR D 130 PHE 0.029 0.002 PHE D 320 TRP 0.012 0.002 TRP C 30 HIS 0.007 0.001 HIS A 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.20 (16386) covalent geometry : angle 0.63823 / 0.35 (22134) hydrogen bonds : bond 0.04714 / 2.98 ( 871) hydrogen bonds : angle 5.11626 / 3.62 ( 2571) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 754 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.9402 (tp30) cc_final: 0.8977 (tp30) REVERT: A 51 LEU cc_start: 0.9522 (tp) cc_final: 0.9284 (pt) REVERT: A 54 LYS cc_start: 0.9628 (ttmm) cc_final: 0.9227 (ttmm) REVERT: A 87 LYS cc_start: 0.9501 (tptt) cc_final: 0.9136 (mmmm) REVERT: A 101 TYR cc_start: 0.9349 (m-10) cc_final: 0.9005 (m-10) REVERT: A 118 TYR cc_start: 0.9163 (t80) cc_final: 0.8673 (t80) REVERT: A 120 ASP cc_start: 0.9125 (m-30) cc_final: 0.8789 (m-30) REVERT: A 122 ILE cc_start: 0.9690 (mt) cc_final: 0.9483 (mt) REVERT: A 139 GLU cc_start: 0.9451 (mm-30) cc_final: 0.9197 (mm-30) REVERT: A 142 ASN cc_start: 0.9427 (m-40) cc_final: 0.9150 (m110) REVERT: A 147 GLN cc_start: 0.8971 (mt0) cc_final: 0.8683 (mt0) REVERT: A 168 VAL cc_start: 0.9382 (t) cc_final: 0.8963 (m) REVERT: A 171 PHE cc_start: 0.9484 (m-80) cc_final: 0.9242 (m-10) REVERT: A 181 ASP cc_start: 0.9017 (m-30) cc_final: 0.8486 (m-30) REVERT: A 184 ARG cc_start: 0.9116 (tpp-160) cc_final: 0.8899 (tpp-160) REVERT: A 202 ASN cc_start: 0.9586 (t0) cc_final: 0.9267 (t0) REVERT: A 204 SER cc_start: 0.9429 (m) cc_final: 0.9118 (p) REVERT: A 223 VAL cc_start: 0.9557 (m) cc_final: 0.9307 (p) REVERT: A 251 LEU cc_start: 0.9593 (tp) cc_final: 0.9336 (tp) REVERT: A 286 ASP cc_start: 0.8613 (m-30) cc_final: 0.8166 (m-30) REVERT: A 291 LEU cc_start: 0.9351 (mt) cc_final: 0.9052 (mt) REVERT: A 293 ARG cc_start: 0.9193 (ttp80) cc_final: 0.8778 (ttp80) REVERT: A 337 ILE cc_start: 0.9488 (tp) cc_final: 0.9178 (tp) REVERT: A 344 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8591 (mt-10) REVERT: A 348 MET cc_start: 0.8968 (ptp) cc_final: 0.8679 (ptp) REVERT: A 349 LEU cc_start: 0.9586 (mt) cc_final: 0.9306 (mt) REVERT: A 362 ASP cc_start: 0.8057 (m-30) cc_final: 0.7444 (m-30) REVERT: A 387 GLN cc_start: 0.9062 (mt0) cc_final: 0.8777 (mt0) REVERT: A 405 LEU cc_start: 0.9120 (mt) cc_final: 0.8914 (mt) REVERT: A 407 ILE cc_start: 0.9202 (mt) cc_final: 0.8832 (mt) REVERT: A 421 GLU cc_start: 0.8204 (pp20) cc_final: 0.7999 (pp20) REVERT: A 441 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8317 (mt-10) REVERT: A 443 THR cc_start: 0.9325 (m) cc_final: 0.9081 (t) REVERT: A 458 MET cc_start: 0.9191 (mmp) cc_final: 0.8632 (mmp) REVERT: A 505 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8924 (mt-10) REVERT: A 550 MET cc_start: 0.7796 (mtt) cc_final: 0.7340 (mtt) REVERT: A 570 MET cc_start: 0.9179 (mtp) cc_final: 0.8927 (mtp) REVERT: A 573 SER cc_start: 0.9476 (p) cc_final: 0.9052 (p) REVERT: A 584 ILE cc_start: 0.9608 (pt) cc_final: 0.9114 (pt) REVERT: A 599 GLU cc_start: 0.8323 (mp0) cc_final: 0.7837 (mp0) REVERT: A 630 TYR cc_start: 0.7919 (m-80) cc_final: 0.7173 (m-10) REVERT: A 632 MET cc_start: 0.8904 (mtm) cc_final: 0.8624 (mtp) REVERT: A 639 ASP cc_start: 0.9194 (m-30) cc_final: 0.8918 (m-30) REVERT: A 650 GLN cc_start: 0.8635 (mt0) cc_final: 0.8317 (tt0) REVERT: A 654 PHE cc_start: 0.9499 (t80) cc_final: 0.9192 (t80) REVERT: A 655 THR cc_start: 0.9278 (m) cc_final: 0.8735 (t) REVERT: A 664 THR cc_start: 0.9173 (p) cc_final: 0.8672 (p) REVERT: A 667 LEU cc_start: 0.9380 (tt) cc_final: 0.9104 (tt) REVERT: A 668 ASN cc_start: 0.9288 (m110) cc_final: 0.9024 (m110) REVERT: A 686 ARG cc_start: 0.8567 (mmt180) cc_final: 0.8284 (mtt-85) REVERT: B 51 LEU cc_start: 0.9485 (tp) cc_final: 0.9257 (tp) REVERT: B 58 LEU cc_start: 0.9676 (mt) cc_final: 0.9448 (mt) REVERT: B 65 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8293 (mp0) REVERT: B 87 LYS cc_start: 0.9293 (tptp) cc_final: 0.8778 (tptp) REVERT: B 95 MET cc_start: 0.9582 (tpt) cc_final: 0.9326 (tpp) REVERT: B 147 GLN cc_start: 0.9146 (mt0) cc_final: 0.8744 (mt0) REVERT: B 149 TYR cc_start: 0.9161 (t80) cc_final: 0.8788 (t80) REVERT: B 181 ASP cc_start: 0.9169 (m-30) cc_final: 0.8932 (m-30) REVERT: B 257 ASP cc_start: 0.9050 (m-30) cc_final: 0.8710 (m-30) REVERT: B 258 ILE cc_start: 0.9504 (tp) cc_final: 0.9298 (tp) REVERT: B 278 LEU cc_start: 0.9282 (tp) cc_final: 0.9016 (tp) REVERT: B 279 SER cc_start: 0.8527 (m) cc_final: 0.7596 (p) REVERT: B 290 GLU cc_start: 0.9273 (tp30) cc_final: 0.9028 (tp30) REVERT: B 316 GLU cc_start: 0.9124 (tt0) cc_final: 0.8895 (tt0) REVERT: B 333 LYS cc_start: 0.9210 (tptp) cc_final: 0.8736 (tttm) REVERT: B 355 TYR cc_start: 0.9036 (m-80) cc_final: 0.8722 (m-80) REVERT: B 381 LEU cc_start: 0.9233 (tp) cc_final: 0.8657 (tp) REVERT: B 413 SER cc_start: 0.9541 (m) cc_final: 0.9037 (t) REVERT: B 415 ASN cc_start: 0.9702 (t0) cc_final: 0.9416 (t0) REVERT: B 459 LYS cc_start: 0.9283 (mttm) cc_final: 0.8438 (mtpt) REVERT: B 460 SER cc_start: 0.8934 (t) cc_final: 0.8717 (t) REVERT: B 471 TYR cc_start: 0.9288 (t80) cc_final: 0.8981 (t80) REVERT: B 487 PHE cc_start: 0.9744 (t80) cc_final: 0.9445 (t80) REVERT: B 493 MET cc_start: 0.9499 (tmm) cc_final: 0.9198 (tmm) REVERT: B 505 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8426 (mt-10) REVERT: B 570 MET cc_start: 0.9112 (mtp) cc_final: 0.8746 (mtp) REVERT: B 599 GLU cc_start: 0.8730 (pt0) cc_final: 0.8505 (pt0) REVERT: B 601 ILE cc_start: 0.9447 (mm) cc_final: 0.9170 (mm) REVERT: B 612 TYR cc_start: 0.8479 (m-10) cc_final: 0.8193 (m-10) REVERT: B 631 ASP cc_start: 0.9034 (t0) cc_final: 0.8530 (t0) REVERT: B 667 LEU cc_start: 0.9424 (tp) cc_final: 0.9190 (tp) REVERT: B 677 ARG cc_start: 0.9487 (mmm-85) cc_final: 0.9159 (mmm-85) REVERT: C 42 LEU cc_start: 0.9034 (mt) cc_final: 0.8827 (mt) REVERT: C 117 THR cc_start: 0.9067 (p) cc_final: 0.8771 (p) REVERT: C 119 ASN cc_start: 0.9094 (t0) cc_final: 0.8825 (t0) REVERT: C 179 TYR cc_start: 0.8590 (t80) cc_final: 0.8351 (t80) REVERT: D 37 LEU cc_start: 0.5152 (tp) cc_final: 0.2830 (tp) REVERT: D 178 PHE cc_start: 0.8810 (m-80) cc_final: 0.8440 (m-80) REVERT: D 252 LEU cc_start: 0.8783 (mt) cc_final: 0.8487 (mt) outliers start: 3 outliers final: 0 residues processed: 755 average time/residue: 0.1181 time to fit residues: 133.8355 Evaluate side-chains 618 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 618 time to evaluate : 0.661 ------------------------------------------------------------------------------- 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: 9.9990 chunk 131 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 182 optimal weight: 0.8980 chunk 159 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN A 19 GLN A 25 GLN A 191 GLN A 338 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 232 ASN B 361 GLN B 387 GLN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.138374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.094531 restraints weight = 39129.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.097865 restraints weight = 20939.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.100085 restraints weight = 13497.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.101651 restraints weight = 9709.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.102650 restraints weight = 7633.353| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16386 Z= 0.210 Angle : 0.616 10.795 22134 Z= 0.331 Chirality : 0.042 0.240 2360 Planarity : 0.004 0.035 2818 Dihedral : 9.255 133.963 2290 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.23 % Allowed : 2.39 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.19), residues: 1932 helix: 1.22 (0.15), residues: 1132 sheet: -0.18 (0.40), residues: 150 loop : 0.40 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 274 TYR 0.043 0.002 TYR D 130 PHE 0.028 0.002 PHE D 320 TRP 0.017 0.002 TRP A 9 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.21 (16386) covalent geometry : angle 0.61574 / 0.33 (22134) hydrogen bonds : bond 0.04242 / 2.71 ( 871) hydrogen bonds : angle 4.96561 / 3.55 ( 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 705 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 701 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9566 (tp) cc_final: 0.9329 (pt) REVERT: A 54 LYS cc_start: 0.9728 (ttmm) cc_final: 0.9277 (ttmm) REVERT: A 64 TYR cc_start: 0.8908 (m-10) cc_final: 0.8385 (m-80) REVERT: A 87 LYS cc_start: 0.9508 (tptt) cc_final: 0.9175 (mmmm) REVERT: A 107 LYS cc_start: 0.9120 (mtpp) cc_final: 0.8838 (mtpp) REVERT: A 118 TYR cc_start: 0.9228 (t80) cc_final: 0.9016 (t80) REVERT: A 120 ASP cc_start: 0.9206 (m-30) cc_final: 0.8896 (m-30) REVERT: A 139 GLU cc_start: 0.9419 (mm-30) cc_final: 0.9132 (mm-30) REVERT: A 142 ASN cc_start: 0.9421 (m-40) cc_final: 0.9142 (m110) REVERT: A 150 GLN cc_start: 0.9441 (tm-30) cc_final: 0.9044 (tm-30) REVERT: A 168 VAL cc_start: 0.9251 (t) cc_final: 0.8944 (m) REVERT: A 184 ARG cc_start: 0.9146 (tpp-160) cc_final: 0.8936 (tpp-160) REVERT: A 223 VAL cc_start: 0.9559 (m) cc_final: 0.9105 (p) REVERT: A 227 MET cc_start: 0.9374 (mtp) cc_final: 0.8957 (mtp) REVERT: A 251 LEU cc_start: 0.9666 (tp) cc_final: 0.9396 (tp) REVERT: A 257 ASP cc_start: 0.9382 (m-30) cc_final: 0.8642 (m-30) REVERT: A 263 ASP cc_start: 0.9076 (m-30) cc_final: 0.8824 (m-30) REVERT: A 286 ASP cc_start: 0.8669 (m-30) cc_final: 0.8242 (m-30) REVERT: A 291 LEU cc_start: 0.9378 (mt) cc_final: 0.9164 (mt) REVERT: A 316 GLU cc_start: 0.8909 (pt0) cc_final: 0.8644 (pp20) REVERT: A 317 MET cc_start: 0.9086 (ptm) cc_final: 0.8855 (ptm) REVERT: A 322 MET cc_start: 0.8658 (mmp) cc_final: 0.8213 (mmm) REVERT: A 337 ILE cc_start: 0.9446 (tp) cc_final: 0.9236 (tp) REVERT: A 344 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8615 (mt-10) REVERT: A 348 MET cc_start: 0.9011 (ptp) cc_final: 0.8718 (ptp) REVERT: A 349 LEU cc_start: 0.9591 (mt) cc_final: 0.9278 (mt) REVERT: A 362 ASP cc_start: 0.8129 (m-30) cc_final: 0.7455 (m-30) REVERT: A 387 GLN cc_start: 0.8983 (mt0) cc_final: 0.8668 (mt0) REVERT: A 398 ASP cc_start: 0.8456 (p0) cc_final: 0.8156 (p0) REVERT: A 403 ILE cc_start: 0.9221 (mm) cc_final: 0.8929 (mm) REVERT: A 407 ILE cc_start: 0.9367 (mt) cc_final: 0.9041 (mt) REVERT: A 421 GLU cc_start: 0.8502 (pp20) cc_final: 0.8241 (pp20) REVERT: A 443 THR cc_start: 0.9439 (m) cc_final: 0.9238 (t) REVERT: A 458 MET cc_start: 0.9375 (mmp) cc_final: 0.8904 (mmm) REVERT: A 485 ARG cc_start: 0.9207 (mtm-85) cc_final: 0.8831 (mtm-85) REVERT: A 490 THR cc_start: 0.9676 (m) cc_final: 0.9341 (p) REVERT: A 505 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8777 (mt-10) REVERT: A 516 GLN cc_start: 0.9467 (mt0) cc_final: 0.8854 (tp-100) REVERT: A 570 MET cc_start: 0.9297 (mtp) cc_final: 0.8963 (mtp) REVERT: A 573 SER cc_start: 0.9424 (p) cc_final: 0.8392 (p) REVERT: A 599 GLU cc_start: 0.8467 (mp0) cc_final: 0.8258 (mp0) REVERT: A 639 ASP cc_start: 0.9117 (m-30) cc_final: 0.8765 (m-30) REVERT: A 645 GLN cc_start: 0.9184 (tp-100) cc_final: 0.8906 (tp40) REVERT: A 650 GLN cc_start: 0.8674 (mt0) cc_final: 0.7989 (mt0) REVERT: A 668 ASN cc_start: 0.9449 (m110) cc_final: 0.9054 (m110) REVERT: B 58 LEU cc_start: 0.9667 (mt) cc_final: 0.9414 (mt) REVERT: B 65 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8401 (mp0) REVERT: B 87 LYS cc_start: 0.9365 (tptp) cc_final: 0.9009 (tptp) REVERT: B 106 LEU cc_start: 0.9516 (tp) cc_final: 0.9295 (tp) REVERT: B 116 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8448 (mp0) REVERT: B 117 ARG cc_start: 0.9034 (ttm110) cc_final: 0.8722 (ttm110) REVERT: B 120 ASP cc_start: 0.8903 (m-30) cc_final: 0.8676 (m-30) REVERT: B 147 GLN cc_start: 0.9176 (mt0) cc_final: 0.8817 (mt0) REVERT: B 149 TYR cc_start: 0.9235 (t80) cc_final: 0.8820 (t80) REVERT: B 172 LEU cc_start: 0.9383 (mp) cc_final: 0.8996 (mp) REVERT: B 191 GLN cc_start: 0.8863 (mm-40) cc_final: 0.8599 (mm-40) REVERT: B 227 MET cc_start: 0.9033 (mtt) cc_final: 0.8556 (mtt) REVERT: B 232 ASN cc_start: 0.8808 (OUTLIER) cc_final: 0.8471 (t0) REVERT: B 257 ASP cc_start: 0.9027 (m-30) cc_final: 0.8740 (m-30) REVERT: B 278 LEU cc_start: 0.9296 (tp) cc_final: 0.9066 (tp) REVERT: B 279 SER cc_start: 0.8463 (m) cc_final: 0.7886 (p) REVERT: B 290 GLU cc_start: 0.9266 (tp30) cc_final: 0.8921 (tp30) REVERT: B 316 GLU cc_start: 0.9122 (tt0) cc_final: 0.8863 (tt0) REVERT: B 333 LYS cc_start: 0.9258 (tptp) cc_final: 0.8736 (tttm) REVERT: B 407 ILE cc_start: 0.9401 (mt) cc_final: 0.9000 (mt) REVERT: B 415 ASN cc_start: 0.9706 (t0) cc_final: 0.9250 (t0) REVERT: B 459 LYS cc_start: 0.9240 (mttm) cc_final: 0.8972 (mttm) REVERT: B 472 LEU cc_start: 0.9698 (mm) cc_final: 0.9483 (mm) REVERT: B 493 MET cc_start: 0.9488 (tmm) cc_final: 0.9192 (tmm) REVERT: B 505 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8369 (mt-10) REVERT: B 515 ASP cc_start: 0.9372 (m-30) cc_final: 0.9125 (m-30) REVERT: B 516 GLN cc_start: 0.9108 (mp10) cc_final: 0.8896 (mp10) REVERT: B 588 GLN cc_start: 0.9440 (mm-40) cc_final: 0.9218 (mm-40) REVERT: B 599 GLU cc_start: 0.8808 (pt0) cc_final: 0.8508 (pt0) REVERT: B 604 ARG cc_start: 0.9407 (tpp80) cc_final: 0.8951 (ttm-80) REVERT: B 631 ASP cc_start: 0.9088 (t0) cc_final: 0.8605 (t0) REVERT: C 74 MET cc_start: 0.8698 (mmp) cc_final: 0.8396 (mmp) REVERT: C 179 TYR cc_start: 0.8575 (t80) cc_final: 0.8237 (t80) REVERT: D 56 MET cc_start: 0.6904 (mmp) cc_final: 0.6698 (mmm) REVERT: D 112 LEU cc_start: 0.6319 (mm) cc_final: 0.5994 (mm) REVERT: D 137 MET cc_start: 0.5199 (mmm) cc_final: 0.4694 (mpp) REVERT: D 158 VAL cc_start: 0.8841 (t) cc_final: 0.7725 (t) REVERT: D 162 TYR cc_start: 0.8595 (m-10) cc_final: 0.8364 (m-80) REVERT: D 178 PHE cc_start: 0.8985 (m-80) cc_final: 0.8484 (m-80) REVERT: D 233 ASN cc_start: 0.8836 (m110) cc_final: 0.8386 (m110) REVERT: D 252 LEU cc_start: 0.8878 (mt) cc_final: 0.8612 (mt) REVERT: D 278 GLU cc_start: 0.8470 (pp20) cc_final: 0.8267 (pp20) outliers start: 4 outliers final: 0 residues processed: 701 average time/residue: 0.1116 time to fit residues: 117.9191 Evaluate side-chains 608 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 607 time to evaluate : 0.574 ------------------------------------------------------------------------------- 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: 1.9990 chunk 157 optimal weight: 30.0000 chunk 168 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 185 optimal weight: 20.0000 chunk 191 optimal weight: 0.8980 chunk 159 optimal weight: 8.9990 chunk 182 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN A 242 GLN A 338 ASN A 361 GLN A 365 ASN A 370 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN B 218 ASN B 232 ASN B 387 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN B 646 GLN ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.138658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.097557 restraints weight = 34537.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.100496 restraints weight = 20179.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.102433 restraints weight = 13734.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.103522 restraints weight = 10498.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.104218 restraints weight = 8802.870| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5786 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= 0.171 Angle : 0.591 10.579 22134 Z= 0.314 Chirality : 0.042 0.385 2360 Planarity : 0.004 0.050 2818 Dihedral : 8.887 134.635 2290 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.17 % Allowed : 1.75 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.19), residues: 1932 helix: 1.13 (0.15), residues: 1138 sheet: 0.04 (0.42), residues: 138 loop : 0.26 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 274 TYR 0.054 0.002 TYR D 130 PHE 0.040 0.002 PHE D 172 TRP 0.010 0.001 TRP A 9 HIS 0.008 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.17 (16386) covalent geometry : angle 0.59138 / 0.31 (22134) hydrogen bonds : bond 0.04037 / 2.56 ( 871) hydrogen bonds : angle 4.84953 / 3.46 ( 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 697 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 694 time to evaluate : 0.607 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 41 ILE cc_start: 0.9523 (mm) cc_final: 0.9193 (mm) REVERT: A 54 LYS cc_start: 0.9678 (ttmm) cc_final: 0.9291 (ttmm) REVERT: A 65 GLU cc_start: 0.8603 (mm-30) cc_final: 0.7787 (mp0) REVERT: A 66 GLU cc_start: 0.8605 (tp30) cc_final: 0.8334 (tp30) REVERT: A 87 LYS cc_start: 0.9515 (tptt) cc_final: 0.9245 (mmmm) REVERT: A 106 LEU cc_start: 0.9534 (tp) cc_final: 0.9164 (tp) REVERT: A 107 LYS cc_start: 0.9196 (mtpp) cc_final: 0.8730 (mtpp) REVERT: A 118 TYR cc_start: 0.9284 (t80) cc_final: 0.8994 (t80) REVERT: A 120 ASP cc_start: 0.9190 (m-30) cc_final: 0.8835 (m-30) REVERT: A 139 GLU cc_start: 0.9418 (mm-30) cc_final: 0.9114 (mm-30) REVERT: A 142 ASN cc_start: 0.9433 (m-40) cc_final: 0.9141 (m110) REVERT: A 147 GLN cc_start: 0.9103 (mt0) cc_final: 0.8716 (mt0) REVERT: A 150 GLN cc_start: 0.9260 (tm-30) cc_final: 0.8885 (tm-30) REVERT: A 157 LEU cc_start: 0.9430 (tp) cc_final: 0.9056 (tp) REVERT: A 168 VAL cc_start: 0.9169 (t) cc_final: 0.8907 (m) REVERT: A 223 VAL cc_start: 0.9585 (m) cc_final: 0.9164 (p) REVERT: A 227 MET cc_start: 0.9355 (mtp) cc_final: 0.8934 (mtp) REVERT: A 251 LEU cc_start: 0.9667 (tp) cc_final: 0.9401 (tp) REVERT: A 257 ASP cc_start: 0.9366 (m-30) cc_final: 0.8615 (m-30) REVERT: A 286 ASP cc_start: 0.8539 (m-30) cc_final: 0.8254 (m-30) REVERT: A 319 MET cc_start: 0.8689 (ttt) cc_final: 0.8117 (ttt) REVERT: A 322 MET cc_start: 0.8579 (mmp) cc_final: 0.7956 (mmm) REVERT: A 344 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8477 (mt-10) REVERT: A 348 MET cc_start: 0.8883 (ptp) cc_final: 0.8673 (ptp) REVERT: A 349 LEU cc_start: 0.9591 (mt) cc_final: 0.9330 (mt) REVERT: A 361 GLN cc_start: 0.8863 (tp40) cc_final: 0.7861 (tp40) REVERT: A 362 ASP cc_start: 0.8019 (m-30) cc_final: 0.7274 (m-30) REVERT: A 365 ASN cc_start: 0.9147 (m110) cc_final: 0.8144 (m-40) REVERT: A 370 ASN cc_start: 0.9464 (m-40) cc_final: 0.9078 (m110) REVERT: A 375 LYS cc_start: 0.9155 (mtpt) cc_final: 0.8839 (mtmm) REVERT: A 403 ILE cc_start: 0.9143 (mm) cc_final: 0.8858 (mm) REVERT: A 407 ILE cc_start: 0.9329 (mt) cc_final: 0.9029 (mt) REVERT: A 418 ASN cc_start: 0.9038 (OUTLIER) cc_final: 0.8538 (m110) REVERT: A 458 MET cc_start: 0.9286 (mmp) cc_final: 0.8906 (mmm) REVERT: A 490 THR cc_start: 0.9676 (m) cc_final: 0.9357 (p) REVERT: A 505 GLU cc_start: 0.9101 (mt-10) cc_final: 0.8783 (mt-10) REVERT: A 570 MET cc_start: 0.9347 (mtp) cc_final: 0.9048 (mtp) REVERT: A 573 SER cc_start: 0.9327 (p) cc_final: 0.8472 (p) REVERT: A 639 ASP cc_start: 0.9108 (m-30) cc_final: 0.8760 (m-30) REVERT: A 643 THR cc_start: 0.9649 (p) cc_final: 0.9202 (t) REVERT: A 645 GLN cc_start: 0.9127 (tp-100) cc_final: 0.8558 (tp40) REVERT: A 650 GLN cc_start: 0.8664 (mt0) cc_final: 0.8037 (mt0) REVERT: A 664 THR cc_start: 0.9171 (p) cc_final: 0.8306 (p) REVERT: A 668 ASN cc_start: 0.9390 (m110) cc_final: 0.8876 (m110) REVERT: A 680 LYS cc_start: 0.8925 (mttt) cc_final: 0.8704 (mttp) REVERT: A 686 ARG cc_start: 0.8546 (mmt180) cc_final: 0.7995 (mmt-90) REVERT: B 31 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8599 (mt-10) REVERT: B 58 LEU cc_start: 0.9670 (mt) cc_final: 0.9462 (mt) REVERT: B 87 LYS cc_start: 0.9365 (tptp) cc_final: 0.9003 (tptp) REVERT: B 116 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8605 (mt-10) REVERT: B 117 ARG cc_start: 0.8994 (ttm110) cc_final: 0.8650 (ttm110) REVERT: B 118 TYR cc_start: 0.9379 (t80) cc_final: 0.9177 (t80) REVERT: B 120 ASP cc_start: 0.8858 (m-30) cc_final: 0.8600 (m-30) REVERT: B 147 GLN cc_start: 0.9096 (mt0) cc_final: 0.8688 (mt0) REVERT: B 149 TYR cc_start: 0.9299 (t80) cc_final: 0.8712 (t80) REVERT: B 172 LEU cc_start: 0.9366 (mp) cc_final: 0.8973 (mp) REVERT: B 191 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8592 (mm-40) REVERT: B 227 MET cc_start: 0.9164 (mtt) cc_final: 0.8694 (mtt) REVERT: B 228 LYS cc_start: 0.8939 (mmtm) cc_final: 0.8634 (mmtt) REVERT: B 232 ASN cc_start: 0.8968 (t160) cc_final: 0.8509 (t0) REVERT: B 257 ASP cc_start: 0.8946 (m-30) cc_final: 0.8721 (m-30) REVERT: B 278 LEU cc_start: 0.9256 (tp) cc_final: 0.9039 (tp) REVERT: B 279 SER cc_start: 0.8111 (m) cc_final: 0.7595 (p) REVERT: B 286 ASP cc_start: 0.8666 (m-30) cc_final: 0.8306 (m-30) REVERT: B 290 GLU cc_start: 0.9089 (tp30) cc_final: 0.8797 (tp30) REVERT: B 319 MET cc_start: 0.9191 (tpp) cc_final: 0.8707 (tpp) REVERT: B 333 LYS cc_start: 0.9270 (tptp) cc_final: 0.8814 (tttm) REVERT: B 348 MET cc_start: 0.9331 (ptp) cc_final: 0.9043 (ptp) REVERT: B 350 ARG cc_start: 0.7682 (mmm160) cc_final: 0.7177 (mmm160) REVERT: B 386 LEU cc_start: 0.9296 (mt) cc_final: 0.9024 (mt) REVERT: B 398 ASP cc_start: 0.8972 (t0) cc_final: 0.8709 (t0) REVERT: B 407 ILE cc_start: 0.9456 (mt) cc_final: 0.9007 (mt) REVERT: B 415 ASN cc_start: 0.9625 (t0) cc_final: 0.9114 (t0) REVERT: B 426 GLU cc_start: 0.8907 (pp20) cc_final: 0.8631 (tm-30) REVERT: B 459 LYS cc_start: 0.9261 (mttm) cc_final: 0.9008 (mttm) REVERT: B 472 LEU cc_start: 0.9639 (mm) cc_final: 0.9375 (mm) REVERT: B 493 MET cc_start: 0.9399 (tmm) cc_final: 0.9101 (tmm) REVERT: B 505 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8295 (mt-10) REVERT: B 515 ASP cc_start: 0.9281 (m-30) cc_final: 0.9071 (m-30) REVERT: B 516 GLN cc_start: 0.9038 (mp10) cc_final: 0.8786 (mp10) REVERT: B 599 GLU cc_start: 0.8733 (pt0) cc_final: 0.8477 (pt0) REVERT: B 604 ARG cc_start: 0.9364 (tpp80) cc_final: 0.8876 (ttm-80) REVERT: B 650 GLN cc_start: 0.8114 (mt0) cc_final: 0.7874 (mt0) REVERT: B 667 LEU cc_start: 0.9472 (tp) cc_final: 0.8929 (tp) REVERT: C 16 ASP cc_start: 0.6163 (p0) cc_final: 0.5592 (p0) REVERT: C 179 TYR cc_start: 0.8636 (t80) cc_final: 0.8345 (t80) REVERT: D 158 VAL cc_start: 0.8888 (t) cc_final: 0.8582 (t) REVERT: D 176 LEU cc_start: 0.9562 (mt) cc_final: 0.9246 (pp) REVERT: D 178 PHE cc_start: 0.8864 (m-80) cc_final: 0.8267 (m-80) REVERT: D 233 ASN cc_start: 0.8781 (m110) cc_final: 0.8286 (m110) REVERT: D 252 LEU cc_start: 0.8751 (mt) cc_final: 0.8412 (mp) REVERT: D 278 GLU cc_start: 0.8145 (pp20) cc_final: 0.7892 (pp20) outliers start: 3 outliers final: 0 residues processed: 695 average time/residue: 0.1260 time to fit residues: 131.1681 Evaluate side-chains 611 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 610 time to evaluate : 0.610 ------------------------------------------------------------------------------- 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: 5.9990 chunk 46 optimal weight: 6.9990 chunk 120 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 32 optimal weight: 0.0770 chunk 122 optimal weight: 10.0000 chunk 115 optimal weight: 0.1980 chunk 168 optimal weight: 10.0000 chunk 157 optimal weight: 30.0000 overall best weight: 2.8544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN A 242 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN B 19 GLN B 218 ASN B 232 ASN B 304 HIS B 320 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN B 646 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 80 HIS D 216 GLN D 249 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.132009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.090704 restraints weight = 39866.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.093979 restraints weight = 21498.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.096148 restraints weight = 13644.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.097533 restraints weight = 9703.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.098419 restraints weight = 7593.338| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.6272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16386 Z= 0.234 Angle : 0.635 9.284 22134 Z= 0.338 Chirality : 0.043 0.254 2360 Planarity : 0.004 0.040 2818 Dihedral : 8.901 135.973 2290 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.17 % Allowed : 1.98 % Favored : 97.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.19), residues: 1932 helix: 1.01 (0.15), residues: 1155 sheet: -0.44 (0.39), residues: 164 loop : 0.13 (0.24), residues: 613 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 196 TYR 0.034 0.002 TYR D 130 PHE 0.027 0.002 PHE C 168 TRP 0.012 0.002 TRP A 623 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.23 (16386) covalent geometry : angle 0.63478 / 0.34 (22134) hydrogen bonds : bond 0.04038 / 2.57 ( 871) hydrogen bonds : angle 4.94848 / 3.52 ( 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 685 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 682 time to evaluate : 0.646 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 15 GLU cc_start: 0.9234 (tt0) cc_final: 0.8293 (tm-30) REVERT: A 18 ILE cc_start: 0.9400 (mm) cc_final: 0.8990 (mm) REVERT: A 41 ILE cc_start: 0.9606 (mm) cc_final: 0.9293 (mm) REVERT: A 64 TYR cc_start: 0.9104 (m-10) cc_final: 0.8770 (m-10) REVERT: A 65 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8592 (mm-30) REVERT: A 87 LYS cc_start: 0.9529 (tptt) cc_final: 0.9265 (mmmm) REVERT: A 107 LYS cc_start: 0.9110 (mtpp) cc_final: 0.8690 (mtpp) REVERT: A 118 TYR cc_start: 0.9352 (t80) cc_final: 0.9126 (t80) REVERT: A 120 ASP cc_start: 0.9091 (m-30) cc_final: 0.8760 (m-30) REVERT: A 139 GLU cc_start: 0.9397 (mm-30) cc_final: 0.9117 (mm-30) REVERT: A 142 ASN cc_start: 0.9405 (m-40) cc_final: 0.9131 (m110) REVERT: A 147 GLN cc_start: 0.9172 (mt0) cc_final: 0.8817 (mt0) REVERT: A 150 GLN cc_start: 0.9296 (tm-30) cc_final: 0.8985 (tm-30) REVERT: A 181 ASP cc_start: 0.9011 (m-30) cc_final: 0.8626 (m-30) REVERT: A 214 LYS cc_start: 0.9257 (mmmt) cc_final: 0.9054 (mmmt) REVERT: A 223 VAL cc_start: 0.9597 (m) cc_final: 0.9146 (p) REVERT: A 227 MET cc_start: 0.9360 (mtp) cc_final: 0.8893 (mtp) REVERT: A 251 LEU cc_start: 0.9637 (tp) cc_final: 0.9332 (tp) REVERT: A 257 ASP cc_start: 0.9354 (m-30) cc_final: 0.8664 (m-30) REVERT: A 286 ASP cc_start: 0.8726 (m-30) cc_final: 0.8375 (m-30) REVERT: A 321 GLU cc_start: 0.8572 (pp20) cc_final: 0.8323 (pp20) REVERT: A 322 MET cc_start: 0.8672 (mmp) cc_final: 0.8225 (mmm) REVERT: A 349 LEU cc_start: 0.9636 (mt) cc_final: 0.9348 (mt) REVERT: A 361 GLN cc_start: 0.9165 (tp40) cc_final: 0.8029 (tp-100) REVERT: A 362 ASP cc_start: 0.8261 (m-30) cc_final: 0.7406 (m-30) REVERT: A 365 ASN cc_start: 0.9297 (m110) cc_final: 0.8005 (m-40) REVERT: A 381 LEU cc_start: 0.9554 (tp) cc_final: 0.9343 (tp) REVERT: A 403 ILE cc_start: 0.9237 (mm) cc_final: 0.8939 (mm) REVERT: A 407 ILE cc_start: 0.9423 (mt) cc_final: 0.9129 (mt) REVERT: A 458 MET cc_start: 0.9176 (mmp) cc_final: 0.8887 (mmm) REVERT: A 490 THR cc_start: 0.9673 (m) cc_final: 0.9409 (p) REVERT: A 505 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8758 (mt-10) REVERT: A 570 MET cc_start: 0.9250 (mtp) cc_final: 0.9010 (mtp) REVERT: A 573 SER cc_start: 0.9305 (p) cc_final: 0.8546 (p) REVERT: A 632 MET cc_start: 0.8836 (mtp) cc_final: 0.8531 (mtp) REVERT: A 636 LYS cc_start: 0.9650 (mmmm) cc_final: 0.8909 (mmmm) REVERT: A 639 ASP cc_start: 0.9208 (m-30) cc_final: 0.8840 (m-30) REVERT: A 643 THR cc_start: 0.9579 (p) cc_final: 0.9292 (t) REVERT: A 646 GLN cc_start: 0.9197 (pt0) cc_final: 0.8913 (pt0) REVERT: A 650 GLN cc_start: 0.8690 (mt0) cc_final: 0.8224 (mt0) REVERT: A 667 LEU cc_start: 0.9524 (tt) cc_final: 0.9291 (tt) REVERT: A 668 ASN cc_start: 0.9448 (m110) cc_final: 0.9117 (m110) REVERT: A 686 ARG cc_start: 0.8800 (mmt180) cc_final: 0.8265 (mmt-90) REVERT: B 18 ILE cc_start: 0.9531 (mp) cc_final: 0.9277 (mp) REVERT: B 25 GLN cc_start: 0.9229 (mt0) cc_final: 0.8632 (mt0) REVERT: B 31 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8567 (mt-10) REVERT: B 58 LEU cc_start: 0.9697 (mt) cc_final: 0.9468 (mt) REVERT: B 65 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8221 (mp0) REVERT: B 87 LYS cc_start: 0.9405 (tptp) cc_final: 0.9028 (tptp) REVERT: B 95 MET cc_start: 0.9565 (tpt) cc_final: 0.9342 (tpp) REVERT: B 120 ASP cc_start: 0.8931 (m-30) cc_final: 0.8719 (m-30) REVERT: B 147 GLN cc_start: 0.9313 (mt0) cc_final: 0.9030 (mt0) REVERT: B 149 TYR cc_start: 0.9353 (t80) cc_final: 0.8881 (t80) REVERT: B 172 LEU cc_start: 0.9430 (mp) cc_final: 0.9125 (mp) REVERT: B 174 GLU cc_start: 0.8360 (mm-30) cc_final: 0.8059 (mm-30) REVERT: B 191 GLN cc_start: 0.8938 (mm-40) cc_final: 0.8638 (mm-40) REVERT: B 228 LYS cc_start: 0.8995 (mmtm) cc_final: 0.8469 (mmtt) REVERT: B 232 ASN cc_start: 0.9079 (t160) cc_final: 0.8634 (t0) REVERT: B 238 ASP cc_start: 0.8483 (p0) cc_final: 0.8047 (p0) REVERT: B 278 LEU cc_start: 0.9294 (tp) cc_final: 0.9076 (tp) REVERT: B 279 SER cc_start: 0.8304 (m) cc_final: 0.7788 (p) REVERT: B 286 ASP cc_start: 0.8731 (m-30) cc_final: 0.8419 (m-30) REVERT: B 290 GLU cc_start: 0.9230 (tp30) cc_final: 0.8899 (tp30) REVERT: B 312 GLN cc_start: 0.9078 (pm20) cc_final: 0.8460 (pm20) REVERT: B 333 LYS cc_start: 0.9271 (tptp) cc_final: 0.8962 (tttp) REVERT: B 384 GLU cc_start: 0.8573 (pm20) cc_final: 0.7842 (pm20) REVERT: B 398 ASP cc_start: 0.8851 (t0) cc_final: 0.8646 (t0) REVERT: B 413 SER cc_start: 0.9592 (m) cc_final: 0.9155 (t) REVERT: B 415 ASN cc_start: 0.9682 (t0) cc_final: 0.9194 (t0) REVERT: B 426 GLU cc_start: 0.8956 (pp20) cc_final: 0.8649 (tm-30) REVERT: B 493 MET cc_start: 0.9392 (tmm) cc_final: 0.9108 (tmm) REVERT: B 496 ASN cc_start: 0.9435 (t0) cc_final: 0.8848 (t0) REVERT: B 500 ILE cc_start: 0.9696 (mp) cc_final: 0.9311 (mp) REVERT: B 505 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8274 (mt-10) REVERT: B 515 ASP cc_start: 0.9377 (m-30) cc_final: 0.9112 (m-30) REVERT: B 516 GLN cc_start: 0.9193 (mp10) cc_final: 0.8919 (mp10) REVERT: B 575 ARG cc_start: 0.8863 (mtm110) cc_final: 0.8439 (mtm110) REVERT: B 595 MET cc_start: 0.9409 (mmm) cc_final: 0.9134 (mmm) REVERT: B 599 GLU cc_start: 0.8777 (pt0) cc_final: 0.8492 (pt0) REVERT: B 601 ILE cc_start: 0.9531 (mm) cc_final: 0.9305 (mm) REVERT: B 628 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8320 (mm-30) REVERT: B 632 MET cc_start: 0.8789 (mtp) cc_final: 0.8017 (mtp) REVERT: B 636 LYS cc_start: 0.9705 (mmtp) cc_final: 0.9408 (mmtm) REVERT: B 646 GLN cc_start: 0.9545 (pt0) cc_final: 0.8837 (pm20) REVERT: B 650 GLN cc_start: 0.8088 (mt0) cc_final: 0.7731 (mt0) REVERT: C 16 ASP cc_start: 0.6581 (p0) cc_final: 0.6039 (p0) REVERT: C 179 TYR cc_start: 0.8782 (t80) cc_final: 0.8495 (t80) REVERT: D 158 VAL cc_start: 0.8234 (t) cc_final: 0.7242 (m) REVERT: D 233 ASN cc_start: 0.8847 (m110) cc_final: 0.8457 (m110) outliers start: 3 outliers final: 0 residues processed: 682 average time/residue: 0.1227 time to fit residues: 126.2785 Evaluate side-chains 604 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 604 time to evaluate : 0.439 ------------------------------------------------------------------------------- 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: 0.9990 chunk 183 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 172 optimal weight: 20.0000 chunk 52 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 232 ASN B 387 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.134975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.093258 restraints weight = 40056.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.096716 restraints weight = 21004.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.098876 restraints weight = 13008.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.100215 restraints weight = 9285.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.101256 restraints weight = 7328.106| |-----------------------------------------------------------------------------| r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.6561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 16386 Z= 0.182 Angle : 0.611 7.834 22134 Z= 0.327 Chirality : 0.043 0.243 2360 Planarity : 0.004 0.040 2818 Dihedral : 8.703 136.497 2290 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.06 % Allowed : 1.57 % Favored : 98.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.19), residues: 1932 helix: 1.02 (0.15), residues: 1141 sheet: -0.25 (0.41), residues: 152 loop : 0.04 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 196 TYR 0.048 0.002 TYR D 162 PHE 0.028 0.002 PHE C 178 TRP 0.020 0.002 TRP C 44 HIS 0.004 0.001 HIS B 438 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (16386) covalent geometry : angle 0.61140 / 0.33 (22134) hydrogen bonds : bond 0.03904 / 2.49 ( 871) hydrogen bonds : angle 4.85461 / 3.50 ( 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 695 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 694 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ILE cc_start: 0.9620 (mm) cc_final: 0.9349 (mm) REVERT: A 54 LYS cc_start: 0.9721 (ttmm) cc_final: 0.9398 (ttmm) REVERT: A 64 TYR cc_start: 0.9033 (m-10) cc_final: 0.8782 (m-10) REVERT: A 87 LYS cc_start: 0.9525 (tptt) cc_final: 0.9254 (mmmm) REVERT: A 107 LYS cc_start: 0.9023 (mtpp) cc_final: 0.8589 (mtpp) REVERT: A 118 TYR cc_start: 0.9379 (t80) cc_final: 0.9131 (t80) REVERT: A 120 ASP cc_start: 0.8977 (m-30) cc_final: 0.8662 (m-30) REVERT: A 139 GLU cc_start: 0.9389 (mm-30) cc_final: 0.9106 (mm-30) REVERT: A 142 ASN cc_start: 0.9409 (m-40) cc_final: 0.9118 (m110) REVERT: A 147 GLN cc_start: 0.9069 (mt0) cc_final: 0.8634 (mt0) REVERT: A 150 GLN cc_start: 0.9338 (tm-30) cc_final: 0.9053 (tm-30) REVERT: A 181 ASP cc_start: 0.8959 (m-30) cc_final: 0.8538 (m-30) REVERT: A 223 VAL cc_start: 0.9594 (m) cc_final: 0.9152 (p) REVERT: A 227 MET cc_start: 0.9354 (mtp) cc_final: 0.8882 (mtp) REVERT: A 251 LEU cc_start: 0.9641 (tp) cc_final: 0.9315 (tp) REVERT: A 257 ASP cc_start: 0.9378 (m-30) cc_final: 0.8661 (m-30) REVERT: A 268 SER cc_start: 0.9103 (m) cc_final: 0.8803 (p) REVERT: A 286 ASP cc_start: 0.8676 (m-30) cc_final: 0.8345 (m-30) REVERT: A 321 GLU cc_start: 0.8609 (pp20) cc_final: 0.8058 (pp20) REVERT: A 322 MET cc_start: 0.8645 (mmp) cc_final: 0.7811 (mmm) REVERT: A 349 LEU cc_start: 0.9606 (mt) cc_final: 0.9314 (mt) REVERT: A 361 GLN cc_start: 0.9081 (tp40) cc_final: 0.7886 (tp-100) REVERT: A 362 ASP cc_start: 0.8268 (m-30) cc_final: 0.7432 (m-30) REVERT: A 365 ASN cc_start: 0.9283 (m110) cc_final: 0.7986 (m-40) REVERT: A 403 ILE cc_start: 0.9184 (mm) cc_final: 0.8888 (mm) REVERT: A 407 ILE cc_start: 0.9400 (mt) cc_final: 0.9111 (mt) REVERT: A 437 THR cc_start: 0.9673 (m) cc_final: 0.9440 (m) REVERT: A 441 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8698 (mt-10) REVERT: A 474 GLN cc_start: 0.9159 (mm-40) cc_final: 0.8922 (mm-40) REVERT: A 479 TYR cc_start: 0.9445 (t80) cc_final: 0.9131 (t80) REVERT: A 505 GLU cc_start: 0.9081 (mt-10) cc_final: 0.8775 (mt-10) REVERT: A 516 GLN cc_start: 0.9453 (mt0) cc_final: 0.8956 (tp-100) REVERT: A 570 MET cc_start: 0.9255 (mtp) cc_final: 0.8960 (mtp) REVERT: A 573 SER cc_start: 0.9294 (p) cc_final: 0.8901 (p) REVERT: A 632 MET cc_start: 0.8738 (mtp) cc_final: 0.8447 (mtp) REVERT: A 636 LYS cc_start: 0.9628 (mmmm) cc_final: 0.9018 (mmmm) REVERT: A 643 THR cc_start: 0.9587 (p) cc_final: 0.9294 (t) REVERT: A 646 GLN cc_start: 0.9165 (pt0) cc_final: 0.8911 (pt0) REVERT: A 650 GLN cc_start: 0.8751 (mt0) cc_final: 0.7885 (mt0) REVERT: A 664 THR cc_start: 0.9301 (p) cc_final: 0.8515 (p) REVERT: A 667 LEU cc_start: 0.9540 (tt) cc_final: 0.9272 (tt) REVERT: A 668 ASN cc_start: 0.9380 (m110) cc_final: 0.8988 (m110) REVERT: B 18 ILE cc_start: 0.9537 (mp) cc_final: 0.9252 (mp) REVERT: B 25 GLN cc_start: 0.9258 (mt0) cc_final: 0.8657 (mt0) REVERT: B 31 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8550 (mt-10) REVERT: B 58 LEU cc_start: 0.9693 (mt) cc_final: 0.9460 (mt) REVERT: B 87 LYS cc_start: 0.9394 (tptp) cc_final: 0.9056 (tptp) REVERT: B 117 ARG cc_start: 0.8863 (mtt180) cc_final: 0.8588 (ttm110) REVERT: B 147 GLN cc_start: 0.9241 (mt0) cc_final: 0.8798 (mt0) REVERT: B 149 TYR cc_start: 0.9419 (t80) cc_final: 0.8849 (t80) REVERT: B 172 LEU cc_start: 0.9428 (mp) cc_final: 0.9023 (mp) REVERT: B 174 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7981 (mm-30) REVERT: B 227 MET cc_start: 0.9229 (mtm) cc_final: 0.8945 (mtm) REVERT: B 235 ARG cc_start: 0.9267 (tpp80) cc_final: 0.9000 (ttm-80) REVERT: B 238 ASP cc_start: 0.8512 (p0) cc_final: 0.8059 (p0) REVERT: B 257 ASP cc_start: 0.9056 (m-30) cc_final: 0.8831 (m-30) REVERT: B 279 SER cc_start: 0.8220 (m) cc_final: 0.7749 (p) REVERT: B 286 ASP cc_start: 0.8731 (m-30) cc_final: 0.8485 (m-30) REVERT: B 290 GLU cc_start: 0.9268 (tp30) cc_final: 0.8823 (tp30) REVERT: B 312 GLN cc_start: 0.9082 (pm20) cc_final: 0.8156 (pm20) REVERT: B 317 MET cc_start: 0.8391 (ptp) cc_final: 0.7886 (ptp) REVERT: B 333 LYS cc_start: 0.9275 (tptp) cc_final: 0.8989 (tttp) REVERT: B 348 MET cc_start: 0.9286 (ptp) cc_final: 0.9020 (ptp) REVERT: B 350 ARG cc_start: 0.7657 (mmm160) cc_final: 0.6892 (mmm160) REVERT: B 384 GLU cc_start: 0.8627 (pm20) cc_final: 0.7972 (pm20) REVERT: B 398 ASP cc_start: 0.8814 (t0) cc_final: 0.8605 (t0) REVERT: B 407 ILE cc_start: 0.9513 (mt) cc_final: 0.9053 (mt) REVERT: B 415 ASN cc_start: 0.9651 (t0) cc_final: 0.9194 (t0) REVERT: B 426 GLU cc_start: 0.8930 (pp20) cc_final: 0.8612 (tm-30) REVERT: B 427 LYS cc_start: 0.9416 (tppt) cc_final: 0.9104 (mmmm) REVERT: B 458 MET cc_start: 0.9360 (mmp) cc_final: 0.9064 (mmp) REVERT: B 459 LYS cc_start: 0.9269 (mttp) cc_final: 0.8698 (mtmm) REVERT: B 474 GLN cc_start: 0.9096 (mm-40) cc_final: 0.8886 (mm-40) REVERT: B 493 MET cc_start: 0.9398 (tmm) cc_final: 0.9138 (tmm) REVERT: B 501 GLN cc_start: 0.9389 (tt0) cc_final: 0.8923 (tt0) REVERT: B 505 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8153 (mt-10) REVERT: B 515 ASP cc_start: 0.9386 (m-30) cc_final: 0.9066 (m-30) REVERT: B 516 GLN cc_start: 0.9217 (mp10) cc_final: 0.8952 (mp10) REVERT: B 588 GLN cc_start: 0.9479 (mm-40) cc_final: 0.9266 (mm-40) REVERT: B 595 MET cc_start: 0.9334 (mmm) cc_final: 0.9123 (mmm) REVERT: B 601 ILE cc_start: 0.9528 (mm) cc_final: 0.9321 (mm) REVERT: B 604 ARG cc_start: 0.9194 (tpp80) cc_final: 0.8946 (ttm-80) REVERT: B 628 GLU cc_start: 0.8889 (mm-30) cc_final: 0.8408 (mm-30) REVERT: B 646 GLN cc_start: 0.9487 (pt0) cc_final: 0.9225 (pt0) REVERT: B 667 LEU cc_start: 0.9416 (tp) cc_final: 0.9151 (tp) REVERT: C 16 ASP cc_start: 0.6639 (p0) cc_final: 0.6086 (p0) REVERT: C 179 TYR cc_start: 0.8733 (t80) cc_final: 0.8475 (t80) REVERT: D 112 LEU cc_start: 0.6353 (mm) cc_final: 0.5989 (mm) REVERT: D 158 VAL cc_start: 0.8162 (t) cc_final: 0.7920 (m) REVERT: D 162 TYR cc_start: 0.8506 (m-80) cc_final: 0.8228 (m-80) REVERT: D 178 PHE cc_start: 0.9163 (m-80) cc_final: 0.8625 (m-80) REVERT: D 233 ASN cc_start: 0.8638 (m110) cc_final: 0.8436 (m-40) REVERT: D 252 LEU cc_start: 0.8815 (mt) cc_final: 0.8487 (mp) outliers start: 1 outliers final: 0 residues processed: 694 average time/residue: 0.1231 time to fit residues: 128.5572 Evaluate side-chains 598 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 598 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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: 2.9990 chunk 51 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 56 optimal weight: 0.6980 chunk 186 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 45 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 156 optimal weight: 5.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN A 44 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 GLN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.130514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.088881 restraints weight = 40140.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.092084 restraints weight = 21509.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.094174 restraints weight = 13654.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.095521 restraints weight = 9827.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.096424 restraints weight = 7733.917| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.6836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 16386 Z= 0.274 Angle : 0.685 9.784 22134 Z= 0.365 Chirality : 0.045 0.204 2360 Planarity : 0.004 0.066 2818 Dihedral : 8.901 137.943 2290 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.06 % Allowed : 1.69 % Favored : 98.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.18), residues: 1932 helix: 0.75 (0.15), residues: 1162 sheet: -0.52 (0.40), residues: 152 loop : -0.15 (0.24), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 274 TYR 0.038 0.002 TYR D 162 PHE 0.029 0.002 PHE B 378 TRP 0.014 0.002 TRP A 623 HIS 0.005 0.001 HIS A 647 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.27 (16386) covalent geometry : angle 0.68480 / 0.37 (22134) hydrogen bonds : bond 0.04135 / 2.64 ( 871) hydrogen bonds : angle 5.03059 / 3.60 ( 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 665 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 664 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.9730 (ttmm) cc_final: 0.9382 (ttmm) REVERT: A 64 TYR cc_start: 0.9254 (m-10) cc_final: 0.8686 (m-10) REVERT: A 65 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8077 (mp0) REVERT: A 87 LYS cc_start: 0.9533 (tptt) cc_final: 0.9235 (mmmm) REVERT: A 107 LYS cc_start: 0.9015 (mtpp) cc_final: 0.8548 (mtpp) REVERT: A 120 ASP cc_start: 0.8980 (m-30) cc_final: 0.8719 (m-30) REVERT: A 139 GLU cc_start: 0.9412 (mm-30) cc_final: 0.9127 (mm-30) REVERT: A 142 ASN cc_start: 0.9414 (m-40) cc_final: 0.9123 (m110) REVERT: A 147 GLN cc_start: 0.9259 (mt0) cc_final: 0.8902 (mt0) REVERT: A 150 GLN cc_start: 0.9388 (tm-30) cc_final: 0.9075 (tm-30) REVERT: A 214 LYS cc_start: 0.9497 (mmmt) cc_final: 0.9212 (mmmt) REVERT: A 218 ASN cc_start: 0.9226 (t0) cc_final: 0.8587 (p0) REVERT: A 223 VAL cc_start: 0.9579 (m) cc_final: 0.9160 (p) REVERT: A 227 MET cc_start: 0.9386 (mtp) cc_final: 0.8907 (mtp) REVERT: A 235 ARG cc_start: 0.8578 (ttm110) cc_final: 0.8074 (ttm110) REVERT: A 251 LEU cc_start: 0.9673 (tp) cc_final: 0.9358 (tp) REVERT: A 257 ASP cc_start: 0.9381 (m-30) cc_final: 0.8904 (m-30) REVERT: A 263 ASP cc_start: 0.9026 (m-30) cc_final: 0.8724 (m-30) REVERT: A 286 ASP cc_start: 0.8718 (m-30) cc_final: 0.8354 (m-30) REVERT: A 321 GLU cc_start: 0.8731 (pp20) cc_final: 0.8358 (pp20) REVERT: A 322 MET cc_start: 0.8705 (mmp) cc_final: 0.8069 (mmm) REVERT: A 333 LYS cc_start: 0.9209 (tttt) cc_final: 0.8966 (tptm) REVERT: A 349 LEU cc_start: 0.9639 (mt) cc_final: 0.9322 (mt) REVERT: A 361 GLN cc_start: 0.9151 (tp40) cc_final: 0.7991 (tp-100) REVERT: A 362 ASP cc_start: 0.8345 (m-30) cc_final: 0.7488 (m-30) REVERT: A 365 ASN cc_start: 0.9304 (m110) cc_final: 0.8058 (m-40) REVERT: A 386 LEU cc_start: 0.9695 (mt) cc_final: 0.9453 (mt) REVERT: A 403 ILE cc_start: 0.9203 (mm) cc_final: 0.8936 (mm) REVERT: A 405 LEU cc_start: 0.9086 (mt) cc_final: 0.8884 (mt) REVERT: A 407 ILE cc_start: 0.9245 (mt) cc_final: 0.8967 (mt) REVERT: A 421 GLU cc_start: 0.8541 (pp20) cc_final: 0.8310 (pp20) REVERT: A 437 THR cc_start: 0.9690 (m) cc_final: 0.9446 (m) REVERT: A 458 MET cc_start: 0.9402 (mmm) cc_final: 0.8639 (mmm) REVERT: A 505 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8759 (mt-10) REVERT: A 516 GLN cc_start: 0.9449 (mt0) cc_final: 0.8899 (tp-100) REVERT: A 599 GLU cc_start: 0.8236 (mp0) cc_final: 0.7970 (mp0) REVERT: A 615 MET cc_start: 0.9019 (mmp) cc_final: 0.8758 (mmp) REVERT: A 632 MET cc_start: 0.8843 (mtp) cc_final: 0.8469 (mtp) REVERT: A 636 LYS cc_start: 0.9593 (mmmm) cc_final: 0.8925 (mmmm) REVERT: A 639 ASP cc_start: 0.9177 (m-30) cc_final: 0.8844 (m-30) REVERT: A 643 THR cc_start: 0.9627 (p) cc_final: 0.9229 (t) REVERT: A 646 GLN cc_start: 0.9169 (pt0) cc_final: 0.8905 (pt0) REVERT: A 650 GLN cc_start: 0.8745 (mt0) cc_final: 0.7957 (mt0) REVERT: A 667 LEU cc_start: 0.9590 (tt) cc_final: 0.9380 (tt) REVERT: A 668 ASN cc_start: 0.9456 (m110) cc_final: 0.9156 (m110) REVERT: A 686 ARG cc_start: 0.8925 (mmt180) cc_final: 0.8296 (mmt180) REVERT: B 18 ILE cc_start: 0.9553 (mp) cc_final: 0.9281 (mp) REVERT: B 25 GLN cc_start: 0.9257 (mt0) cc_final: 0.8727 (mt0) REVERT: B 31 GLU cc_start: 0.8868 (mt-10) cc_final: 0.8586 (mt-10) REVERT: B 58 LEU cc_start: 0.9685 (mt) cc_final: 0.9481 (mt) REVERT: B 87 LYS cc_start: 0.9433 (tptp) cc_final: 0.9123 (tptp) REVERT: B 117 ARG cc_start: 0.8939 (mtt180) cc_final: 0.8680 (ttm110) REVERT: B 120 ASP cc_start: 0.8970 (m-30) cc_final: 0.8672 (m-30) REVERT: B 147 GLN cc_start: 0.9309 (mt0) cc_final: 0.8789 (mt0) REVERT: B 149 TYR cc_start: 0.9427 (t80) cc_final: 0.8793 (t80) REVERT: B 174 GLU cc_start: 0.8259 (mm-30) cc_final: 0.7999 (mm-30) REVERT: B 232 ASN cc_start: 0.9005 (t0) cc_final: 0.8528 (t0) REVERT: B 238 ASP cc_start: 0.8648 (p0) cc_final: 0.8280 (p0) REVERT: B 257 ASP cc_start: 0.8944 (m-30) cc_final: 0.8737 (m-30) REVERT: B 274 ARG cc_start: 0.7948 (mmt-90) cc_final: 0.7622 (mpt180) REVERT: B 286 ASP cc_start: 0.8729 (m-30) cc_final: 0.8496 (m-30) REVERT: B 312 GLN cc_start: 0.9062 (pm20) cc_final: 0.8322 (pm20) REVERT: B 317 MET cc_start: 0.8580 (ptp) cc_final: 0.8095 (ptp) REVERT: B 333 LYS cc_start: 0.9267 (tptp) cc_final: 0.8921 (tttm) REVERT: B 345 LYS cc_start: 0.9559 (tttt) cc_final: 0.9352 (tttt) REVERT: B 348 MET cc_start: 0.9273 (ptp) cc_final: 0.9041 (ptp) REVERT: B 384 GLU cc_start: 0.8651 (pm20) cc_final: 0.7901 (pm20) REVERT: B 398 ASP cc_start: 0.8907 (t0) cc_final: 0.8687 (t0) REVERT: B 407 ILE cc_start: 0.9516 (mt) cc_final: 0.9265 (mt) REVERT: B 413 SER cc_start: 0.9585 (m) cc_final: 0.9129 (t) REVERT: B 414 LEU cc_start: 0.9696 (mt) cc_final: 0.9462 (mt) REVERT: B 415 ASN cc_start: 0.9601 (t0) cc_final: 0.9241 (t0) REVERT: B 426 GLU cc_start: 0.8974 (pp20) cc_final: 0.8651 (tm-30) REVERT: B 427 LYS cc_start: 0.9425 (tppt) cc_final: 0.9118 (mmmm) REVERT: B 458 MET cc_start: 0.9373 (mmp) cc_final: 0.9093 (mmp) REVERT: B 459 LYS cc_start: 0.9337 (mttp) cc_final: 0.8784 (mtmm) REVERT: B 467 ASN cc_start: 0.9269 (m-40) cc_final: 0.9044 (m-40) REVERT: B 493 MET cc_start: 0.9390 (tmm) cc_final: 0.9152 (tmm) REVERT: B 494 MET cc_start: 0.9505 (mmm) cc_final: 0.9165 (mmt) REVERT: B 501 GLN cc_start: 0.9379 (tt0) cc_final: 0.9136 (tt0) REVERT: B 515 ASP cc_start: 0.9405 (m-30) cc_final: 0.9081 (m-30) REVERT: B 516 GLN cc_start: 0.9267 (mp10) cc_final: 0.8987 (mp10) REVERT: B 588 GLN cc_start: 0.9495 (mm-40) cc_final: 0.9232 (mm-40) REVERT: B 599 GLU cc_start: 0.8810 (pt0) cc_final: 0.8522 (pt0) REVERT: B 628 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8280 (mm-30) REVERT: B 646 GLN cc_start: 0.9479 (pt0) cc_final: 0.9210 (pt0) REVERT: C 16 ASP cc_start: 0.6883 (p0) cc_final: 0.6350 (p0) REVERT: C 74 MET cc_start: 0.6287 (ptt) cc_final: 0.6018 (ptp) REVERT: C 179 TYR cc_start: 0.8834 (t80) cc_final: 0.8573 (t80) REVERT: C 214 ASN cc_start: 0.8576 (p0) cc_final: 0.7875 (p0) REVERT: D 158 VAL cc_start: 0.8230 (t) cc_final: 0.7450 (m) REVERT: D 162 TYR cc_start: 0.8533 (m-80) cc_final: 0.7996 (m-80) REVERT: D 233 ASN cc_start: 0.8808 (m110) cc_final: 0.8274 (m110) REVERT: D 321 TYR cc_start: 0.9000 (m-80) cc_final: 0.8606 (m-80) outliers start: 1 outliers final: 0 residues processed: 664 average time/residue: 0.1177 time to fit residues: 117.8785 Evaluate side-chains 592 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 592 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 42 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 153 optimal weight: 10.0000 chunk 11 optimal weight: 0.9980 chunk 158 optimal weight: 20.0000 chunk 97 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 13 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 GLN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN C 201 HIS ** C 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.135547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.093331 restraints weight = 39703.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.096760 restraints weight = 20832.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.098955 restraints weight = 12900.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.100346 restraints weight = 9197.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.101282 restraints weight = 7212.202| |-----------------------------------------------------------------------------| r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.7036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16386 Z= 0.145 Angle : 0.619 8.708 22134 Z= 0.329 Chirality : 0.043 0.235 2360 Planarity : 0.004 0.041 2818 Dihedral : 8.401 137.311 2290 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.12 % Allowed : 1.11 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.19), residues: 1932 helix: 0.97 (0.15), residues: 1147 sheet: -0.40 (0.41), residues: 148 loop : -0.23 (0.24), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 196 TYR 0.036 0.002 TYR D 162 PHE 0.023 0.002 PHE C 168 TRP 0.054 0.002 TRP D 124 HIS 0.017 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (16386) covalent geometry : angle 0.61927 / 0.33 (22134) hydrogen bonds : bond 0.03915 / 2.53 ( 871) hydrogen bonds : angle 4.83503 / 3.47 ( 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 676 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 674 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.9272 (tt0) cc_final: 0.8479 (tm-30) REVERT: A 16 ILE cc_start: 0.9455 (mm) cc_final: 0.9248 (mm) REVERT: A 18 ILE cc_start: 0.9416 (mm) cc_final: 0.8945 (mm) REVERT: A 54 LYS cc_start: 0.9700 (ttmm) cc_final: 0.9394 (ttmm) REVERT: A 64 TYR cc_start: 0.9181 (m-10) cc_final: 0.8429 (m-10) REVERT: A 65 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8072 (mp0) REVERT: A 66 GLU cc_start: 0.8673 (tp30) cc_final: 0.8468 (tp30) REVERT: A 87 LYS cc_start: 0.9515 (tptt) cc_final: 0.9249 (mmmm) REVERT: A 99 LYS cc_start: 0.9439 (mmmt) cc_final: 0.9144 (mmmm) REVERT: A 107 LYS cc_start: 0.9070 (mtpp) cc_final: 0.8611 (mtpp) REVERT: A 117 ARG cc_start: 0.8946 (mtt-85) cc_final: 0.8642 (mtp85) REVERT: A 120 ASP cc_start: 0.8886 (m-30) cc_final: 0.8665 (m-30) REVERT: A 124 ILE cc_start: 0.9708 (mm) cc_final: 0.9397 (mm) REVERT: A 139 GLU cc_start: 0.9375 (mm-30) cc_final: 0.9075 (mm-30) REVERT: A 142 ASN cc_start: 0.9399 (m-40) cc_final: 0.9088 (m110) REVERT: A 147 GLN cc_start: 0.9080 (mt0) cc_final: 0.8578 (mt0) REVERT: A 150 GLN cc_start: 0.9410 (tm-30) cc_final: 0.8410 (tm-30) REVERT: A 214 LYS cc_start: 0.9463 (mmmt) cc_final: 0.9224 (mmmm) REVERT: A 223 VAL cc_start: 0.9565 (m) cc_final: 0.9142 (p) REVERT: A 227 MET cc_start: 0.9365 (mtp) cc_final: 0.8881 (mtp) REVERT: A 251 LEU cc_start: 0.9639 (tp) cc_final: 0.9325 (tp) REVERT: A 286 ASP cc_start: 0.8639 (m-30) cc_final: 0.8307 (m-30) REVERT: A 322 MET cc_start: 0.8690 (mmp) cc_final: 0.8187 (mmm) REVERT: A 345 LYS cc_start: 0.9436 (tttt) cc_final: 0.9235 (tttt) REVERT: A 349 LEU cc_start: 0.9577 (mt) cc_final: 0.9264 (mt) REVERT: A 361 GLN cc_start: 0.9100 (tp40) cc_final: 0.8556 (tp-100) REVERT: A 362 ASP cc_start: 0.8286 (m-30) cc_final: 0.7515 (m-30) REVERT: A 365 ASN cc_start: 0.9257 (m110) cc_final: 0.8550 (m110) REVERT: A 386 LEU cc_start: 0.9659 (mt) cc_final: 0.9419 (mt) REVERT: A 403 ILE cc_start: 0.9167 (mm) cc_final: 0.8906 (mm) REVERT: A 407 ILE cc_start: 0.9281 (mt) cc_final: 0.9004 (mt) REVERT: A 410 ASN cc_start: 0.8928 (OUTLIER) cc_final: 0.8409 (t160) REVERT: A 421 GLU cc_start: 0.8370 (pp20) cc_final: 0.8102 (pp20) REVERT: A 437 THR cc_start: 0.9636 (m) cc_final: 0.9351 (m) REVERT: A 441 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8740 (mt-10) REVERT: A 458 MET cc_start: 0.9356 (mmm) cc_final: 0.8597 (mmm) REVERT: A 505 GLU cc_start: 0.9114 (mt-10) cc_final: 0.8776 (mt-10) REVERT: A 516 GLN cc_start: 0.9448 (mt0) cc_final: 0.8960 (tp-100) REVERT: A 585 SER cc_start: 0.9493 (p) cc_final: 0.8884 (t) REVERT: A 632 MET cc_start: 0.8796 (mtp) cc_final: 0.8124 (mtp) REVERT: A 636 LYS cc_start: 0.9544 (mmmm) cc_final: 0.9077 (mmmm) REVERT: A 643 THR cc_start: 0.9573 (p) cc_final: 0.9300 (t) REVERT: A 646 GLN cc_start: 0.9164 (pt0) cc_final: 0.8809 (pt0) REVERT: A 650 GLN cc_start: 0.8683 (mt0) cc_final: 0.7791 (mt0) REVERT: A 664 THR cc_start: 0.9338 (p) cc_final: 0.8556 (p) REVERT: A 667 LEU cc_start: 0.9563 (tt) cc_final: 0.9273 (tt) REVERT: A 668 ASN cc_start: 0.9416 (m110) cc_final: 0.9084 (m110) REVERT: B 18 ILE cc_start: 0.9536 (mp) cc_final: 0.9292 (mp) REVERT: B 25 GLN cc_start: 0.9118 (mt0) cc_final: 0.8629 (mt0) REVERT: B 31 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8557 (mt-10) REVERT: B 71 LEU cc_start: 0.9720 (mm) cc_final: 0.9483 (mp) REVERT: B 87 LYS cc_start: 0.9398 (tptp) cc_final: 0.9063 (tptp) REVERT: B 117 ARG cc_start: 0.8863 (mtt180) cc_final: 0.8634 (ttm110) REVERT: B 120 ASP cc_start: 0.8944 (m-30) cc_final: 0.8678 (m-30) REVERT: B 147 GLN cc_start: 0.9285 (mt0) cc_final: 0.8815 (mt0) REVERT: B 149 TYR cc_start: 0.9429 (t80) cc_final: 0.8554 (t80) REVERT: B 174 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7907 (mm-30) REVERT: B 191 GLN cc_start: 0.8537 (mm-40) cc_final: 0.7862 (mt0) REVERT: B 227 MET cc_start: 0.9406 (mtp) cc_final: 0.9137 (mtp) REVERT: B 232 ASN cc_start: 0.8975 (t0) cc_final: 0.8495 (t0) REVERT: B 235 ARG cc_start: 0.9261 (tpp80) cc_final: 0.9040 (ttm-80) REVERT: B 238 ASP cc_start: 0.8631 (p0) cc_final: 0.8244 (p0) REVERT: B 257 ASP cc_start: 0.8908 (m-30) cc_final: 0.8669 (m-30) REVERT: B 258 ILE cc_start: 0.9599 (tp) cc_final: 0.9398 (tp) REVERT: B 286 ASP cc_start: 0.8704 (m-30) cc_final: 0.8465 (m-30) REVERT: B 312 GLN cc_start: 0.9110 (pm20) cc_final: 0.8688 (pm20) REVERT: B 333 LYS cc_start: 0.9294 (tptp) cc_final: 0.9044 (tttp) REVERT: B 348 MET cc_start: 0.9253 (ptp) cc_final: 0.9015 (ptp) REVERT: B 381 LEU cc_start: 0.9135 (tp) cc_final: 0.8689 (tp) REVERT: B 384 GLU cc_start: 0.8811 (pm20) cc_final: 0.7997 (pm20) REVERT: B 415 ASN cc_start: 0.9581 (t0) cc_final: 0.9221 (t0) REVERT: B 426 GLU cc_start: 0.8982 (pp20) cc_final: 0.8728 (tm-30) REVERT: B 427 LYS cc_start: 0.9454 (tppt) cc_final: 0.9173 (mmmm) REVERT: B 458 MET cc_start: 0.9346 (mmp) cc_final: 0.8969 (mmp) REVERT: B 459 LYS cc_start: 0.9344 (mttp) cc_final: 0.8790 (mtmm) REVERT: B 467 ASN cc_start: 0.9302 (m-40) cc_final: 0.9085 (m-40) REVERT: B 493 MET cc_start: 0.9383 (tmm) cc_final: 0.9118 (tmm) REVERT: B 494 MET cc_start: 0.9491 (mmm) cc_final: 0.9239 (mmt) REVERT: B 501 GLN cc_start: 0.9602 (tt0) cc_final: 0.8763 (tt0) REVERT: B 515 ASP cc_start: 0.9359 (m-30) cc_final: 0.9037 (m-30) REVERT: B 516 GLN cc_start: 0.9224 (mp10) cc_final: 0.8938 (mp10) REVERT: B 570 MET cc_start: 0.8768 (mtp) cc_final: 0.8458 (mtp) REVERT: B 588 GLN cc_start: 0.9468 (mm-40) cc_final: 0.9175 (mm-40) REVERT: B 628 GLU cc_start: 0.8879 (mm-30) cc_final: 0.8308 (mm-30) REVERT: B 645 GLN cc_start: 0.9360 (tp40) cc_final: 0.9054 (tp-100) REVERT: B 683 TYR cc_start: 0.8944 (t80) cc_final: 0.8604 (t80) REVERT: C 16 ASP cc_start: 0.6817 (p0) cc_final: 0.6275 (p0) REVERT: C 179 TYR cc_start: 0.8783 (t80) cc_final: 0.8550 (t80) REVERT: C 201 HIS cc_start: 0.7744 (m-70) cc_final: 0.7431 (m-70) REVERT: D 112 LEU cc_start: 0.6694 (mm) cc_final: 0.6452 (mm) REVERT: D 129 LYS cc_start: 0.8937 (tptp) cc_final: 0.8633 (tmtt) REVERT: D 158 VAL cc_start: 0.8223 (t) cc_final: 0.7976 (m) REVERT: D 162 TYR cc_start: 0.8440 (m-80) cc_final: 0.7927 (m-80) REVERT: D 176 LEU cc_start: 0.9453 (mt) cc_final: 0.9098 (pp) REVERT: D 178 PHE cc_start: 0.9029 (m-80) cc_final: 0.8426 (m-80) REVERT: D 208 LEU cc_start: 0.8828 (mt) cc_final: 0.8433 (mt) REVERT: D 233 ASN cc_start: 0.8785 (m110) cc_final: 0.8211 (m110) REVERT: D 252 LEU cc_start: 0.8894 (mt) cc_final: 0.8509 (mp) REVERT: D 321 TYR cc_start: 0.9006 (m-80) cc_final: 0.8687 (m-80) outliers start: 2 outliers final: 0 residues processed: 675 average time/residue: 0.1208 time to fit residues: 123.9802 Evaluate side-chains 594 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 593 time to evaluate : 0.593 ------------------------------------------------------------------------------- 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: 2.9990 chunk 133 optimal weight: 0.3980 chunk 149 optimal weight: 4.9990 chunk 16 optimal weight: 0.0010 chunk 114 optimal weight: 0.1980 chunk 86 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN B 232 ASN B 361 GLN B 387 GLN B 501 GLN C 181 GLN C 254 HIS ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.137913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.095723 restraints weight = 39011.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.099211 restraints weight = 20559.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.101422 restraints weight = 12863.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.102841 restraints weight = 9199.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.103815 restraints weight = 7188.218| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.7208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16386 Z= 0.135 Angle : 0.635 8.649 22134 Z= 0.338 Chirality : 0.043 0.240 2360 Planarity : 0.004 0.040 2818 Dihedral : 8.153 138.115 2290 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.06 % Allowed : 0.47 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.19), residues: 1932 helix: 0.94 (0.15), residues: 1137 sheet: -0.44 (0.41), residues: 148 loop : -0.14 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 485 TYR 0.037 0.002 TYR D 174 PHE 0.043 0.002 PHE A 171 TRP 0.045 0.002 TRP D 124 HIS 0.013 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.14 (16386) covalent geometry : angle 0.63477 / 0.34 (22134) hydrogen bonds : bond 0.03926 / 2.56 ( 871) hydrogen bonds : angle 4.91840 / 3.55 ( 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 681 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 680 time to evaluate : 0.583 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 15 GLU cc_start: 0.9276 (tt0) cc_final: 0.8521 (tm-30) REVERT: A 16 ILE cc_start: 0.9445 (mm) cc_final: 0.9231 (mm) REVERT: A 18 ILE cc_start: 0.9387 (mm) cc_final: 0.9028 (mm) REVERT: A 54 LYS cc_start: 0.9684 (ttmm) cc_final: 0.9408 (ttmm) REVERT: A 64 TYR cc_start: 0.9119 (m-10) cc_final: 0.8377 (m-10) REVERT: A 65 GLU cc_start: 0.8823 (mm-30) cc_final: 0.8061 (mp0) REVERT: A 66 GLU cc_start: 0.8685 (tp30) cc_final: 0.8388 (tp30) REVERT: A 87 LYS cc_start: 0.9483 (tptt) cc_final: 0.9207 (mmmm) REVERT: A 99 LYS cc_start: 0.9424 (mmmt) cc_final: 0.9156 (mmmm) REVERT: A 107 LYS cc_start: 0.9042 (mtpp) cc_final: 0.8556 (mtpp) REVERT: A 117 ARG cc_start: 0.8959 (mtt-85) cc_final: 0.8670 (mtp85) REVERT: A 124 ILE cc_start: 0.9708 (mm) cc_final: 0.9410 (mm) REVERT: A 139 GLU cc_start: 0.9351 (mm-30) cc_final: 0.9059 (mm-30) REVERT: A 142 ASN cc_start: 0.9434 (m-40) cc_final: 0.9140 (m110) REVERT: A 147 GLN cc_start: 0.9081 (mt0) cc_final: 0.8534 (mm-40) REVERT: A 150 GLN cc_start: 0.9440 (tm-30) cc_final: 0.8417 (tm-30) REVERT: A 214 LYS cc_start: 0.9452 (mmmt) cc_final: 0.9211 (mmmm) REVERT: A 223 VAL cc_start: 0.9560 (m) cc_final: 0.9160 (p) REVERT: A 227 MET cc_start: 0.9326 (mtp) cc_final: 0.8901 (mtp) REVERT: A 236 TYR cc_start: 0.9038 (t80) cc_final: 0.8815 (t80) REVERT: A 251 LEU cc_start: 0.9649 (tp) cc_final: 0.9366 (tp) REVERT: A 283 VAL cc_start: 0.9319 (t) cc_final: 0.9023 (m) REVERT: A 286 ASP cc_start: 0.8600 (m-30) cc_final: 0.8314 (m-30) REVERT: A 322 MET cc_start: 0.8653 (mmp) cc_final: 0.8225 (mmm) REVERT: A 333 LYS cc_start: 0.9543 (ttmt) cc_final: 0.9224 (ttmm) REVERT: A 345 LYS cc_start: 0.9408 (tttt) cc_final: 0.9179 (tttt) REVERT: A 349 LEU cc_start: 0.9590 (mt) cc_final: 0.9259 (mt) REVERT: A 361 GLN cc_start: 0.9115 (tp40) cc_final: 0.8273 (tp-100) REVERT: A 362 ASP cc_start: 0.8272 (m-30) cc_final: 0.7656 (m-30) REVERT: A 403 ILE cc_start: 0.9192 (mm) cc_final: 0.8934 (mm) REVERT: A 407 ILE cc_start: 0.9258 (mt) cc_final: 0.8996 (mt) REVERT: A 417 LEU cc_start: 0.9713 (tt) cc_final: 0.9493 (tt) REVERT: A 421 GLU cc_start: 0.8368 (pp20) cc_final: 0.8070 (pp20) REVERT: A 431 LEU cc_start: 0.9247 (mm) cc_final: 0.9038 (mm) REVERT: A 437 THR cc_start: 0.9649 (m) cc_final: 0.9313 (p) REVERT: A 458 MET cc_start: 0.9255 (mmm) cc_final: 0.8497 (mmm) REVERT: A 505 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8811 (mt-10) REVERT: A 615 MET cc_start: 0.8902 (mmp) cc_final: 0.8698 (mmp) REVERT: A 636 LYS cc_start: 0.9571 (mmmm) cc_final: 0.9021 (mmmm) REVERT: A 639 ASP cc_start: 0.9105 (m-30) cc_final: 0.8652 (m-30) REVERT: A 643 THR cc_start: 0.9577 (p) cc_final: 0.9270 (t) REVERT: A 646 GLN cc_start: 0.9105 (pt0) cc_final: 0.8839 (pt0) REVERT: A 664 THR cc_start: 0.9121 (p) cc_final: 0.8331 (p) REVERT: A 667 LEU cc_start: 0.9573 (tt) cc_final: 0.9290 (tt) REVERT: A 668 ASN cc_start: 0.9406 (m110) cc_final: 0.9130 (m110) REVERT: B 18 ILE cc_start: 0.9557 (mp) cc_final: 0.9278 (mp) REVERT: B 25 GLN cc_start: 0.9200 (mt0) cc_final: 0.8600 (mt0) REVERT: B 31 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8558 (mt-10) REVERT: B 71 LEU cc_start: 0.9717 (mm) cc_final: 0.9516 (mp) REVERT: B 87 LYS cc_start: 0.9372 (tptp) cc_final: 0.9054 (tptp) REVERT: B 147 GLN cc_start: 0.9291 (mt0) cc_final: 0.8944 (mt0) REVERT: B 149 TYR cc_start: 0.9415 (t80) cc_final: 0.8567 (t80) REVERT: B 171 PHE cc_start: 0.9359 (m-80) cc_final: 0.9154 (m-80) REVERT: B 172 LEU cc_start: 0.9341 (mp) cc_final: 0.8911 (mp) REVERT: B 174 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7875 (mm-30) REVERT: B 192 LEU cc_start: 0.9360 (mt) cc_final: 0.9156 (mt) REVERT: B 227 MET cc_start: 0.9346 (mtp) cc_final: 0.9068 (mtp) REVERT: B 232 ASN cc_start: 0.8973 (t0) cc_final: 0.8483 (t0) REVERT: B 235 ARG cc_start: 0.9242 (tpp80) cc_final: 0.9004 (ttm-80) REVERT: B 238 ASP cc_start: 0.8590 (p0) cc_final: 0.8268 (p0) REVERT: B 257 ASP cc_start: 0.8937 (m-30) cc_final: 0.8663 (m-30) REVERT: B 286 ASP cc_start: 0.8725 (m-30) cc_final: 0.8510 (m-30) REVERT: B 321 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8147 (tm-30) REVERT: B 322 MET cc_start: 0.9044 (tpp) cc_final: 0.7963 (tpp) REVERT: B 333 LYS cc_start: 0.9294 (tptp) cc_final: 0.9015 (tptp) REVERT: B 348 MET cc_start: 0.9205 (ptp) cc_final: 0.8961 (ptp) REVERT: B 381 LEU cc_start: 0.9127 (tp) cc_final: 0.8737 (tp) REVERT: B 384 GLU cc_start: 0.8027 (pm20) cc_final: 0.7799 (pm20) REVERT: B 407 ILE cc_start: 0.9375 (mt) cc_final: 0.9141 (mt) REVERT: B 415 ASN cc_start: 0.9588 (t0) cc_final: 0.9263 (t0) REVERT: B 426 GLU cc_start: 0.8949 (pp20) cc_final: 0.8568 (tm-30) REVERT: B 427 LYS cc_start: 0.9465 (tppt) cc_final: 0.9190 (mmmm) REVERT: B 447 ASN cc_start: 0.8701 (m-40) cc_final: 0.8497 (m-40) REVERT: B 458 MET cc_start: 0.9307 (mmp) cc_final: 0.8875 (mmp) REVERT: B 459 LYS cc_start: 0.9339 (mttp) cc_final: 0.8804 (mtmm) REVERT: B 467 ASN cc_start: 0.9391 (m-40) cc_final: 0.9178 (m-40) REVERT: B 493 MET cc_start: 0.9387 (tmm) cc_final: 0.9080 (tmm) REVERT: B 494 MET cc_start: 0.9491 (mmm) cc_final: 0.9194 (mmt) REVERT: B 501 GLN cc_start: 0.9441 (tt0) cc_final: 0.9140 (tt0) REVERT: B 505 GLU cc_start: 0.9017 (mp0) cc_final: 0.8752 (mp0) REVERT: B 515 ASP cc_start: 0.9337 (m-30) cc_final: 0.9025 (m-30) REVERT: B 516 GLN cc_start: 0.9178 (mp10) cc_final: 0.8884 (mp10) REVERT: B 570 MET cc_start: 0.8710 (mtp) cc_final: 0.8228 (mtp) REVERT: B 588 GLN cc_start: 0.9432 (mm-40) cc_final: 0.9226 (mm-40) REVERT: B 595 MET cc_start: 0.9271 (mmm) cc_final: 0.8998 (mmm) REVERT: B 628 GLU cc_start: 0.8881 (mm-30) cc_final: 0.8376 (mm-30) REVERT: C 16 ASP cc_start: 0.6786 (p0) cc_final: 0.6210 (p0) REVERT: C 42 LEU cc_start: 0.8707 (pt) cc_final: 0.8478 (pt) REVERT: C 179 TYR cc_start: 0.8797 (t80) cc_final: 0.8490 (t80) REVERT: D 112 LEU cc_start: 0.6768 (mm) cc_final: 0.6560 (mm) REVERT: D 129 LYS cc_start: 0.8930 (tptp) cc_final: 0.8666 (tmtt) REVERT: D 158 VAL cc_start: 0.8255 (t) cc_final: 0.7668 (m) REVERT: D 162 TYR cc_start: 0.8479 (m-80) cc_final: 0.7918 (m-80) REVERT: D 178 PHE cc_start: 0.9005 (m-80) cc_final: 0.8568 (m-80) REVERT: D 208 LEU cc_start: 0.8716 (mt) cc_final: 0.8462 (mt) REVERT: D 233 ASN cc_start: 0.8728 (m110) cc_final: 0.8122 (m-40) REVERT: D 252 LEU cc_start: 0.8864 (mt) cc_final: 0.8476 (mp) REVERT: D 269 MET cc_start: 0.7429 (ptm) cc_final: 0.7135 (ppp) REVERT: D 321 TYR cc_start: 0.9064 (m-80) cc_final: 0.8785 (m-80) outliers start: 1 outliers final: 0 residues processed: 680 average time/residue: 0.1162 time to fit residues: 119.8085 Evaluate side-chains 593 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 593 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 71 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 189 optimal weight: 9.9990 chunk 181 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN B 646 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** 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 = 0.3671 r_free = 0.3671 target = 0.133619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.091481 restraints weight = 40424.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.094785 restraints weight = 21461.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.096884 restraints weight = 13515.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.098293 restraints weight = 9772.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.099105 restraints weight = 7712.112| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.7343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 16386 Z= 0.216 Angle : 0.694 10.251 22134 Z= 0.368 Chirality : 0.045 0.223 2360 Planarity : 0.004 0.043 2818 Dihedral : 8.281 140.069 2290 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.06 % Allowed : 0.41 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.19), residues: 1932 helix: 0.82 (0.15), residues: 1150 sheet: -0.59 (0.40), residues: 148 loop : -0.33 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 117 TYR 0.037 0.002 TYR B 613 PHE 0.034 0.002 PHE B 378 TRP 0.039 0.002 TRP D 124 HIS 0.018 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.22 (16386) covalent geometry : angle 0.69368 / 0.37 (22134) hydrogen bonds : bond 0.04062 / 2.63 ( 871) hydrogen bonds : angle 4.97467 / 3.58 ( 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 639 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 638 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.9711 (ttmm) cc_final: 0.9402 (ttmm) REVERT: A 64 TYR cc_start: 0.9199 (m-10) cc_final: 0.8481 (m-10) REVERT: A 65 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8144 (mp0) REVERT: A 66 GLU cc_start: 0.8743 (tp30) cc_final: 0.8535 (tp30) REVERT: A 87 LYS cc_start: 0.9494 (tptt) cc_final: 0.9260 (mmmm) REVERT: A 107 LYS cc_start: 0.9063 (mtpp) cc_final: 0.8590 (mtpp) REVERT: A 117 ARG cc_start: 0.8969 (mtt-85) cc_final: 0.8621 (mtp85) REVERT: A 120 ASP cc_start: 0.8945 (m-30) cc_final: 0.8682 (m-30) REVERT: A 124 ILE cc_start: 0.9732 (mm) cc_final: 0.9486 (mm) REVERT: A 139 GLU cc_start: 0.9384 (mm-30) cc_final: 0.9082 (mm-30) REVERT: A 142 ASN cc_start: 0.9417 (m-40) cc_final: 0.9088 (m110) REVERT: A 147 GLN cc_start: 0.9256 (mt0) cc_final: 0.8744 (mt0) REVERT: A 150 GLN cc_start: 0.9429 (tm-30) cc_final: 0.9129 (tm-30) REVERT: A 158 ASN cc_start: 0.9456 (m-40) cc_final: 0.9174 (m-40) REVERT: A 214 LYS cc_start: 0.9501 (mmmt) cc_final: 0.9250 (mmmm) REVERT: A 223 VAL cc_start: 0.9569 (m) cc_final: 0.9101 (p) REVERT: A 227 MET cc_start: 0.9339 (mtp) cc_final: 0.8872 (mtp) REVERT: A 251 LEU cc_start: 0.9668 (tp) cc_final: 0.9346 (tp) REVERT: A 257 ASP cc_start: 0.9388 (m-30) cc_final: 0.8741 (m-30) REVERT: A 277 THR cc_start: 0.8732 (p) cc_final: 0.8119 (t) REVERT: A 279 SER cc_start: 0.8841 (m) cc_final: 0.8565 (t) REVERT: A 286 ASP cc_start: 0.8625 (m-30) cc_final: 0.8306 (m-30) REVERT: A 322 MET cc_start: 0.8678 (mmp) cc_final: 0.8243 (mmm) REVERT: A 349 LEU cc_start: 0.9603 (mt) cc_final: 0.9337 (mt) REVERT: A 361 GLN cc_start: 0.9164 (tp40) cc_final: 0.8287 (tp-100) REVERT: A 362 ASP cc_start: 0.8565 (m-30) cc_final: 0.7593 (m-30) REVERT: A 365 ASN cc_start: 0.9275 (m110) cc_final: 0.8268 (m-40) REVERT: A 403 ILE cc_start: 0.9148 (mm) cc_final: 0.8893 (mm) REVERT: A 407 ILE cc_start: 0.9357 (mt) cc_final: 0.9101 (mt) REVERT: A 421 GLU cc_start: 0.8392 (pp20) cc_final: 0.8117 (pp20) REVERT: A 431 LEU cc_start: 0.9227 (mm) cc_final: 0.9003 (mm) REVERT: A 437 THR cc_start: 0.9687 (m) cc_final: 0.9371 (p) REVERT: A 458 MET cc_start: 0.9255 (mmm) cc_final: 0.8565 (mmm) REVERT: A 505 GLU cc_start: 0.9117 (mt-10) cc_final: 0.8648 (mt-10) REVERT: A 601 ILE cc_start: 0.9369 (tp) cc_final: 0.9119 (tp) REVERT: A 636 LYS cc_start: 0.9561 (mmmm) cc_final: 0.9021 (mmmm) REVERT: A 639 ASP cc_start: 0.9139 (m-30) cc_final: 0.8823 (m-30) REVERT: A 643 THR cc_start: 0.9608 (p) cc_final: 0.9336 (t) REVERT: A 646 GLN cc_start: 0.9142 (pt0) cc_final: 0.8788 (pt0) REVERT: A 650 GLN cc_start: 0.8807 (mt0) cc_final: 0.7984 (tt0) REVERT: A 667 LEU cc_start: 0.9623 (tt) cc_final: 0.9383 (tt) REVERT: A 668 ASN cc_start: 0.9462 (m110) cc_final: 0.9169 (m110) REVERT: A 680 LYS cc_start: 0.8829 (mttt) cc_final: 0.8618 (mttp) REVERT: B 31 GLU cc_start: 0.8884 (mt-10) cc_final: 0.8623 (mt-10) REVERT: B 71 LEU cc_start: 0.9737 (mm) cc_final: 0.9504 (mp) REVERT: B 87 LYS cc_start: 0.9438 (tptp) cc_final: 0.9121 (tptp) REVERT: B 120 ASP cc_start: 0.8948 (m-30) cc_final: 0.8717 (m-30) REVERT: B 147 GLN cc_start: 0.9330 (mt0) cc_final: 0.8884 (mt0) REVERT: B 149 TYR cc_start: 0.9431 (t80) cc_final: 0.8634 (t80) REVERT: B 172 LEU cc_start: 0.9339 (mp) cc_final: 0.8925 (mp) REVERT: B 174 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7879 (mm-30) REVERT: B 227 MET cc_start: 0.9385 (mtp) cc_final: 0.9081 (mtp) REVERT: B 232 ASN cc_start: 0.9018 (t0) cc_final: 0.8544 (t0) REVERT: B 238 ASP cc_start: 0.8654 (p0) cc_final: 0.8262 (p0) REVERT: B 257 ASP cc_start: 0.8902 (m-30) cc_final: 0.8672 (m-30) REVERT: B 286 ASP cc_start: 0.8679 (m-30) cc_final: 0.8458 (m-30) REVERT: B 321 GLU cc_start: 0.8763 (tm-30) cc_final: 0.8157 (tm-30) REVERT: B 322 MET cc_start: 0.9030 (tpp) cc_final: 0.7959 (tpp) REVERT: B 333 LYS cc_start: 0.9322 (tptp) cc_final: 0.9022 (tttp) REVERT: B 348 MET cc_start: 0.9229 (ptp) cc_final: 0.9006 (ptp) REVERT: B 381 LEU cc_start: 0.9301 (tp) cc_final: 0.8903 (tp) REVERT: B 384 GLU cc_start: 0.8181 (pm20) cc_final: 0.7399 (pm20) REVERT: B 407 ILE cc_start: 0.9398 (mt) cc_final: 0.9143 (mt) REVERT: B 415 ASN cc_start: 0.9596 (t0) cc_final: 0.9242 (t0) REVERT: B 426 GLU cc_start: 0.8950 (pp20) cc_final: 0.8610 (tm-30) REVERT: B 427 LYS cc_start: 0.9439 (tppt) cc_final: 0.9184 (mmmm) REVERT: B 458 MET cc_start: 0.9347 (mmp) cc_final: 0.8977 (mmp) REVERT: B 459 LYS cc_start: 0.9358 (mttp) cc_final: 0.8773 (mtmm) REVERT: B 493 MET cc_start: 0.9361 (tmm) cc_final: 0.9086 (tmm) REVERT: B 505 GLU cc_start: 0.9051 (mp0) cc_final: 0.8802 (mp0) REVERT: B 515 ASP cc_start: 0.9385 (m-30) cc_final: 0.9074 (m-30) REVERT: B 516 GLN cc_start: 0.9283 (mp10) cc_final: 0.8964 (mp10) REVERT: B 550 MET cc_start: 0.8844 (mmt) cc_final: 0.8613 (mmt) REVERT: B 570 MET cc_start: 0.8872 (mtp) cc_final: 0.8440 (mtp) REVERT: B 588 GLN cc_start: 0.9445 (mm-40) cc_final: 0.9152 (mm-40) REVERT: B 595 MET cc_start: 0.9320 (mmm) cc_final: 0.9111 (mmm) REVERT: B 628 GLU cc_start: 0.8906 (mm-30) cc_final: 0.8425 (mm-30) REVERT: B 650 GLN cc_start: 0.8221 (mt0) cc_final: 0.7862 (mt0) REVERT: C 16 ASP cc_start: 0.6992 (p0) cc_final: 0.6466 (p0) REVERT: C 179 TYR cc_start: 0.8929 (t80) cc_final: 0.8667 (t80) REVERT: D 129 LYS cc_start: 0.8970 (tptp) cc_final: 0.8717 (tmtt) REVERT: D 158 VAL cc_start: 0.8357 (t) cc_final: 0.7679 (m) REVERT: D 162 TYR cc_start: 0.8647 (m-80) cc_final: 0.8184 (m-80) REVERT: D 233 ASN cc_start: 0.8743 (m110) cc_final: 0.8279 (m110) REVERT: D 269 MET cc_start: 0.7407 (ptm) cc_final: 0.7065 (ppp) REVERT: D 321 TYR cc_start: 0.9135 (m-80) cc_final: 0.8828 (m-80) outliers start: 1 outliers final: 0 residues processed: 638 average time/residue: 0.1172 time to fit residues: 114.2740 Evaluate side-chains 575 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 575 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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: 3.9990 chunk 48 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 148 optimal weight: 0.9980 chunk 125 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN B 232 ASN B 387 GLN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** 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 = 0.3712 r_free = 0.3712 target = 0.137468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.095352 restraints weight = 39364.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.098731 restraints weight = 20922.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.100893 restraints weight = 13267.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.102319 restraints weight = 9550.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.103246 restraints weight = 7492.568| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.7534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 16386 Z= 0.142 Angle : 0.654 9.461 22134 Z= 0.347 Chirality : 0.044 0.213 2360 Planarity : 0.004 0.044 2818 Dihedral : 8.031 139.856 2290 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % 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 are not related in a simple way. whole: 0.47 (0.19), residues: 1932 helix: 0.82 (0.15), residues: 1148 sheet: -0.53 (0.40), residues: 144 loop : -0.21 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 117 TYR 0.036 0.002 TYR A 498 PHE 0.029 0.002 PHE A 171 TRP 0.037 0.002 TRP D 124 HIS 0.017 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 (16386) covalent geometry : angle 0.65393 / 0.35 (22134) hydrogen bonds : bond 0.03924 / 2.54 ( 871) hydrogen bonds : angle 4.93369 / 3.55 ( 2571) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3287.53 seconds wall clock time: 57 minutes 43.87 seconds (3463.87 seconds total)