Starting phenix.real_space_refine on Fri Jul 3 19:43:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzf_45066/07_2026/9bzf_45066_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzf_45066/07_2026/9bzf_45066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bzf_45066/07_2026/9bzf_45066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzf_45066/07_2026/9bzf_45066.map" model { file = "/net/cci-nas-00/data/ceres_data/9bzf_45066/07_2026/9bzf_45066_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzf_45066/07_2026/9bzf_45066_neut.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 0 Ad-hoc single atom residues: {' MN': 2} Chain breaks: 2 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 3.54, per 1000 atoms: 0.22 Number of scatterers: 16038 At special positions: 0 Unit cell: (100.386, 126.75, 130.806, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 675.2 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: 0.34 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.985A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.953A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.664A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.695A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.393A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.628A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.676A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.646A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.027A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.067A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.934A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.669A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.876A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.360A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.478A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.185A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.049A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.09 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4889 1.34 - 1.46: 3089 1.46 - 1.58: 8227 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" O3B TTP A 803 " pdb=" PG TTP A 803 " ideal model delta sigma weight residual 1.748 1.609 0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" O3B TTP B 801 " pdb=" PG TTP B 801 " ideal model delta sigma weight residual 1.748 1.610 0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -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 1.18e+01 bond pdb=" O3A TTP B 801 " pdb=" PB TTP B 801 " ideal model delta sigma weight residual 1.675 1.607 0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 21521 2.10 - 4.19: 532 4.19 - 6.29: 64 6.29 - 8.39: 8 8.39 - 10.49: 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 110.54 116.61 -6.07 1.36e+00 5.41e-01 1.99e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.09 -4.38 1.15e+00 7.56e-01 1.45e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.83 -4.33 1.23e+00 6.61e-01 1.24e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.67 -3.96 1.15e+00 7.56e-01 1.18e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.55 3.64 1.06e+00 8.90e-01 1.18e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.06: 9089 25.06 - 50.13: 656 50.13 - 75.19: 125 75.19 - 100.26: 26 100.26 - 125.32: 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 -98.30 125.32 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 -95.58 122.60 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 -134.36 12.36 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: 2136 0.093 - 0.187: 192 0.187 - 0.280: 27 0.280 - 0.373: 3 0.373 - 0.466: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.44e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO D 75 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.018 2.00e-02 2.50e+03 1.13e-02 2.22e+00 pdb=" CG PHE D 92 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 177 " -0.017 2.00e-02 2.50e+03 9.84e-03 1.94e+00 pdb=" CG TYR C 177 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR C 177 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 177 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 177 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 177 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 177 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 177 " -0.010 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 132 2.51 - 3.11: 11553 3.11 - 3.70: 27046 3.70 - 4.30: 41515 4.30 - 4.90: 65404 Nonbonded interactions: 145650 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 3.060 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 3.060 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 3.060 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 3.060 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.012 3.040 ... (remaining 145645 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.930 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5783 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 10.486 22134 Z= 0.471 Chirality : 0.058 0.466 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.681 125.324 6202 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.34 % Allowed : 15.33 % Favored : 83.33 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.18), residues: 1932 helix: 0.59 (0.14), residues: 1151 sheet: 0.47 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 196 TYR 0.020 0.002 TYR D 179 PHE 0.021 0.002 PHE C 227 TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.33 (16386) covalent geometry : angle 0.78778 / 0.47 (22134) hydrogen bonds : bond 0.15420 / 9.51 ( 871) hydrogen bonds : angle 6.51691 / 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 901 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 878 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.8173 (t0) cc_final: 0.7969 (t70) REVERT: A 37 PHE cc_start: 0.6566 (m-80) cc_final: 0.6213 (m-10) REVERT: A 41 ILE cc_start: 0.8350 (mm) cc_final: 0.8058 (mm) REVERT: A 101 TYR cc_start: 0.7570 (m-80) cc_final: 0.7216 (m-10) REVERT: A 119 GLU cc_start: 0.7561 (mp0) cc_final: 0.6800 (mp0) REVERT: A 143 LEU cc_start: 0.8763 (tp) cc_final: 0.8409 (tp) REVERT: A 168 VAL cc_start: 0.8904 (t) cc_final: 0.8646 (t) REVERT: A 181 ASP cc_start: 0.8597 (m-30) cc_final: 0.8144 (m-30) REVERT: A 191 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7519 (mm110) REVERT: A 258 ILE cc_start: 0.8700 (tp) cc_final: 0.8402 (tp) REVERT: A 264 THR cc_start: 0.8999 (p) cc_final: 0.8787 (m) REVERT: A 278 LEU cc_start: 0.8386 (tp) cc_final: 0.8154 (tp) REVERT: A 322 MET cc_start: 0.7510 (mmp) cc_final: 0.6584 (mmm) REVERT: A 362 ASP cc_start: 0.5877 (m-30) cc_final: 0.4814 (m-30) REVERT: A 425 ILE cc_start: 0.9125 (mt) cc_final: 0.8814 (mt) REVERT: A 431 LEU cc_start: 0.9210 (mt) cc_final: 0.8870 (mm) REVERT: A 436 LEU cc_start: 0.9165 (mt) cc_final: 0.8809 (mt) REVERT: A 447 ASN cc_start: 0.7619 (m-40) cc_final: 0.6724 (m110) REVERT: A 493 MET cc_start: 0.7568 (tmm) cc_final: 0.7062 (tmm) REVERT: A 494 MET cc_start: 0.7764 (mtp) cc_final: 0.7300 (mtp) REVERT: A 500 ILE cc_start: 0.9352 (mt) cc_final: 0.9024 (mt) REVERT: A 522 TYR cc_start: 0.7435 (m-80) cc_final: 0.6453 (m-10) REVERT: A 531 TYR cc_start: 0.6454 (m-80) cc_final: 0.6064 (m-80) REVERT: A 558 TRP cc_start: 0.8229 (m100) cc_final: 0.6925 (m100) REVERT: A 561 LEU cc_start: 0.8853 (tp) cc_final: 0.8601 (tp) REVERT: A 571 TYR cc_start: 0.6916 (t80) cc_final: 0.6597 (t80) REVERT: A 575 ARG cc_start: 0.8503 (mtm110) cc_final: 0.7973 (ptp90) REVERT: A 655 THR cc_start: 0.8855 (m) cc_final: 0.8483 (t) REVERT: A 684 TYR cc_start: 0.5726 (m-80) cc_final: 0.4260 (m-80) REVERT: B 41 ILE cc_start: 0.8888 (mm) cc_final: 0.8442 (mm) REVERT: B 51 LEU cc_start: 0.8225 (tp) cc_final: 0.7878 (tp) REVERT: B 78 LYS cc_start: 0.8360 (tttp) cc_final: 0.8114 (tttt) REVERT: B 95 MET cc_start: 0.6967 (tpp) cc_final: 0.6615 (tpp) REVERT: B 99 LYS cc_start: 0.8995 (mmtt) cc_final: 0.8748 (mmtt) REVERT: B 121 ARG cc_start: 0.8271 (tpm170) cc_final: 0.7560 (tpp-160) REVERT: B 122 ILE cc_start: 0.9011 (mt) cc_final: 0.8360 (mt) REVERT: B 147 GLN cc_start: 0.8114 (mt0) cc_final: 0.6125 (mt0) REVERT: B 157 LEU cc_start: 0.8161 (tp) cc_final: 0.7915 (tp) REVERT: B 172 LEU cc_start: 0.9041 (mp) cc_final: 0.8742 (mp) REVERT: B 181 ASP cc_start: 0.8259 (m-30) cc_final: 0.7808 (m-30) REVERT: B 191 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7852 (mm-40) REVERT: B 204 SER cc_start: 0.8945 (m) cc_final: 0.8457 (p) REVERT: B 258 ILE cc_start: 0.8950 (tp) cc_final: 0.8705 (tp) REVERT: B 291 LEU cc_start: 0.9105 (mt) cc_final: 0.8877 (mt) REVERT: B 319 MET cc_start: 0.7375 (tpp) cc_final: 0.7014 (mmp) REVERT: B 322 MET cc_start: 0.7547 (mmm) cc_final: 0.7007 (mmm) REVERT: B 467 ASN cc_start: 0.8417 (t0) cc_final: 0.8183 (m-40) REVERT: B 469 HIS cc_start: 0.8278 (t-170) cc_final: 0.7981 (t70) REVERT: B 515 ASP cc_start: 0.8433 (m-30) cc_final: 0.8185 (m-30) REVERT: B 522 TYR cc_start: 0.7414 (m-80) cc_final: 0.6996 (m-10) REVERT: B 570 MET cc_start: 0.6616 (mtm) cc_final: 0.5996 (mtm) REVERT: B 587 VAL cc_start: 0.8980 (t) cc_final: 0.8642 (t) REVERT: B 588 GLN cc_start: 0.7762 (mm-40) cc_final: 0.6652 (mm-40) REVERT: B 589 SER cc_start: 0.8503 (m) cc_final: 0.8043 (p) REVERT: B 627 LYS cc_start: 0.8225 (tttt) cc_final: 0.7889 (tttp) REVERT: B 631 ASP cc_start: 0.7629 (m-30) cc_final: 0.7177 (t0) REVERT: B 644 ILE cc_start: 0.8499 (mt) cc_final: 0.8200 (mt) REVERT: B 655 THR cc_start: 0.9341 (m) cc_final: 0.8555 (t) REVERT: C 56 MET cc_start: -0.0067 (mmm) cc_final: -0.0509 (ttp) REVERT: C 90 LEU cc_start: 0.5964 (mt) cc_final: 0.5475 (mt) REVERT: C 95 MET cc_start: 0.5795 (tmm) cc_final: 0.5481 (tmm) REVERT: D 185 MET cc_start: 0.2872 (mmm) cc_final: 0.0368 (mpp) outliers start: 23 outliers final: 6 residues processed: 887 average time/residue: 0.1330 time to fit residues: 169.9466 Evaluate side-chains 612 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 606 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.0970 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 overall best weight: 1.5382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 242 GLN A 320 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 516 GLN A 645 GLN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 GLN B 150 GLN B 218 ASN B 313 HIS ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN B 645 GLN C 24 GLN C 28 GLN C 186 GLN C 238 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.143315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.096056 restraints weight = 43407.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.099310 restraints weight = 26518.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.101524 restraints weight = 18784.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.103184 restraints weight = 14045.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.104380 restraints weight = 11133.734| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (12 function evaluations) r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16386 Z= 0.168 Angle : 0.615 8.786 22134 Z= 0.329 Chirality : 0.042 0.211 2360 Planarity : 0.004 0.038 2818 Dihedral : 9.584 126.452 2290 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 16.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.29 % Allowed : 2.56 % Favored : 97.14 % 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: 1.51 (0.19), residues: 1932 helix: 1.52 (0.15), residues: 1121 sheet: -0.30 (0.39), residues: 148 loop : 0.61 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 161 TYR 0.028 0.002 TYR A 498 PHE 0.032 0.002 PHE D 320 TRP 0.009 0.001 TRP C 30 HIS 0.011 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (16386) covalent geometry : angle 0.61484 / 0.33 (22134) hydrogen bonds : bond 0.04602 / 2.92 ( 871) hydrogen bonds : angle 5.03217 / 3.58 ( 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 742 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 737 time to evaluate : 0.677 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: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9317 (t0) cc_final: 0.9009 (t70) REVERT: A 51 LEU cc_start: 0.9370 (tp) cc_final: 0.9027 (tp) REVERT: A 89 PHE cc_start: 0.8862 (t80) cc_final: 0.8096 (t80) REVERT: A 119 GLU cc_start: 0.9181 (mp0) cc_final: 0.8438 (tm-30) REVERT: A 143 LEU cc_start: 0.9362 (tp) cc_final: 0.8915 (tp) REVERT: A 148 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8500 (mt-10) REVERT: A 181 ASP cc_start: 0.9129 (m-30) cc_final: 0.8916 (m-30) REVERT: A 191 GLN cc_start: 0.9424 (mm-40) cc_final: 0.9061 (mm-40) REVERT: A 195 LEU cc_start: 0.9555 (mt) cc_final: 0.9307 (mt) REVERT: A 227 MET cc_start: 0.9240 (mtm) cc_final: 0.9031 (mtm) REVERT: A 235 ARG cc_start: 0.8771 (mtm110) cc_final: 0.8569 (mtm110) REVERT: A 252 ASN cc_start: 0.9364 (t0) cc_final: 0.8911 (t0) REVERT: A 307 TYR cc_start: 0.9542 (t80) cc_final: 0.9307 (t80) REVERT: A 322 MET cc_start: 0.9115 (mmp) cc_final: 0.8856 (mmm) REVERT: A 335 GLU cc_start: 0.8435 (mm-30) cc_final: 0.7685 (mm-30) REVERT: A 350 ARG cc_start: 0.8501 (mmm-85) cc_final: 0.8029 (mmm-85) REVERT: A 370 ASN cc_start: 0.9375 (m-40) cc_final: 0.9020 (m110) REVERT: A 402 GLU cc_start: 0.8524 (mp0) cc_final: 0.8242 (mp0) REVERT: A 447 ASN cc_start: 0.8886 (m-40) cc_final: 0.8240 (m-40) REVERT: A 468 LEU cc_start: 0.9789 (tp) cc_final: 0.9503 (tp) REVERT: A 472 LEU cc_start: 0.9731 (mt) cc_final: 0.9448 (mt) REVERT: A 500 ILE cc_start: 0.9651 (mt) cc_final: 0.9240 (mt) REVERT: A 515 ASP cc_start: 0.9211 (m-30) cc_final: 0.8866 (m-30) REVERT: A 522 TYR cc_start: 0.9225 (m-80) cc_final: 0.8751 (m-10) REVERT: A 570 MET cc_start: 0.8972 (mtp) cc_final: 0.7591 (mtp) REVERT: A 575 ARG cc_start: 0.9113 (mtm110) cc_final: 0.8264 (ptp90) REVERT: A 598 MET cc_start: 0.9225 (mtp) cc_final: 0.8568 (mmt) REVERT: A 615 MET cc_start: 0.8679 (mmp) cc_final: 0.8208 (mmp) REVERT: A 632 MET cc_start: 0.8898 (mtp) cc_final: 0.8470 (mtm) REVERT: A 645 GLN cc_start: 0.8758 (tp40) cc_final: 0.8527 (tp-100) REVERT: A 650 GLN cc_start: 0.8778 (mt0) cc_final: 0.8198 (mt0) REVERT: A 657 PHE cc_start: 0.8454 (m-80) cc_final: 0.7635 (m-80) REVERT: B 15 GLU cc_start: 0.9168 (tp30) cc_final: 0.8603 (tp30) REVERT: B 51 LEU cc_start: 0.9225 (tp) cc_final: 0.8789 (tp) REVERT: B 62 GLN cc_start: 0.9616 (mp-120) cc_final: 0.9003 (mp10) REVERT: B 95 MET cc_start: 0.9134 (tpp) cc_final: 0.8526 (tpp) REVERT: B 99 LYS cc_start: 0.9521 (mmmt) cc_final: 0.9008 (mmmt) REVERT: B 115 LEU cc_start: 0.9442 (mt) cc_final: 0.9195 (mt) REVERT: B 117 ARG cc_start: 0.9053 (ttm110) cc_final: 0.8788 (ttm110) REVERT: B 119 GLU cc_start: 0.9264 (mp0) cc_final: 0.8901 (mp0) REVERT: B 144 MET cc_start: 0.9256 (mtm) cc_final: 0.8892 (mtm) REVERT: B 147 GLN cc_start: 0.9241 (mt0) cc_final: 0.8775 (mt0) REVERT: B 205 LYS cc_start: 0.9401 (mmmt) cc_final: 0.8966 (mmmm) REVERT: B 211 GLU cc_start: 0.8665 (mm-30) cc_final: 0.8189 (mm-30) REVERT: B 227 MET cc_start: 0.9410 (mtp) cc_final: 0.9163 (mtp) REVERT: B 236 TYR cc_start: 0.8975 (t80) cc_final: 0.8595 (t80) REVERT: B 251 LEU cc_start: 0.9478 (tp) cc_final: 0.9120 (tp) REVERT: B 286 ASP cc_start: 0.8696 (m-30) cc_final: 0.8178 (m-30) REVERT: B 288 PHE cc_start: 0.9423 (t80) cc_final: 0.9185 (t80) REVERT: B 291 LEU cc_start: 0.9610 (mt) cc_final: 0.9312 (mt) REVERT: B 308 LYS cc_start: 0.9381 (mtmt) cc_final: 0.9142 (ptpp) REVERT: B 322 MET cc_start: 0.9308 (mmm) cc_final: 0.8744 (mmm) REVERT: B 342 LEU cc_start: 0.9668 (tp) cc_final: 0.9307 (tp) REVERT: B 345 LYS cc_start: 0.9458 (tttt) cc_final: 0.9207 (tttt) REVERT: B 348 MET cc_start: 0.9269 (tpp) cc_final: 0.8613 (tpp) REVERT: B 362 ASP cc_start: 0.8992 (m-30) cc_final: 0.8101 (m-30) REVERT: B 373 ILE cc_start: 0.9659 (mt) cc_final: 0.9450 (tp) REVERT: B 375 LYS cc_start: 0.9213 (mmtm) cc_final: 0.8779 (mmtm) REVERT: B 393 SER cc_start: 0.9691 (t) cc_final: 0.9076 (p) REVERT: B 398 ASP cc_start: 0.8783 (t70) cc_final: 0.8410 (t70) REVERT: B 403 ILE cc_start: 0.9360 (mp) cc_final: 0.9030 (tp) REVERT: B 427 LYS cc_start: 0.9586 (ptpp) cc_final: 0.9226 (ptpp) REVERT: B 430 LYS cc_start: 0.9133 (ptpp) cc_final: 0.8881 (mtmm) REVERT: B 444 ASP cc_start: 0.7998 (t70) cc_final: 0.7744 (t0) REVERT: B 458 MET cc_start: 0.9424 (mmm) cc_final: 0.8911 (mmm) REVERT: B 494 MET cc_start: 0.9449 (mtt) cc_final: 0.9158 (mtt) REVERT: B 500 ILE cc_start: 0.9759 (mt) cc_final: 0.9408 (mt) REVERT: B 522 TYR cc_start: 0.9060 (m-80) cc_final: 0.8742 (m-10) REVERT: B 570 MET cc_start: 0.9414 (mtp) cc_final: 0.8405 (mtp) REVERT: B 586 TYR cc_start: 0.9361 (m-80) cc_final: 0.8758 (m-80) REVERT: B 599 GLU cc_start: 0.8426 (pm20) cc_final: 0.8152 (pm20) REVERT: B 615 MET cc_start: 0.8748 (mmp) cc_final: 0.8234 (mmp) REVERT: B 631 ASP cc_start: 0.9409 (m-30) cc_final: 0.9099 (t0) REVERT: B 667 LEU cc_start: 0.9043 (tp) cc_final: 0.8633 (tp) REVERT: B 668 ASN cc_start: 0.9360 (m-40) cc_final: 0.8863 (m-40) REVERT: B 677 ARG cc_start: 0.9636 (mmm160) cc_final: 0.9257 (mmm-85) REVERT: C 74 MET cc_start: 0.8175 (mtt) cc_final: 0.7779 (mtt) REVERT: C 93 MET cc_start: 0.9324 (mtm) cc_final: 0.8959 (tpt) REVERT: C 100 VAL cc_start: 0.8941 (t) cc_final: 0.8530 (t) REVERT: C 101 HIS cc_start: 0.7726 (m90) cc_final: 0.7055 (m90) REVERT: C 136 GLN cc_start: 0.0116 (mt0) cc_final: -0.0225 (tp40) REVERT: C 185 MET cc_start: 0.2115 (tmm) cc_final: 0.1536 (mmm) REVERT: D 69 GLN cc_start: 0.8630 (tp40) cc_final: 0.7946 (tp40) REVERT: D 74 MET cc_start: 0.7744 (mmt) cc_final: 0.7444 (mmt) REVERT: D 179 TYR cc_start: 0.6496 (t80) cc_final: 0.6073 (t80) REVERT: D 185 MET cc_start: 0.1463 (mmm) cc_final: 0.0874 (mpp) REVERT: D 212 ILE cc_start: 0.8799 (pt) cc_final: 0.8565 (pt) outliers start: 5 outliers final: 0 residues processed: 739 average time/residue: 0.1390 time to fit residues: 150.8661 Evaluate side-chains 594 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 594 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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: 6.9990 chunk 131 optimal weight: 5.9990 chunk 164 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 182 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 158 optimal weight: 30.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 14 ASN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN B 150 GLN B 410 ASN B 475 ASN ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 127 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.126011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.083085 restraints weight = 47954.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.086198 restraints weight = 28595.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.088178 restraints weight = 19166.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.089558 restraints weight = 14274.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.090514 restraints weight = 11287.521| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (13 function evaluations) r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.5692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 16386 Z= 0.294 Angle : 0.717 8.051 22134 Z= 0.382 Chirality : 0.044 0.165 2360 Planarity : 0.005 0.118 2818 Dihedral : 9.470 126.517 2290 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 20.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.12 % Allowed : 3.38 % Favored : 96.50 % 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: 1.18 (0.19), residues: 1932 helix: 1.26 (0.15), residues: 1115 sheet: -0.66 (0.38), residues: 152 loop : 0.55 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 665 TYR 0.039 0.002 TYR B 612 PHE 0.021 0.002 PHE D 320 TRP 0.030 0.002 TRP C 124 HIS 0.008 0.002 HIS A 368 Details of bonding type rmsd/Z covalent geometry : bond 0.00595 / 0.29 (16386) covalent geometry : angle 0.71729 / 0.38 (22134) hydrogen bonds : bond 0.04462 / 2.84 ( 871) hydrogen bonds : angle 5.21458 / 3.72 ( 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 652 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 650 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9468 (t0) cc_final: 0.9225 (t70) REVERT: A 89 PHE cc_start: 0.9305 (t80) cc_final: 0.8989 (t80) REVERT: A 116 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8567 (tt0) REVERT: A 117 ARG cc_start: 0.9314 (mtp180) cc_final: 0.9032 (mtt180) REVERT: A 119 GLU cc_start: 0.9299 (mp0) cc_final: 0.8547 (tm-30) REVERT: A 143 LEU cc_start: 0.9430 (tp) cc_final: 0.9070 (tp) REVERT: A 147 GLN cc_start: 0.9184 (mm110) cc_final: 0.8510 (mm-40) REVERT: A 148 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8428 (mt-10) REVERT: A 172 LEU cc_start: 0.9268 (mp) cc_final: 0.8908 (mp) REVERT: A 181 ASP cc_start: 0.9195 (m-30) cc_final: 0.8879 (m-30) REVERT: A 195 LEU cc_start: 0.9656 (mt) cc_final: 0.9404 (mt) REVERT: A 227 MET cc_start: 0.9355 (mtm) cc_final: 0.9106 (mtm) REVERT: A 250 TYR cc_start: 0.8702 (m-80) cc_final: 0.8367 (m-80) REVERT: A 252 ASN cc_start: 0.9555 (t0) cc_final: 0.9068 (t0) REVERT: A 307 TYR cc_start: 0.9576 (t80) cc_final: 0.9075 (t80) REVERT: A 322 MET cc_start: 0.9201 (mmp) cc_final: 0.8481 (mmm) REVERT: A 350 ARG cc_start: 0.8712 (mmm-85) cc_final: 0.8121 (mmm-85) REVERT: A 359 MET cc_start: 0.8982 (ttp) cc_final: 0.8633 (ttp) REVERT: A 361 GLN cc_start: 0.9530 (tt0) cc_final: 0.9121 (tp40) REVERT: A 370 ASN cc_start: 0.9687 (m-40) cc_final: 0.9475 (m-40) REVERT: A 387 GLN cc_start: 0.9015 (mt0) cc_final: 0.8580 (mp10) REVERT: A 394 TYR cc_start: 0.9351 (m-80) cc_final: 0.8944 (m-80) REVERT: A 402 GLU cc_start: 0.8684 (mp0) cc_final: 0.8428 (mp0) REVERT: A 406 ASP cc_start: 0.8877 (m-30) cc_final: 0.8590 (m-30) REVERT: A 415 ASN cc_start: 0.9524 (t0) cc_final: 0.9323 (t0) REVERT: A 417 LEU cc_start: 0.9818 (tt) cc_final: 0.9611 (tt) REVERT: A 418 ASN cc_start: 0.9483 (m-40) cc_final: 0.8836 (m110) REVERT: A 425 ILE cc_start: 0.9479 (mp) cc_final: 0.9182 (mp) REVERT: A 468 LEU cc_start: 0.9789 (tp) cc_final: 0.9396 (tp) REVERT: A 472 LEU cc_start: 0.9733 (mt) cc_final: 0.9415 (mt) REVERT: A 479 TYR cc_start: 0.9040 (t80) cc_final: 0.8838 (t80) REVERT: A 494 MET cc_start: 0.9456 (mtp) cc_final: 0.9230 (ttm) REVERT: A 499 SER cc_start: 0.9948 (t) cc_final: 0.9676 (p) REVERT: A 515 ASP cc_start: 0.9304 (m-30) cc_final: 0.9048 (m-30) REVERT: A 522 TYR cc_start: 0.9259 (m-80) cc_final: 0.8804 (m-10) REVERT: A 570 MET cc_start: 0.9318 (mtp) cc_final: 0.7785 (mtp) REVERT: A 575 ARG cc_start: 0.9346 (mtm110) cc_final: 0.8302 (ptp90) REVERT: A 576 LEU cc_start: 0.9332 (mt) cc_final: 0.9043 (mt) REVERT: A 588 GLN cc_start: 0.9319 (mm-40) cc_final: 0.8769 (tp40) REVERT: A 598 MET cc_start: 0.9238 (mtp) cc_final: 0.8782 (mmm) REVERT: A 612 TYR cc_start: 0.8870 (m-10) cc_final: 0.8351 (m-80) REVERT: A 613 TYR cc_start: 0.8953 (t80) cc_final: 0.8642 (t80) REVERT: A 615 MET cc_start: 0.8858 (mmp) cc_final: 0.8578 (mmp) REVERT: A 632 MET cc_start: 0.8632 (mtt) cc_final: 0.8430 (mtm) REVERT: A 645 GLN cc_start: 0.9070 (tp40) cc_final: 0.8867 (tp-100) REVERT: A 650 GLN cc_start: 0.8768 (mt0) cc_final: 0.7492 (mt0) REVERT: A 657 PHE cc_start: 0.8669 (m-80) cc_final: 0.8315 (m-80) REVERT: B 15 GLU cc_start: 0.9159 (tp30) cc_final: 0.8938 (tp30) REVERT: B 51 LEU cc_start: 0.9326 (tp) cc_final: 0.9109 (tp) REVERT: B 95 MET cc_start: 0.9362 (tpp) cc_final: 0.8742 (tpp) REVERT: B 99 LYS cc_start: 0.9572 (mmmt) cc_final: 0.9033 (mmmt) REVERT: B 115 LEU cc_start: 0.9575 (mt) cc_final: 0.9293 (mt) REVERT: B 136 LYS cc_start: 0.9644 (mmtp) cc_final: 0.9389 (mmmm) REVERT: B 139 GLU cc_start: 0.9495 (mp0) cc_final: 0.9215 (mp0) REVERT: B 144 MET cc_start: 0.9263 (mtm) cc_final: 0.8939 (mtm) REVERT: B 147 GLN cc_start: 0.9314 (mt0) cc_final: 0.8733 (mt0) REVERT: B 157 LEU cc_start: 0.9564 (tp) cc_final: 0.9359 (tp) REVERT: B 158 ASN cc_start: 0.9559 (m110) cc_final: 0.9267 (p0) REVERT: B 161 ARG cc_start: 0.8938 (ttm110) cc_final: 0.8288 (mtp85) REVERT: B 211 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8364 (mm-30) REVERT: B 227 MET cc_start: 0.9424 (mtp) cc_final: 0.9156 (mtp) REVERT: B 251 LEU cc_start: 0.9469 (tp) cc_final: 0.9201 (tp) REVERT: B 286 ASP cc_start: 0.8798 (m-30) cc_final: 0.8306 (m-30) REVERT: B 290 GLU cc_start: 0.9348 (pp20) cc_final: 0.8632 (pp20) REVERT: B 291 LEU cc_start: 0.9552 (mt) cc_final: 0.9283 (mt) REVERT: B 296 LYS cc_start: 0.8987 (mmpt) cc_final: 0.8574 (mtmm) REVERT: B 308 LYS cc_start: 0.9410 (mtmt) cc_final: 0.9168 (ptpp) REVERT: B 312 GLN cc_start: 0.9241 (pm20) cc_final: 0.8868 (pm20) REVERT: B 322 MET cc_start: 0.8796 (mmm) cc_final: 0.8426 (mmm) REVERT: B 345 LYS cc_start: 0.9593 (tttt) cc_final: 0.9266 (tttt) REVERT: B 350 ARG cc_start: 0.8781 (mtp85) cc_final: 0.8134 (mtp85) REVERT: B 362 ASP cc_start: 0.9113 (m-30) cc_final: 0.8008 (m-30) REVERT: B 370 ASN cc_start: 0.9609 (m-40) cc_final: 0.9273 (m110) REVERT: B 373 ILE cc_start: 0.9689 (mt) cc_final: 0.9367 (mt) REVERT: B 398 ASP cc_start: 0.8897 (t70) cc_final: 0.8606 (t70) REVERT: B 407 ILE cc_start: 0.8882 (mt) cc_final: 0.8664 (mt) REVERT: B 443 THR cc_start: 0.9282 (m) cc_final: 0.9066 (t) REVERT: B 455 ASN cc_start: 0.9550 (t0) cc_final: 0.9260 (t0) REVERT: B 494 MET cc_start: 0.9558 (mtt) cc_final: 0.9120 (mtt) REVERT: B 501 GLN cc_start: 0.9722 (tt0) cc_final: 0.9031 (tp-100) REVERT: B 522 TYR cc_start: 0.9269 (m-80) cc_final: 0.9047 (m-10) REVERT: B 570 MET cc_start: 0.9423 (mtp) cc_final: 0.8855 (mtp) REVERT: B 588 GLN cc_start: 0.9606 (mm110) cc_final: 0.9293 (mm110) REVERT: B 606 TYR cc_start: 0.8653 (m-80) cc_final: 0.8261 (m-10) REVERT: B 615 MET cc_start: 0.8889 (mmp) cc_final: 0.8577 (mmp) REVERT: B 631 ASP cc_start: 0.9561 (m-30) cc_final: 0.9283 (m-30) REVERT: B 634 MET cc_start: 0.9400 (mmm) cc_final: 0.9097 (mmt) REVERT: B 648 ILE cc_start: 0.9555 (mm) cc_final: 0.9315 (mm) REVERT: B 668 ASN cc_start: 0.9407 (m-40) cc_final: 0.9007 (m-40) REVERT: B 677 ARG cc_start: 0.9677 (mmm160) cc_final: 0.9373 (mmm-85) REVERT: C 56 MET cc_start: -0.1168 (ttp) cc_final: -0.1479 (ttp) REVERT: C 100 VAL cc_start: 0.9015 (t) cc_final: 0.8803 (t) REVERT: C 101 HIS cc_start: 0.8335 (m90) cc_final: 0.7908 (m90) REVERT: C 124 TRP cc_start: 0.7870 (t60) cc_final: 0.7253 (t60) REVERT: D 69 GLN cc_start: 0.9451 (tp40) cc_final: 0.8777 (tp-100) REVERT: D 100 VAL cc_start: 0.4440 (t) cc_final: 0.4114 (t) REVERT: D 157 MET cc_start: 0.8745 (mtm) cc_final: 0.8467 (mtm) REVERT: D 179 TYR cc_start: 0.7013 (t80) cc_final: 0.6719 (t80) REVERT: D 185 MET cc_start: 0.2098 (mmm) cc_final: 0.1592 (mpp) outliers start: 2 outliers final: 0 residues processed: 650 average time/residue: 0.1306 time to fit residues: 127.4750 Evaluate side-chains 569 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 569 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 29 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 60 optimal weight: 0.5980 chunk 185 optimal weight: 3.9990 chunk 191 optimal weight: 10.0000 chunk 159 optimal weight: 20.0000 chunk 182 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 14 ASN A 147 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 HIS ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.129738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.086052 restraints weight = 46876.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.089154 restraints weight = 27641.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.091194 restraints weight = 18300.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.092531 restraints weight = 13542.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.093601 restraints weight = 10794.222| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (11 function evaluations) r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.6056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16386 Z= 0.179 Angle : 0.602 11.239 22134 Z= 0.322 Chirality : 0.042 0.205 2360 Planarity : 0.004 0.089 2818 Dihedral : 9.148 125.003 2290 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.19), residues: 1932 helix: 1.19 (0.15), residues: 1134 sheet: -0.80 (0.37), residues: 154 loop : 0.43 (0.25), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 117 TYR 0.029 0.002 TYR B 612 PHE 0.024 0.002 PHE D 109 TRP 0.017 0.001 TRP C 124 HIS 0.006 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (16386) covalent geometry : angle 0.60236 / 0.32 (22134) hydrogen bonds : bond 0.03919 / 2.47 ( 871) hydrogen bonds : angle 4.96604 / 3.54 ( 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 653 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 653 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9517 (t0) cc_final: 0.9184 (t70) REVERT: A 89 PHE cc_start: 0.9182 (t80) cc_final: 0.8915 (t80) REVERT: A 95 MET cc_start: 0.9124 (tpt) cc_final: 0.8573 (tpp) REVERT: A 99 LYS cc_start: 0.9558 (mmtt) cc_final: 0.9184 (mmtt) REVERT: A 116 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8469 (tt0) REVERT: A 143 LEU cc_start: 0.9578 (tp) cc_final: 0.9345 (tp) REVERT: A 147 GLN cc_start: 0.9119 (mm-40) cc_final: 0.8218 (mm-40) REVERT: A 172 LEU cc_start: 0.9306 (mp) cc_final: 0.9014 (mp) REVERT: A 195 LEU cc_start: 0.9596 (mt) cc_final: 0.9357 (mt) REVERT: A 204 SER cc_start: 0.9390 (m) cc_final: 0.9106 (m) REVERT: A 227 MET cc_start: 0.9331 (mtm) cc_final: 0.9018 (mtm) REVERT: A 235 ARG cc_start: 0.8660 (mtm110) cc_final: 0.8407 (mtt90) REVERT: A 251 LEU cc_start: 0.9607 (tp) cc_final: 0.9337 (tp) REVERT: A 252 ASN cc_start: 0.9519 (t0) cc_final: 0.9007 (t0) REVERT: A 255 HIS cc_start: 0.8999 (t-90) cc_final: 0.8563 (t-90) REVERT: A 307 TYR cc_start: 0.9613 (t80) cc_final: 0.9149 (t80) REVERT: A 322 MET cc_start: 0.9231 (mmp) cc_final: 0.8912 (mmm) REVERT: A 337 ILE cc_start: 0.9437 (mp) cc_final: 0.9066 (mp) REVERT: A 348 MET cc_start: 0.9349 (ptp) cc_final: 0.9105 (ptp) REVERT: A 350 ARG cc_start: 0.8854 (mmm-85) cc_final: 0.8231 (mmm-85) REVERT: A 361 GLN cc_start: 0.9516 (tt0) cc_final: 0.9206 (tp40) REVERT: A 377 LYS cc_start: 0.8946 (mttt) cc_final: 0.8586 (mtmt) REVERT: A 387 GLN cc_start: 0.8935 (mt0) cc_final: 0.8419 (mp10) REVERT: A 394 TYR cc_start: 0.9337 (m-80) cc_final: 0.8691 (m-80) REVERT: A 402 GLU cc_start: 0.8759 (mp0) cc_final: 0.8553 (mp0) REVERT: A 406 ASP cc_start: 0.8864 (m-30) cc_final: 0.8590 (m-30) REVERT: A 407 ILE cc_start: 0.9223 (mt) cc_final: 0.8836 (mt) REVERT: A 421 GLU cc_start: 0.9275 (tm-30) cc_final: 0.9067 (tm-30) REVERT: A 468 LEU cc_start: 0.9688 (tp) cc_final: 0.9386 (tp) REVERT: A 472 LEU cc_start: 0.9738 (mt) cc_final: 0.9455 (mt) REVERT: A 494 MET cc_start: 0.9407 (mtp) cc_final: 0.9178 (mtp) REVERT: A 496 ASN cc_start: 0.9689 (t0) cc_final: 0.9168 (t0) REVERT: A 499 SER cc_start: 0.9942 (t) cc_final: 0.9708 (p) REVERT: A 500 ILE cc_start: 0.9754 (mt) cc_final: 0.9209 (mt) REVERT: A 515 ASP cc_start: 0.9290 (m-30) cc_final: 0.9012 (m-30) REVERT: A 522 TYR cc_start: 0.9221 (m-80) cc_final: 0.8704 (m-10) REVERT: A 570 MET cc_start: 0.9427 (mtp) cc_final: 0.7354 (mtp) REVERT: A 575 ARG cc_start: 0.9367 (mtm110) cc_final: 0.8529 (ptp90) REVERT: A 588 GLN cc_start: 0.9266 (mm-40) cc_final: 0.8455 (tp-100) REVERT: A 598 MET cc_start: 0.9227 (mtp) cc_final: 0.8977 (mmt) REVERT: A 602 GLU cc_start: 0.8182 (pt0) cc_final: 0.7542 (pt0) REVERT: A 612 TYR cc_start: 0.8987 (m-10) cc_final: 0.8391 (m-80) REVERT: A 645 GLN cc_start: 0.9125 (tp40) cc_final: 0.8895 (tp-100) REVERT: A 650 GLN cc_start: 0.8774 (mt0) cc_final: 0.7631 (mt0) REVERT: B 15 GLU cc_start: 0.9206 (tp30) cc_final: 0.8814 (tp30) REVERT: B 17 MET cc_start: 0.8846 (mpp) cc_final: 0.8276 (mpp) REVERT: B 51 LEU cc_start: 0.9280 (tp) cc_final: 0.9012 (tp) REVERT: B 87 LYS cc_start: 0.9143 (mtpt) cc_final: 0.8893 (mtpt) REVERT: B 95 MET cc_start: 0.9259 (tpp) cc_final: 0.8702 (tpp) REVERT: B 99 LYS cc_start: 0.9566 (mmmt) cc_final: 0.9093 (mmmt) REVERT: B 107 LYS cc_start: 0.9624 (mptt) cc_final: 0.9300 (mmtt) REVERT: B 115 LEU cc_start: 0.9586 (mt) cc_final: 0.9341 (mt) REVERT: B 119 GLU cc_start: 0.9261 (mp0) cc_final: 0.8848 (tm-30) REVERT: B 120 ASP cc_start: 0.9298 (m-30) cc_final: 0.8893 (m-30) REVERT: B 136 LYS cc_start: 0.9634 (mmtp) cc_final: 0.9341 (mmmm) REVERT: B 144 MET cc_start: 0.9195 (mtm) cc_final: 0.8842 (mtm) REVERT: B 157 LEU cc_start: 0.9584 (tp) cc_final: 0.9334 (tp) REVERT: B 158 ASN cc_start: 0.9554 (m110) cc_final: 0.9038 (p0) REVERT: B 161 ARG cc_start: 0.8820 (ttm110) cc_final: 0.8333 (mtp85) REVERT: B 211 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8220 (mm-30) REVERT: B 218 ASN cc_start: 0.9649 (t0) cc_final: 0.9239 (t0) REVERT: B 227 MET cc_start: 0.9348 (mtp) cc_final: 0.9108 (mtp) REVERT: B 251 LEU cc_start: 0.9444 (tp) cc_final: 0.9121 (tp) REVERT: B 286 ASP cc_start: 0.8799 (m-30) cc_final: 0.8131 (m-30) REVERT: B 296 LYS cc_start: 0.8987 (mmpt) cc_final: 0.8607 (mtmm) REVERT: B 312 GLN cc_start: 0.9269 (pm20) cc_final: 0.8552 (pm20) REVERT: B 322 MET cc_start: 0.8722 (mmm) cc_final: 0.8494 (mmm) REVERT: B 345 LYS cc_start: 0.9650 (tttt) cc_final: 0.9415 (tttt) REVERT: B 350 ARG cc_start: 0.8744 (mtp85) cc_final: 0.8164 (mtp85) REVERT: B 355 TYR cc_start: 0.9264 (m-10) cc_final: 0.9023 (m-10) REVERT: B 362 ASP cc_start: 0.9160 (m-30) cc_final: 0.8077 (m-30) REVERT: B 370 ASN cc_start: 0.9613 (m-40) cc_final: 0.9216 (m110) REVERT: B 373 ILE cc_start: 0.9691 (mt) cc_final: 0.9370 (mt) REVERT: B 375 LYS cc_start: 0.9259 (mmtm) cc_final: 0.8925 (mmtm) REVERT: B 390 GLN cc_start: 0.9350 (mt0) cc_final: 0.9033 (mm-40) REVERT: B 393 SER cc_start: 0.9580 (t) cc_final: 0.9033 (t) REVERT: B 398 ASP cc_start: 0.8788 (t70) cc_final: 0.8415 (t70) REVERT: B 399 GLU cc_start: 0.8886 (mp0) cc_final: 0.8402 (mp0) REVERT: B 402 GLU cc_start: 0.8656 (mp0) cc_final: 0.8356 (mp0) REVERT: B 443 THR cc_start: 0.9351 (m) cc_final: 0.9034 (t) REVERT: B 455 ASN cc_start: 0.9586 (t0) cc_final: 0.9308 (t0) REVERT: B 494 MET cc_start: 0.9521 (mtt) cc_final: 0.9028 (mtt) REVERT: B 570 MET cc_start: 0.9411 (mtp) cc_final: 0.8641 (mtp) REVERT: B 585 SER cc_start: 0.9108 (p) cc_final: 0.8612 (t) REVERT: B 591 THR cc_start: 0.9241 (p) cc_final: 0.8946 (p) REVERT: B 606 TYR cc_start: 0.8511 (m-80) cc_final: 0.8051 (m-10) REVERT: B 615 MET cc_start: 0.8809 (mmp) cc_final: 0.8571 (mmp) REVERT: B 631 ASP cc_start: 0.9370 (m-30) cc_final: 0.9125 (m-30) REVERT: B 636 LYS cc_start: 0.9749 (mmtm) cc_final: 0.9512 (mmmt) REVERT: B 648 ILE cc_start: 0.9585 (mm) cc_final: 0.9319 (mm) REVERT: B 657 PHE cc_start: 0.8665 (m-80) cc_final: 0.8173 (m-80) REVERT: B 667 LEU cc_start: 0.9324 (tp) cc_final: 0.9037 (tp) REVERT: B 668 ASN cc_start: 0.9351 (m-40) cc_final: 0.8635 (m110) REVERT: B 677 ARG cc_start: 0.9653 (mmm160) cc_final: 0.9318 (mmm-85) REVERT: C 93 MET cc_start: 0.9475 (mtm) cc_final: 0.9144 (tpt) REVERT: C 100 VAL cc_start: 0.8984 (t) cc_final: 0.8632 (t) REVERT: C 124 TRP cc_start: 0.7541 (t60) cc_final: 0.7215 (t60) REVERT: D 69 GLN cc_start: 0.9473 (tp-100) cc_final: 0.9029 (tm-30) REVERT: D 100 VAL cc_start: 0.4502 (t) cc_final: 0.3745 (p) REVERT: D 185 MET cc_start: 0.2223 (mmm) cc_final: 0.1684 (mpp) REVERT: D 204 TYR cc_start: 0.9149 (t80) cc_final: 0.8930 (t80) REVERT: D 205 VAL cc_start: 0.9584 (t) cc_final: 0.9202 (t) REVERT: D 312 VAL cc_start: 0.9757 (p) cc_final: 0.9542 (p) outliers start: 0 outliers final: 0 residues processed: 653 average time/residue: 0.1320 time to fit residues: 129.0246 Evaluate side-chains 568 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 568 time to evaluate : 0.635 ------------------------------------------------------------------------------- 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: 6.9990 chunk 46 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 122 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 157 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN D 91 ASN ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.130639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.087131 restraints weight = 46484.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.090077 restraints weight = 27336.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.092196 restraints weight = 18369.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.093617 restraints weight = 13498.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.094597 restraints weight = 10639.561| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.6407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16386 Z= 0.167 Angle : 0.593 9.167 22134 Z= 0.316 Chirality : 0.042 0.238 2360 Planarity : 0.004 0.077 2818 Dihedral : 8.857 125.763 2290 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.19), residues: 1932 helix: 1.15 (0.15), residues: 1146 sheet: -0.67 (0.38), residues: 140 loop : 0.22 (0.24), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 117 TYR 0.023 0.002 TYR B 683 PHE 0.028 0.002 PHE B 81 TRP 0.011 0.001 TRP C 124 HIS 0.005 0.001 HIS A 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 (16386) covalent geometry : angle 0.59304 / 0.32 (22134) hydrogen bonds : bond 0.03802 / 2.40 ( 871) hydrogen bonds : angle 4.94300 / 3.55 ( 2571) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 646 time to evaluate : 0.633 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: A 29 ASP cc_start: 0.9525 (t0) cc_final: 0.9121 (t70) REVERT: A 89 PHE cc_start: 0.9173 (t80) cc_final: 0.8839 (t80) REVERT: A 119 GLU cc_start: 0.9222 (mp0) cc_final: 0.8285 (tm-30) REVERT: A 139 GLU cc_start: 0.9216 (mt-10) cc_final: 0.8957 (pt0) REVERT: A 143 LEU cc_start: 0.9617 (tp) cc_final: 0.9258 (tp) REVERT: A 147 GLN cc_start: 0.9131 (mm-40) cc_final: 0.8145 (mm110) REVERT: A 164 ARG cc_start: 0.8435 (ptm-80) cc_final: 0.7670 (ptm-80) REVERT: A 172 LEU cc_start: 0.9328 (mp) cc_final: 0.9009 (mp) REVERT: A 195 LEU cc_start: 0.9597 (mt) cc_final: 0.9368 (mt) REVERT: A 204 SER cc_start: 0.9413 (m) cc_final: 0.9102 (m) REVERT: A 227 MET cc_start: 0.9355 (mtm) cc_final: 0.9070 (mtm) REVERT: A 252 ASN cc_start: 0.9501 (t0) cc_final: 0.9011 (t0) REVERT: A 255 HIS cc_start: 0.8957 (t-90) cc_final: 0.8564 (t-90) REVERT: A 307 TYR cc_start: 0.9607 (t80) cc_final: 0.9163 (t80) REVERT: A 322 MET cc_start: 0.9207 (mmp) cc_final: 0.8831 (mmm) REVERT: A 348 MET cc_start: 0.9340 (ptp) cc_final: 0.9078 (ptp) REVERT: A 350 ARG cc_start: 0.8853 (mmm-85) cc_final: 0.8216 (mmm-85) REVERT: A 361 GLN cc_start: 0.9511 (tt0) cc_final: 0.9186 (tp40) REVERT: A 370 ASN cc_start: 0.9606 (m-40) cc_final: 0.9348 (m110) REVERT: A 387 GLN cc_start: 0.9010 (mt0) cc_final: 0.8447 (mp10) REVERT: A 394 TYR cc_start: 0.9289 (m-80) cc_final: 0.8570 (m-80) REVERT: A 406 ASP cc_start: 0.8932 (m-30) cc_final: 0.8678 (m-30) REVERT: A 407 ILE cc_start: 0.9226 (mt) cc_final: 0.8835 (mt) REVERT: A 415 ASN cc_start: 0.9510 (t0) cc_final: 0.8920 (t0) REVERT: A 418 ASN cc_start: 0.9512 (m-40) cc_final: 0.8883 (m-40) REVERT: A 421 GLU cc_start: 0.9245 (tm-30) cc_final: 0.8985 (tm-30) REVERT: A 468 LEU cc_start: 0.9627 (tp) cc_final: 0.9347 (tp) REVERT: A 472 LEU cc_start: 0.9762 (mt) cc_final: 0.9512 (mt) REVERT: A 494 MET cc_start: 0.9390 (mtp) cc_final: 0.9141 (mtp) REVERT: A 496 ASN cc_start: 0.9675 (t0) cc_final: 0.9123 (t0) REVERT: A 499 SER cc_start: 0.9939 (t) cc_final: 0.9707 (p) REVERT: A 500 ILE cc_start: 0.9773 (mt) cc_final: 0.9235 (mt) REVERT: A 515 ASP cc_start: 0.9306 (m-30) cc_final: 0.9008 (m-30) REVERT: A 522 TYR cc_start: 0.9221 (m-80) cc_final: 0.8726 (m-10) REVERT: A 558 TRP cc_start: 0.9225 (m100) cc_final: 0.8626 (m100) REVERT: A 570 MET cc_start: 0.9460 (mtp) cc_final: 0.7401 (mtp) REVERT: A 575 ARG cc_start: 0.9403 (mtm110) cc_final: 0.8596 (ptp90) REVERT: A 586 TYR cc_start: 0.8904 (m-10) cc_final: 0.8629 (m-10) REVERT: A 588 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8156 (tp40) REVERT: A 615 MET cc_start: 0.8708 (mmp) cc_final: 0.8453 (mmp) REVERT: A 639 ASP cc_start: 0.9231 (m-30) cc_final: 0.8968 (m-30) REVERT: A 645 GLN cc_start: 0.9135 (tp40) cc_final: 0.8897 (tp-100) REVERT: A 650 GLN cc_start: 0.8835 (mt0) cc_final: 0.7594 (mt0) REVERT: B 15 GLU cc_start: 0.9194 (tp30) cc_final: 0.8884 (tp30) REVERT: B 51 LEU cc_start: 0.9359 (tp) cc_final: 0.8311 (tp) REVERT: B 55 LEU cc_start: 0.9635 (mt) cc_final: 0.9380 (mt) REVERT: B 87 LYS cc_start: 0.9124 (mtpt) cc_final: 0.8872 (mtpt) REVERT: B 95 MET cc_start: 0.9281 (tpp) cc_final: 0.8847 (tpp) REVERT: B 99 LYS cc_start: 0.9583 (mmmt) cc_final: 0.9128 (mmmt) REVERT: B 107 LYS cc_start: 0.9658 (mptt) cc_final: 0.9362 (mmtt) REVERT: B 115 LEU cc_start: 0.9604 (mt) cc_final: 0.9336 (mt) REVERT: B 136 LYS cc_start: 0.9632 (mmtp) cc_final: 0.9304 (mmmm) REVERT: B 144 MET cc_start: 0.9122 (mtm) cc_final: 0.8819 (mtm) REVERT: B 147 GLN cc_start: 0.9330 (mt0) cc_final: 0.8962 (mt0) REVERT: B 157 LEU cc_start: 0.9520 (tp) cc_final: 0.9073 (tp) REVERT: B 158 ASN cc_start: 0.9613 (m110) cc_final: 0.9033 (p0) REVERT: B 161 ARG cc_start: 0.8859 (ttm110) cc_final: 0.8236 (mtt180) REVERT: B 164 ARG cc_start: 0.9175 (ttp80) cc_final: 0.8632 (ttp80) REVERT: B 200 SER cc_start: 0.9070 (t) cc_final: 0.8869 (t) REVERT: B 209 LYS cc_start: 0.9196 (tptp) cc_final: 0.8949 (tptp) REVERT: B 211 GLU cc_start: 0.8358 (mm-30) cc_final: 0.7532 (mm-30) REVERT: B 218 ASN cc_start: 0.9638 (t0) cc_final: 0.9357 (t0) REVERT: B 251 LEU cc_start: 0.9452 (tp) cc_final: 0.9122 (tp) REVERT: B 283 VAL cc_start: 0.9276 (t) cc_final: 0.8969 (t) REVERT: B 286 ASP cc_start: 0.8681 (m-30) cc_final: 0.7990 (m-30) REVERT: B 296 LYS cc_start: 0.9096 (mmpt) cc_final: 0.8750 (mtmm) REVERT: B 322 MET cc_start: 0.8749 (mmm) cc_final: 0.8494 (mmm) REVERT: B 333 LYS cc_start: 0.9436 (ttmm) cc_final: 0.9118 (ttmm) REVERT: B 345 LYS cc_start: 0.9687 (tttt) cc_final: 0.9396 (tttt) REVERT: B 350 ARG cc_start: 0.8686 (mtp85) cc_final: 0.8019 (mtp85) REVERT: B 359 MET cc_start: 0.9030 (ttm) cc_final: 0.8748 (ttm) REVERT: B 362 ASP cc_start: 0.9091 (m-30) cc_final: 0.8102 (m-30) REVERT: B 370 ASN cc_start: 0.9620 (m-40) cc_final: 0.9289 (m110) REVERT: B 375 LYS cc_start: 0.9256 (mmtm) cc_final: 0.8911 (mmtm) REVERT: B 393 SER cc_start: 0.9603 (t) cc_final: 0.9062 (t) REVERT: B 398 ASP cc_start: 0.8806 (t70) cc_final: 0.8601 (t70) REVERT: B 399 GLU cc_start: 0.8890 (mp0) cc_final: 0.8532 (mp0) REVERT: B 402 GLU cc_start: 0.8651 (mp0) cc_final: 0.8329 (mp0) REVERT: B 413 SER cc_start: 0.9501 (m) cc_final: 0.9038 (t) REVERT: B 471 TYR cc_start: 0.9401 (t80) cc_final: 0.9201 (t80) REVERT: B 494 MET cc_start: 0.9428 (mtt) cc_final: 0.9109 (mtt) REVERT: B 500 ILE cc_start: 0.9696 (mt) cc_final: 0.9491 (mt) REVERT: B 570 MET cc_start: 0.9254 (mtp) cc_final: 0.8915 (mtp) REVERT: B 585 SER cc_start: 0.9207 (p) cc_final: 0.8721 (t) REVERT: B 591 THR cc_start: 0.9216 (p) cc_final: 0.8902 (p) REVERT: B 606 TYR cc_start: 0.8444 (m-80) cc_final: 0.7983 (m-10) REVERT: B 615 MET cc_start: 0.8892 (mmp) cc_final: 0.8567 (mmp) REVERT: B 631 ASP cc_start: 0.9356 (m-30) cc_final: 0.9148 (m-30) REVERT: B 636 LYS cc_start: 0.9750 (mmtm) cc_final: 0.9524 (mmmt) REVERT: B 645 GLN cc_start: 0.9475 (tp-100) cc_final: 0.9134 (tp-100) REVERT: B 648 ILE cc_start: 0.9556 (mm) cc_final: 0.9280 (mm) REVERT: B 667 LEU cc_start: 0.9410 (tp) cc_final: 0.9146 (tt) REVERT: B 668 ASN cc_start: 0.9406 (m-40) cc_final: 0.9047 (m-40) REVERT: B 671 ASP cc_start: 0.9327 (m-30) cc_final: 0.9102 (m-30) REVERT: B 677 ARG cc_start: 0.9619 (mmm160) cc_final: 0.9320 (mmm-85) REVERT: C 100 VAL cc_start: 0.9176 (t) cc_final: 0.8964 (t) REVERT: C 124 TRP cc_start: 0.7892 (t60) cc_final: 0.7315 (t60) REVERT: D 69 GLN cc_start: 0.9452 (tp-100) cc_final: 0.8961 (tm-30) REVERT: D 100 VAL cc_start: 0.4519 (t) cc_final: 0.3695 (p) REVERT: D 204 TYR cc_start: 0.9091 (t80) cc_final: 0.8876 (t80) outliers start: 0 outliers final: 0 residues processed: 646 average time/residue: 0.1321 time to fit residues: 127.9516 Evaluate side-chains 586 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 586 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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: 0.5980 chunk 183 optimal weight: 9.9990 chunk 72 optimal weight: 0.0770 chunk 172 optimal weight: 30.0000 chunk 52 optimal weight: 7.9990 chunk 28 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 77 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 overall best weight: 0.9340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 13 ASN A 14 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.134662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.090338 restraints weight = 45321.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.093466 restraints weight = 26810.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.095580 restraints weight = 17907.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.097041 restraints weight = 13201.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.098105 restraints weight = 10455.439| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.6717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16386 Z= 0.131 Angle : 0.584 10.813 22134 Z= 0.313 Chirality : 0.042 0.193 2360 Planarity : 0.003 0.051 2818 Dihedral : 8.616 131.424 2290 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: 0.87 (0.19), residues: 1932 helix: 1.14 (0.15), residues: 1141 sheet: -0.64 (0.38), residues: 140 loop : 0.05 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 161 TYR 0.023 0.002 TYR B 612 PHE 0.028 0.002 PHE B 81 TRP 0.008 0.001 TRP C 124 HIS 0.007 0.001 HIS C 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (16386) covalent geometry : angle 0.58382 / 0.31 (22134) hydrogen bonds : bond 0.03732 / 2.33 ( 871) hydrogen bonds : angle 4.88022 / 3.51 ( 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 659 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 658 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9493 (t0) cc_final: 0.9154 (t70) REVERT: A 89 PHE cc_start: 0.9107 (t80) cc_final: 0.8831 (t80) REVERT: A 116 GLU cc_start: 0.8527 (tt0) cc_final: 0.7766 (tt0) REVERT: A 117 ARG cc_start: 0.8927 (mmt90) cc_final: 0.8719 (mmm160) REVERT: A 119 GLU cc_start: 0.9066 (mp0) cc_final: 0.8735 (mt-10) REVERT: A 139 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8930 (pt0) REVERT: A 143 LEU cc_start: 0.9597 (tp) cc_final: 0.9242 (tp) REVERT: A 147 GLN cc_start: 0.9123 (mm-40) cc_final: 0.8698 (mm110) REVERT: A 172 LEU cc_start: 0.9359 (mp) cc_final: 0.8984 (mp) REVERT: A 176 ASN cc_start: 0.9065 (t0) cc_final: 0.8596 (m-40) REVERT: A 195 LEU cc_start: 0.9566 (mt) cc_final: 0.9353 (mt) REVERT: A 204 SER cc_start: 0.9389 (m) cc_final: 0.8857 (p) REVERT: A 251 LEU cc_start: 0.9612 (tp) cc_final: 0.9310 (tp) REVERT: A 252 ASN cc_start: 0.9424 (t0) cc_final: 0.8881 (t0) REVERT: A 255 HIS cc_start: 0.8904 (t-90) cc_final: 0.8524 (t-90) REVERT: A 266 LYS cc_start: 0.9374 (mttp) cc_final: 0.8868 (mttp) REVERT: A 307 TYR cc_start: 0.9620 (t80) cc_final: 0.9142 (t80) REVERT: A 322 MET cc_start: 0.9208 (mmp) cc_final: 0.8828 (mmm) REVERT: A 342 LEU cc_start: 0.9619 (tp) cc_final: 0.9397 (tp) REVERT: A 348 MET cc_start: 0.9281 (ptp) cc_final: 0.9050 (ptp) REVERT: A 350 ARG cc_start: 0.8840 (mmm-85) cc_final: 0.8382 (mmm-85) REVERT: A 361 GLN cc_start: 0.9502 (tt0) cc_final: 0.9203 (tp40) REVERT: A 370 ASN cc_start: 0.9557 (m-40) cc_final: 0.9244 (m110) REVERT: A 387 GLN cc_start: 0.8904 (mt0) cc_final: 0.8472 (mp10) REVERT: A 394 TYR cc_start: 0.9279 (m-80) cc_final: 0.8547 (m-80) REVERT: A 406 ASP cc_start: 0.8964 (m-30) cc_final: 0.8757 (m-30) REVERT: A 415 ASN cc_start: 0.9533 (t0) cc_final: 0.8802 (t0) REVERT: A 418 ASN cc_start: 0.9464 (m110) cc_final: 0.8750 (m-40) REVERT: A 421 GLU cc_start: 0.9212 (tm-30) cc_final: 0.8924 (tm-30) REVERT: A 468 LEU cc_start: 0.9630 (tp) cc_final: 0.9351 (tp) REVERT: A 472 LEU cc_start: 0.9762 (mt) cc_final: 0.9557 (mt) REVERT: A 494 MET cc_start: 0.9415 (mtp) cc_final: 0.9153 (mtp) REVERT: A 496 ASN cc_start: 0.9658 (t0) cc_final: 0.9106 (t0) REVERT: A 499 SER cc_start: 0.9934 (t) cc_final: 0.9701 (p) REVERT: A 500 ILE cc_start: 0.9764 (mt) cc_final: 0.9365 (mt) REVERT: A 515 ASP cc_start: 0.9314 (m-30) cc_final: 0.8991 (m-30) REVERT: A 522 TYR cc_start: 0.9213 (m-80) cc_final: 0.8699 (m-10) REVERT: A 558 TRP cc_start: 0.9251 (m100) cc_final: 0.8678 (m100) REVERT: A 570 MET cc_start: 0.9489 (mtp) cc_final: 0.7865 (mtp) REVERT: A 575 ARG cc_start: 0.9436 (mtm110) cc_final: 0.8922 (ptp90) REVERT: A 612 TYR cc_start: 0.8903 (m-80) cc_final: 0.8294 (m-80) REVERT: A 639 ASP cc_start: 0.9226 (m-30) cc_final: 0.8884 (m-30) REVERT: A 640 MET cc_start: 0.9014 (tpp) cc_final: 0.8811 (tpp) REVERT: A 645 GLN cc_start: 0.9149 (tp40) cc_final: 0.8905 (tp-100) REVERT: A 650 GLN cc_start: 0.8836 (mt0) cc_final: 0.7669 (mt0) REVERT: A 655 THR cc_start: 0.8691 (m) cc_final: 0.8270 (m) REVERT: A 657 PHE cc_start: 0.8711 (m-80) cc_final: 0.8416 (m-80) REVERT: A 683 TYR cc_start: 0.8002 (t80) cc_final: 0.7602 (t80) REVERT: A 684 TYR cc_start: 0.7325 (m-10) cc_final: 0.7018 (m-80) REVERT: B 15 GLU cc_start: 0.9231 (tp30) cc_final: 0.8737 (tp30) REVERT: B 95 MET cc_start: 0.9168 (tpp) cc_final: 0.8809 (mmm) REVERT: B 99 LYS cc_start: 0.9549 (mmmt) cc_final: 0.9056 (mmmt) REVERT: B 119 GLU cc_start: 0.9237 (mp0) cc_final: 0.8813 (tm-30) REVERT: B 120 ASP cc_start: 0.9308 (m-30) cc_final: 0.8822 (m-30) REVERT: B 136 LYS cc_start: 0.9662 (mmtp) cc_final: 0.9369 (mmmm) REVERT: B 144 MET cc_start: 0.9031 (mtm) cc_final: 0.8714 (mtm) REVERT: B 157 LEU cc_start: 0.9507 (tp) cc_final: 0.9137 (tp) REVERT: B 158 ASN cc_start: 0.9586 (m110) cc_final: 0.9023 (p0) REVERT: B 161 ARG cc_start: 0.8722 (ttm110) cc_final: 0.8231 (mtt180) REVERT: B 164 ARG cc_start: 0.9063 (ttp80) cc_final: 0.8650 (ttp80) REVERT: B 200 SER cc_start: 0.9047 (t) cc_final: 0.8840 (t) REVERT: B 209 LYS cc_start: 0.9202 (tptp) cc_final: 0.8957 (tptp) REVERT: B 211 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7554 (mm-30) REVERT: B 217 GLU cc_start: 0.9214 (pp20) cc_final: 0.8883 (tm-30) REVERT: B 218 ASN cc_start: 0.9589 (t0) cc_final: 0.9331 (t0) REVERT: B 227 MET cc_start: 0.9345 (mtm) cc_final: 0.9112 (mtm) REVERT: B 251 LEU cc_start: 0.9445 (tp) cc_final: 0.9161 (tp) REVERT: B 283 VAL cc_start: 0.9178 (t) cc_final: 0.8950 (t) REVERT: B 286 ASP cc_start: 0.8764 (m-30) cc_final: 0.7958 (m-30) REVERT: B 296 LYS cc_start: 0.8986 (mmpt) cc_final: 0.8668 (mtmm) REVERT: B 306 ILE cc_start: 0.9602 (mt) cc_final: 0.9382 (tp) REVERT: B 312 GLN cc_start: 0.9306 (pm20) cc_final: 0.8942 (pm20) REVERT: B 322 MET cc_start: 0.8806 (mmm) cc_final: 0.8553 (mmm) REVERT: B 333 LYS cc_start: 0.9461 (ttmm) cc_final: 0.9133 (ttmm) REVERT: B 335 GLU cc_start: 0.9187 (pt0) cc_final: 0.8479 (pp20) REVERT: B 337 ILE cc_start: 0.9453 (mp) cc_final: 0.8863 (mp) REVERT: B 345 LYS cc_start: 0.9709 (tttt) cc_final: 0.9416 (tttt) REVERT: B 350 ARG cc_start: 0.8687 (mtp85) cc_final: 0.8104 (mtp85) REVERT: B 359 MET cc_start: 0.8973 (ttm) cc_final: 0.8712 (ttm) REVERT: B 362 ASP cc_start: 0.9119 (m-30) cc_final: 0.8090 (m-30) REVERT: B 373 ILE cc_start: 0.9667 (mt) cc_final: 0.9180 (mt) REVERT: B 375 LYS cc_start: 0.9191 (mmtm) cc_final: 0.8845 (mmtm) REVERT: B 390 GLN cc_start: 0.9349 (mt0) cc_final: 0.9132 (mm-40) REVERT: B 393 SER cc_start: 0.9589 (t) cc_final: 0.9062 (t) REVERT: B 399 GLU cc_start: 0.8963 (mp0) cc_final: 0.8624 (mp0) REVERT: B 402 GLU cc_start: 0.8679 (mp0) cc_final: 0.8350 (mp0) REVERT: B 443 THR cc_start: 0.9372 (m) cc_final: 0.9097 (t) REVERT: B 458 MET cc_start: 0.9512 (mmm) cc_final: 0.9180 (mmm) REVERT: B 471 TYR cc_start: 0.9389 (t80) cc_final: 0.9177 (t80) REVERT: B 493 MET cc_start: 0.9355 (tmm) cc_final: 0.8878 (tmm) REVERT: B 501 GLN cc_start: 0.9505 (mt0) cc_final: 0.9280 (mt0) REVERT: B 585 SER cc_start: 0.9190 (p) cc_final: 0.8774 (t) REVERT: B 591 THR cc_start: 0.9102 (p) cc_final: 0.8752 (p) REVERT: B 598 MET cc_start: 0.8179 (mmt) cc_final: 0.7928 (mmm) REVERT: B 606 TYR cc_start: 0.8296 (m-80) cc_final: 0.8071 (m-80) REVERT: B 615 MET cc_start: 0.8924 (mmp) cc_final: 0.8611 (mmp) REVERT: B 636 LYS cc_start: 0.9757 (mmtm) cc_final: 0.9526 (mmmt) REVERT: B 645 GLN cc_start: 0.9486 (tp-100) cc_final: 0.9270 (tp-100) REVERT: B 646 GLN cc_start: 0.9286 (pm20) cc_final: 0.9084 (pm20) REVERT: B 658 LEU cc_start: 0.9242 (mm) cc_final: 0.8846 (mm) REVERT: B 668 ASN cc_start: 0.9406 (m-40) cc_final: 0.8777 (m110) REVERT: B 677 ARG cc_start: 0.9607 (mmm160) cc_final: 0.9320 (mmm-85) REVERT: C 124 TRP cc_start: 0.8049 (t60) cc_final: 0.7749 (t60) REVERT: C 260 ILE cc_start: 0.2500 (pt) cc_final: 0.2130 (pt) REVERT: D 69 GLN cc_start: 0.9488 (tp-100) cc_final: 0.9131 (tm-30) REVERT: D 100 VAL cc_start: 0.4438 (t) cc_final: 0.3671 (p) REVERT: D 204 TYR cc_start: 0.9146 (t80) cc_final: 0.8917 (t80) outliers start: 1 outliers final: 0 residues processed: 658 average time/residue: 0.1313 time to fit residues: 129.7638 Evaluate side-chains 563 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 563 time to evaluate : 0.666 ------------------------------------------------------------------------------- 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: 3.9990 chunk 51 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 186 optimal weight: 0.9980 chunk 140 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 68 optimal weight: 10.0000 chunk 156 optimal weight: 20.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 HIS ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.129594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.086877 restraints weight = 46388.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.089910 restraints weight = 27365.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.091938 restraints weight = 18196.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.093306 restraints weight = 13415.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.094268 restraints weight = 10579.823| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.7033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16386 Z= 0.193 Angle : 0.631 8.679 22134 Z= 0.337 Chirality : 0.043 0.211 2360 Planarity : 0.004 0.048 2818 Dihedral : 8.621 131.649 2290 Min Nonbonded Distance : 1.776 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.06 % Allowed : 1.05 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.19), residues: 1932 helix: 1.05 (0.15), residues: 1149 sheet: -0.62 (0.38), residues: 140 loop : 0.11 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 575 TYR 0.042 0.002 TYR C 142 PHE 0.022 0.002 PHE B 81 TRP 0.009 0.002 TRP B 9 HIS 0.009 0.001 HIS B 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.19 (16386) covalent geometry : angle 0.63143 / 0.34 (22134) hydrogen bonds : bond 0.03800 / 2.40 ( 871) hydrogen bonds : angle 4.98394 / 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 630 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 629 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9479 (t0) cc_final: 0.9162 (t70) REVERT: A 143 LEU cc_start: 0.9590 (tp) cc_final: 0.9216 (tp) REVERT: A 150 GLN cc_start: 0.9370 (tp40) cc_final: 0.9140 (tp-100) REVERT: A 172 LEU cc_start: 0.9364 (mp) cc_final: 0.9018 (mp) REVERT: A 176 ASN cc_start: 0.9065 (t0) cc_final: 0.8578 (m-40) REVERT: A 195 LEU cc_start: 0.9559 (mt) cc_final: 0.9333 (mt) REVERT: A 204 SER cc_start: 0.9387 (m) cc_final: 0.8916 (p) REVERT: A 251 LEU cc_start: 0.9597 (tp) cc_final: 0.9315 (tp) REVERT: A 252 ASN cc_start: 0.9481 (t0) cc_final: 0.8900 (t0) REVERT: A 255 HIS cc_start: 0.8936 (t-90) cc_final: 0.8508 (t-90) REVERT: A 301 PHE cc_start: 0.9329 (m-10) cc_final: 0.8828 (m-10) REVERT: A 307 TYR cc_start: 0.9619 (t80) cc_final: 0.9098 (t80) REVERT: A 322 MET cc_start: 0.9165 (mmp) cc_final: 0.8810 (mmm) REVERT: A 345 LYS cc_start: 0.9721 (tttt) cc_final: 0.9436 (mttt) REVERT: A 348 MET cc_start: 0.9280 (ptp) cc_final: 0.9047 (ptp) REVERT: A 350 ARG cc_start: 0.8893 (mmm-85) cc_final: 0.8456 (mmm-85) REVERT: A 361 GLN cc_start: 0.9544 (tt0) cc_final: 0.9234 (tp40) REVERT: A 370 ASN cc_start: 0.9627 (m-40) cc_final: 0.9320 (m110) REVERT: A 387 GLN cc_start: 0.8986 (mt0) cc_final: 0.8579 (mp10) REVERT: A 394 TYR cc_start: 0.9262 (m-80) cc_final: 0.8480 (m-80) REVERT: A 415 ASN cc_start: 0.9490 (t0) cc_final: 0.9096 (t0) REVERT: A 418 ASN cc_start: 0.9329 (m110) cc_final: 0.8666 (m110) REVERT: A 421 GLU cc_start: 0.9244 (tm-30) cc_final: 0.8940 (tm-30) REVERT: A 468 LEU cc_start: 0.9684 (tp) cc_final: 0.9410 (tp) REVERT: A 472 LEU cc_start: 0.9790 (mt) cc_final: 0.9586 (mt) REVERT: A 494 MET cc_start: 0.9416 (mtp) cc_final: 0.9150 (mtp) REVERT: A 496 ASN cc_start: 0.9698 (t0) cc_final: 0.9104 (t0) REVERT: A 499 SER cc_start: 0.9939 (t) cc_final: 0.9694 (p) REVERT: A 500 ILE cc_start: 0.9794 (mt) cc_final: 0.9389 (mt) REVERT: A 515 ASP cc_start: 0.9328 (m-30) cc_final: 0.9027 (m-30) REVERT: A 522 TYR cc_start: 0.9223 (m-80) cc_final: 0.8720 (m-10) REVERT: A 558 TRP cc_start: 0.9279 (m100) cc_final: 0.8627 (m100) REVERT: A 570 MET cc_start: 0.9444 (mtp) cc_final: 0.7807 (mtp) REVERT: A 575 ARG cc_start: 0.9485 (mtm110) cc_final: 0.8960 (ptp90) REVERT: A 610 LYS cc_start: 0.9311 (ttpp) cc_final: 0.8724 (tmmt) REVERT: A 612 TYR cc_start: 0.8777 (m-80) cc_final: 0.7906 (m-80) REVERT: A 632 MET cc_start: 0.9034 (mtm) cc_final: 0.8613 (mtt) REVERT: A 639 ASP cc_start: 0.9277 (m-30) cc_final: 0.8959 (m-30) REVERT: A 645 GLN cc_start: 0.9135 (tp40) cc_final: 0.8896 (tp-100) REVERT: A 650 GLN cc_start: 0.8855 (mt0) cc_final: 0.7670 (mt0) REVERT: A 655 THR cc_start: 0.8775 (m) cc_final: 0.8544 (m) REVERT: A 657 PHE cc_start: 0.8705 (m-80) cc_final: 0.8463 (m-80) REVERT: B 17 MET cc_start: 0.9014 (mpp) cc_final: 0.8240 (mpp) REVERT: B 29 ASP cc_start: 0.9421 (t70) cc_final: 0.9147 (t70) REVERT: B 51 LEU cc_start: 0.9516 (tp) cc_final: 0.9291 (tp) REVERT: B 95 MET cc_start: 0.9239 (tpp) cc_final: 0.8940 (tpp) REVERT: B 99 LYS cc_start: 0.9548 (mmmt) cc_final: 0.9124 (mmmt) REVERT: B 118 TYR cc_start: 0.9528 (t80) cc_final: 0.9321 (t80) REVERT: B 119 GLU cc_start: 0.9231 (mp0) cc_final: 0.8848 (tm-30) REVERT: B 120 ASP cc_start: 0.9420 (m-30) cc_final: 0.8866 (m-30) REVERT: B 136 LYS cc_start: 0.9668 (mmtp) cc_final: 0.9325 (mmmm) REVERT: B 144 MET cc_start: 0.9114 (mtm) cc_final: 0.8838 (mtm) REVERT: B 147 GLN cc_start: 0.9440 (mt0) cc_final: 0.8952 (mt0) REVERT: B 157 LEU cc_start: 0.9539 (tp) cc_final: 0.8970 (tp) REVERT: B 161 ARG cc_start: 0.8843 (ttm110) cc_final: 0.8195 (mtt180) REVERT: B 200 SER cc_start: 0.8958 (t) cc_final: 0.8753 (t) REVERT: B 209 LYS cc_start: 0.9219 (tptp) cc_final: 0.8978 (tptp) REVERT: B 211 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7447 (mm-30) REVERT: B 227 MET cc_start: 0.9399 (mtm) cc_final: 0.9095 (mtm) REVERT: B 251 LEU cc_start: 0.9463 (tp) cc_final: 0.9204 (tp) REVERT: B 286 ASP cc_start: 0.8764 (m-30) cc_final: 0.8028 (m-30) REVERT: B 296 LYS cc_start: 0.9125 (mmpt) cc_final: 0.8821 (mtmm) REVERT: B 322 MET cc_start: 0.8798 (mmm) cc_final: 0.8515 (mmm) REVERT: B 333 LYS cc_start: 0.9461 (ttmm) cc_final: 0.9109 (ttmm) REVERT: B 345 LYS cc_start: 0.9698 (tttt) cc_final: 0.9436 (tttt) REVERT: B 350 ARG cc_start: 0.8750 (mtp85) cc_final: 0.7950 (mtp85) REVERT: B 362 ASP cc_start: 0.9069 (m-30) cc_final: 0.8103 (m-30) REVERT: B 375 LYS cc_start: 0.9217 (mmtm) cc_final: 0.8890 (mmtm) REVERT: B 393 SER cc_start: 0.9546 (t) cc_final: 0.8854 (t) REVERT: B 399 GLU cc_start: 0.8995 (mp0) cc_final: 0.8601 (mp0) REVERT: B 402 GLU cc_start: 0.8634 (mp0) cc_final: 0.8192 (mp0) REVERT: B 403 ILE cc_start: 0.9195 (mm) cc_final: 0.8803 (tp) REVERT: B 413 SER cc_start: 0.9535 (m) cc_final: 0.9063 (t) REVERT: B 440 SER cc_start: 0.9749 (t) cc_final: 0.9471 (t) REVERT: B 441 GLU cc_start: 0.9092 (pm20) cc_final: 0.8827 (pm20) REVERT: B 458 MET cc_start: 0.9471 (mmm) cc_final: 0.8981 (mmm) REVERT: B 459 LYS cc_start: 0.9212 (mppt) cc_final: 0.8346 (mptt) REVERT: B 494 MET cc_start: 0.9446 (mtt) cc_final: 0.8815 (mtt) REVERT: B 585 SER cc_start: 0.9216 (p) cc_final: 0.8833 (t) REVERT: B 588 GLN cc_start: 0.9584 (mm110) cc_final: 0.9273 (mm-40) REVERT: B 591 THR cc_start: 0.9333 (p) cc_final: 0.9010 (p) REVERT: B 606 TYR cc_start: 0.8446 (m-80) cc_final: 0.8050 (m-80) REVERT: B 615 MET cc_start: 0.8989 (mmp) cc_final: 0.8622 (mmp) REVERT: B 636 LYS cc_start: 0.9729 (mmtm) cc_final: 0.9440 (mmmt) REVERT: B 639 ASP cc_start: 0.9349 (m-30) cc_final: 0.8988 (m-30) REVERT: B 645 GLN cc_start: 0.9450 (tp-100) cc_final: 0.9174 (tp-100) REVERT: B 648 ILE cc_start: 0.9572 (mm) cc_final: 0.9335 (mm) REVERT: B 658 LEU cc_start: 0.9032 (mm) cc_final: 0.8773 (mm) REVERT: B 667 LEU cc_start: 0.9567 (tp) cc_final: 0.9234 (tt) REVERT: B 668 ASN cc_start: 0.9449 (m-40) cc_final: 0.8970 (m-40) REVERT: B 677 ARG cc_start: 0.9609 (mmm160) cc_final: 0.9335 (mmm-85) REVERT: C 100 VAL cc_start: 0.9222 (t) cc_final: 0.8925 (p) REVERT: C 124 TRP cc_start: 0.7857 (t60) cc_final: 0.7631 (t60) REVERT: D 69 GLN cc_start: 0.9527 (tp-100) cc_final: 0.9221 (tm-30) REVERT: D 100 VAL cc_start: 0.4553 (t) cc_final: 0.3764 (p) REVERT: D 204 TYR cc_start: 0.9172 (t80) cc_final: 0.8940 (t80) outliers start: 1 outliers final: 0 residues processed: 629 average time/residue: 0.1284 time to fit residues: 121.6695 Evaluate side-chains 557 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 557 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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: 8.9990 chunk 99 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 158 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN B 191 GLN ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN B 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 GLN C 186 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.130219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.086941 restraints weight = 46682.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.090065 restraints weight = 27495.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.092034 restraints weight = 18169.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.093349 restraints weight = 13434.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.094381 restraints weight = 10730.312| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.7270 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= 0.176 Angle : 0.625 10.353 22134 Z= 0.333 Chirality : 0.043 0.189 2360 Planarity : 0.004 0.075 2818 Dihedral : 8.537 131.335 2290 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.19), residues: 1932 helix: 1.04 (0.15), residues: 1149 sheet: -0.62 (0.39), residues: 140 loop : 0.03 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 117 TYR 0.042 0.002 TYR C 142 PHE 0.023 0.002 PHE B 487 TRP 0.009 0.001 TRP A 623 HIS 0.009 0.001 HIS B 469 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (16386) covalent geometry : angle 0.62454 / 0.33 (22134) hydrogen bonds : bond 0.03763 / 2.37 ( 871) hydrogen bonds : angle 4.96385 / 3.57 ( 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 620 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 620 time to evaluate : 0.760 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9479 (t0) cc_final: 0.9131 (t70) REVERT: A 95 MET cc_start: 0.9054 (tpt) cc_final: 0.8050 (tmm) REVERT: A 99 LYS cc_start: 0.9654 (mmtt) cc_final: 0.9265 (mmtt) REVERT: A 139 GLU cc_start: 0.9219 (mt-10) cc_final: 0.8962 (pt0) REVERT: A 143 LEU cc_start: 0.9610 (tp) cc_final: 0.9219 (tp) REVERT: A 147 GLN cc_start: 0.9234 (mm-40) cc_final: 0.9017 (mm-40) REVERT: A 148 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8695 (mt-10) REVERT: A 176 ASN cc_start: 0.9110 (t0) cc_final: 0.8629 (m-40) REVERT: A 195 LEU cc_start: 0.9570 (mt) cc_final: 0.9337 (mt) REVERT: A 204 SER cc_start: 0.9430 (m) cc_final: 0.8916 (p) REVERT: A 251 LEU cc_start: 0.9637 (tp) cc_final: 0.9369 (tp) REVERT: A 252 ASN cc_start: 0.9487 (t0) cc_final: 0.8929 (t0) REVERT: A 255 HIS cc_start: 0.8902 (t-90) cc_final: 0.8467 (t-90) REVERT: A 301 PHE cc_start: 0.9293 (m-10) cc_final: 0.8700 (m-10) REVERT: A 307 TYR cc_start: 0.9605 (t80) cc_final: 0.9088 (t80) REVERT: A 320 ASN cc_start: 0.9492 (m-40) cc_final: 0.9254 (m-40) REVERT: A 322 MET cc_start: 0.9142 (mmp) cc_final: 0.8773 (mmm) REVERT: A 350 ARG cc_start: 0.8943 (mmm-85) cc_final: 0.8501 (mmm-85) REVERT: A 361 GLN cc_start: 0.9493 (tt0) cc_final: 0.9238 (tp40) REVERT: A 370 ASN cc_start: 0.9600 (m-40) cc_final: 0.9268 (m110) REVERT: A 387 GLN cc_start: 0.8903 (mt0) cc_final: 0.8491 (mp10) REVERT: A 394 TYR cc_start: 0.9265 (m-80) cc_final: 0.8567 (m-80) REVERT: A 407 ILE cc_start: 0.9172 (mt) cc_final: 0.8787 (mt) REVERT: A 415 ASN cc_start: 0.9492 (t0) cc_final: 0.9012 (t0) REVERT: A 418 ASN cc_start: 0.9217 (m110) cc_final: 0.8579 (m-40) REVERT: A 421 GLU cc_start: 0.9187 (tm-30) cc_final: 0.8923 (tm-30) REVERT: A 468 LEU cc_start: 0.9696 (tp) cc_final: 0.9443 (tp) REVERT: A 472 LEU cc_start: 0.9762 (mt) cc_final: 0.9552 (mt) REVERT: A 496 ASN cc_start: 0.9646 (t0) cc_final: 0.9084 (t0) REVERT: A 499 SER cc_start: 0.9931 (t) cc_final: 0.9702 (p) REVERT: A 500 ILE cc_start: 0.9801 (mt) cc_final: 0.9403 (mt) REVERT: A 515 ASP cc_start: 0.9311 (m-30) cc_final: 0.9028 (m-30) REVERT: A 522 TYR cc_start: 0.9191 (m-80) cc_final: 0.8676 (m-10) REVERT: A 558 TRP cc_start: 0.9239 (m100) cc_final: 0.8604 (m100) REVERT: A 570 MET cc_start: 0.9424 (mtp) cc_final: 0.7825 (mtp) REVERT: A 575 ARG cc_start: 0.9473 (mtm110) cc_final: 0.9038 (ptp90) REVERT: A 586 TYR cc_start: 0.9369 (m-10) cc_final: 0.8881 (m-10) REVERT: A 610 LYS cc_start: 0.9301 (ttpp) cc_final: 0.8753 (tmmt) REVERT: A 612 TYR cc_start: 0.8870 (m-80) cc_final: 0.8035 (m-80) REVERT: A 615 MET cc_start: 0.8880 (mmp) cc_final: 0.8034 (mmp) REVERT: A 639 ASP cc_start: 0.9259 (m-30) cc_final: 0.8894 (m-30) REVERT: A 640 MET cc_start: 0.9327 (ttm) cc_final: 0.8692 (tpp) REVERT: A 645 GLN cc_start: 0.9155 (tp40) cc_final: 0.8907 (tp-100) REVERT: A 650 GLN cc_start: 0.8860 (mt0) cc_final: 0.7580 (mt0) REVERT: A 664 THR cc_start: 0.9404 (p) cc_final: 0.9095 (t) REVERT: B 15 GLU cc_start: 0.8975 (tp30) cc_final: 0.8706 (tp30) REVERT: B 17 MET cc_start: 0.8955 (mpp) cc_final: 0.8174 (mpp) REVERT: B 29 ASP cc_start: 0.9363 (t70) cc_final: 0.9071 (t70) REVERT: B 81 PHE cc_start: 0.9461 (m-80) cc_final: 0.9104 (m-80) REVERT: B 95 MET cc_start: 0.9108 (tpp) cc_final: 0.8805 (tpp) REVERT: B 99 LYS cc_start: 0.9540 (mmmt) cc_final: 0.9104 (mmmt) REVERT: B 119 GLU cc_start: 0.9248 (mp0) cc_final: 0.8917 (tm-30) REVERT: B 120 ASP cc_start: 0.9417 (m-30) cc_final: 0.8612 (m-30) REVERT: B 136 LYS cc_start: 0.9665 (mmtp) cc_final: 0.9291 (mmmm) REVERT: B 144 MET cc_start: 0.9036 (mtm) cc_final: 0.8777 (mtm) REVERT: B 147 GLN cc_start: 0.9344 (mt0) cc_final: 0.8699 (mt0) REVERT: B 205 LYS cc_start: 0.9145 (mmmt) cc_final: 0.8839 (mmmm) REVERT: B 209 LYS cc_start: 0.9170 (tptp) cc_final: 0.8923 (tptp) REVERT: B 211 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7483 (mm-30) REVERT: B 218 ASN cc_start: 0.9547 (m110) cc_final: 0.9045 (t0) REVERT: B 227 MET cc_start: 0.9317 (mtm) cc_final: 0.9083 (mtm) REVERT: B 251 LEU cc_start: 0.9494 (tp) cc_final: 0.9214 (tp) REVERT: B 286 ASP cc_start: 0.8737 (m-30) cc_final: 0.7992 (m-30) REVERT: B 296 LYS cc_start: 0.9126 (mmpt) cc_final: 0.8836 (mtmm) REVERT: B 322 MET cc_start: 0.8733 (mmm) cc_final: 0.8491 (mmm) REVERT: B 333 LYS cc_start: 0.9464 (ttmm) cc_final: 0.9103 (ttmm) REVERT: B 335 GLU cc_start: 0.9248 (pt0) cc_final: 0.9026 (pt0) REVERT: B 342 LEU cc_start: 0.9739 (tp) cc_final: 0.9492 (tp) REVERT: B 345 LYS cc_start: 0.9725 (tttt) cc_final: 0.9434 (tttt) REVERT: B 346 LEU cc_start: 0.9716 (mt) cc_final: 0.9508 (mt) REVERT: B 350 ARG cc_start: 0.8745 (mtp85) cc_final: 0.7972 (mtp85) REVERT: B 362 ASP cc_start: 0.9041 (m-30) cc_final: 0.8032 (m-30) REVERT: B 370 ASN cc_start: 0.9495 (m-40) cc_final: 0.8796 (m110) REVERT: B 375 LYS cc_start: 0.9230 (mmtm) cc_final: 0.8853 (mmtm) REVERT: B 393 SER cc_start: 0.9538 (t) cc_final: 0.8823 (t) REVERT: B 398 ASP cc_start: 0.8798 (t70) cc_final: 0.8540 (t70) REVERT: B 402 GLU cc_start: 0.8641 (mp0) cc_final: 0.8188 (mp0) REVERT: B 403 ILE cc_start: 0.9185 (mm) cc_final: 0.8798 (tp) REVERT: B 459 LYS cc_start: 0.9189 (mppt) cc_final: 0.8891 (mmmt) REVERT: B 494 MET cc_start: 0.9408 (mtt) cc_final: 0.8745 (mtt) REVERT: B 585 SER cc_start: 0.9274 (p) cc_final: 0.8883 (t) REVERT: B 588 GLN cc_start: 0.9506 (mm-40) cc_final: 0.9023 (mm-40) REVERT: B 591 THR cc_start: 0.9323 (p) cc_final: 0.9041 (p) REVERT: B 606 TYR cc_start: 0.8424 (m-80) cc_final: 0.8076 (m-80) REVERT: B 615 MET cc_start: 0.8949 (mmp) cc_final: 0.8633 (mmp) REVERT: B 636 LYS cc_start: 0.9705 (mmtm) cc_final: 0.9357 (mmmt) REVERT: B 639 ASP cc_start: 0.9336 (m-30) cc_final: 0.8950 (m-30) REVERT: B 645 GLN cc_start: 0.9359 (tp40) cc_final: 0.9091 (tp-100) REVERT: B 648 ILE cc_start: 0.9561 (mm) cc_final: 0.9316 (mm) REVERT: B 658 LEU cc_start: 0.9122 (mm) cc_final: 0.8847 (mm) REVERT: B 668 ASN cc_start: 0.9422 (m-40) cc_final: 0.8892 (m-40) REVERT: B 677 ARG cc_start: 0.9599 (mmm160) cc_final: 0.9320 (mmm-85) REVERT: C 100 VAL cc_start: 0.8980 (t) cc_final: 0.8763 (p) REVERT: C 194 ILE cc_start: 0.8901 (mt) cc_final: 0.8698 (mt) REVERT: D 69 GLN cc_start: 0.9549 (tp-100) cc_final: 0.9181 (tm-30) REVERT: D 91 ASN cc_start: 0.7916 (m-40) cc_final: 0.7650 (m-40) REVERT: D 96 MET cc_start: 0.8916 (mmp) cc_final: 0.8710 (mpp) REVERT: D 100 VAL cc_start: 0.4705 (t) cc_final: 0.3948 (p) outliers start: 0 outliers final: 0 residues processed: 620 average time/residue: 0.1288 time to fit residues: 120.7939 Evaluate side-chains 562 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 562 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 69 optimal weight: 7.9990 chunk 133 optimal weight: 0.9980 chunk 149 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 GLN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.135868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.092061 restraints weight = 46411.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.095085 restraints weight = 27202.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.097142 restraints weight = 18209.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.098669 restraints weight = 13443.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.099635 restraints weight = 10490.885| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.7513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16386 Z= 0.132 Angle : 0.609 7.906 22134 Z= 0.326 Chirality : 0.043 0.250 2360 Planarity : 0.004 0.062 2818 Dihedral : 8.454 131.039 2290 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % 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: 0.71 (0.18), residues: 1932 helix: 1.03 (0.15), residues: 1150 sheet: 0.06 (0.45), residues: 110 loop : -0.29 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 161 TYR 0.041 0.002 TYR C 142 PHE 0.030 0.002 PHE B 156 TRP 0.015 0.001 TRP C 124 HIS 0.011 0.001 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (16386) covalent geometry : angle 0.60870 / 0.33 (22134) hydrogen bonds : bond 0.03723 / 2.32 ( 871) hydrogen bonds : angle 4.88715 / 3.53 ( 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 630 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 630 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9468 (t0) cc_final: 0.9122 (t70) REVERT: A 91 PHE cc_start: 0.9508 (m-80) cc_final: 0.8842 (m-80) REVERT: A 95 MET cc_start: 0.8930 (tpt) cc_final: 0.6660 (mmm) REVERT: A 98 PHE cc_start: 0.9546 (t80) cc_final: 0.8824 (t80) REVERT: A 99 LYS cc_start: 0.9600 (mmtt) cc_final: 0.9172 (mmtt) REVERT: A 139 GLU cc_start: 0.9226 (mt-10) cc_final: 0.8980 (pt0) REVERT: A 143 LEU cc_start: 0.9603 (tp) cc_final: 0.9214 (tp) REVERT: A 147 GLN cc_start: 0.9206 (mm-40) cc_final: 0.8903 (mm-40) REVERT: A 148 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8670 (mt-10) REVERT: A 176 ASN cc_start: 0.9099 (t0) cc_final: 0.8688 (m-40) REVERT: A 188 ILE cc_start: 0.9560 (mt) cc_final: 0.9350 (mt) REVERT: A 195 LEU cc_start: 0.9559 (mt) cc_final: 0.9349 (mt) REVERT: A 204 SER cc_start: 0.9411 (m) cc_final: 0.8898 (p) REVERT: A 251 LEU cc_start: 0.9613 (tp) cc_final: 0.9394 (tp) REVERT: A 252 ASN cc_start: 0.9428 (t0) cc_final: 0.8901 (t0) REVERT: A 255 HIS cc_start: 0.8827 (t-90) cc_final: 0.8555 (t-90) REVERT: A 301 PHE cc_start: 0.9240 (m-10) cc_final: 0.8703 (m-10) REVERT: A 307 TYR cc_start: 0.9622 (t80) cc_final: 0.9089 (t80) REVERT: A 322 MET cc_start: 0.9189 (mmp) cc_final: 0.8797 (mmm) REVERT: A 350 ARG cc_start: 0.8966 (mmm-85) cc_final: 0.8466 (mmm-85) REVERT: A 370 ASN cc_start: 0.9527 (m-40) cc_final: 0.9134 (m110) REVERT: A 387 GLN cc_start: 0.8864 (mt0) cc_final: 0.8486 (mp10) REVERT: A 394 TYR cc_start: 0.9316 (m-80) cc_final: 0.8518 (m-80) REVERT: A 415 ASN cc_start: 0.9541 (t0) cc_final: 0.8826 (t0) REVERT: A 418 ASN cc_start: 0.9218 (m110) cc_final: 0.8542 (m-40) REVERT: A 421 GLU cc_start: 0.9209 (tm-30) cc_final: 0.8924 (tm-30) REVERT: A 466 MET cc_start: 0.9623 (ptt) cc_final: 0.9042 (ptt) REVERT: A 468 LEU cc_start: 0.9667 (tp) cc_final: 0.9461 (tp) REVERT: A 496 ASN cc_start: 0.9632 (t0) cc_final: 0.9070 (t0) REVERT: A 499 SER cc_start: 0.9928 (t) cc_final: 0.9686 (p) REVERT: A 500 ILE cc_start: 0.9782 (mt) cc_final: 0.9431 (mt) REVERT: A 515 ASP cc_start: 0.9333 (m-30) cc_final: 0.9030 (m-30) REVERT: A 522 TYR cc_start: 0.9181 (m-80) cc_final: 0.8920 (m-10) REVERT: A 558 TRP cc_start: 0.9246 (m100) cc_final: 0.8669 (m100) REVERT: A 570 MET cc_start: 0.9478 (mtp) cc_final: 0.7678 (ttm) REVERT: A 575 ARG cc_start: 0.9407 (mtm110) cc_final: 0.9114 (ptp90) REVERT: A 586 TYR cc_start: 0.9342 (m-10) cc_final: 0.8936 (m-10) REVERT: A 601 ILE cc_start: 0.9405 (tt) cc_final: 0.9114 (tt) REVERT: A 612 TYR cc_start: 0.8774 (m-80) cc_final: 0.8088 (m-80) REVERT: A 613 TYR cc_start: 0.8844 (t80) cc_final: 0.8379 (t80) REVERT: A 615 MET cc_start: 0.8949 (mmp) cc_final: 0.8424 (mmp) REVERT: A 639 ASP cc_start: 0.9259 (m-30) cc_final: 0.8845 (m-30) REVERT: A 640 MET cc_start: 0.9424 (ttm) cc_final: 0.9064 (ttm) REVERT: A 641 ILE cc_start: 0.9860 (mm) cc_final: 0.9659 (mm) REVERT: A 645 GLN cc_start: 0.9116 (tp40) cc_final: 0.8851 (tp-100) REVERT: A 650 GLN cc_start: 0.8787 (mt0) cc_final: 0.7569 (mt0) REVERT: A 679 ILE cc_start: 0.9657 (mm) cc_final: 0.9439 (mm) REVERT: A 682 ILE cc_start: 0.9404 (mp) cc_final: 0.9079 (mp) REVERT: B 15 GLU cc_start: 0.8973 (tp30) cc_final: 0.8677 (tp30) REVERT: B 17 MET cc_start: 0.8982 (mpp) cc_final: 0.8328 (mpp) REVERT: B 29 ASP cc_start: 0.9421 (t70) cc_final: 0.9192 (t70) REVERT: B 71 LEU cc_start: 0.9713 (mm) cc_final: 0.9512 (mp) REVERT: B 99 LYS cc_start: 0.9507 (mmmt) cc_final: 0.9097 (mmmt) REVERT: B 136 LYS cc_start: 0.9660 (mmtp) cc_final: 0.9279 (mmmm) REVERT: B 144 MET cc_start: 0.8939 (mtm) cc_final: 0.8665 (mtm) REVERT: B 147 GLN cc_start: 0.9228 (mt0) cc_final: 0.8581 (mt0) REVERT: B 157 LEU cc_start: 0.9659 (tp) cc_final: 0.9420 (tp) REVERT: B 161 ARG cc_start: 0.8748 (ttm110) cc_final: 0.8281 (mtp85) REVERT: B 191 GLN cc_start: 0.9279 (mm-40) cc_final: 0.8659 (mt0) REVERT: B 200 SER cc_start: 0.9032 (t) cc_final: 0.8812 (t) REVERT: B 209 LYS cc_start: 0.9093 (tptp) cc_final: 0.8826 (tptp) REVERT: B 211 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7425 (mm-30) REVERT: B 218 ASN cc_start: 0.9354 (m110) cc_final: 0.8864 (m-40) REVERT: B 227 MET cc_start: 0.9305 (mtm) cc_final: 0.9099 (mtm) REVERT: B 251 LEU cc_start: 0.9489 (tp) cc_final: 0.9232 (tp) REVERT: B 258 ILE cc_start: 0.9502 (tp) cc_final: 0.9283 (tp) REVERT: B 286 ASP cc_start: 0.8606 (m-30) cc_final: 0.8247 (m-30) REVERT: B 290 GLU cc_start: 0.9201 (pp20) cc_final: 0.8714 (pp20) REVERT: B 291 LEU cc_start: 0.9618 (mt) cc_final: 0.9362 (mt) REVERT: B 296 LYS cc_start: 0.9039 (mmpt) cc_final: 0.8746 (mtmm) REVERT: B 322 MET cc_start: 0.8725 (mmm) cc_final: 0.8448 (mmm) REVERT: B 333 LYS cc_start: 0.9484 (ttmm) cc_final: 0.9148 (ttmm) REVERT: B 345 LYS cc_start: 0.9713 (tttt) cc_final: 0.9443 (tttt) REVERT: B 350 ARG cc_start: 0.8633 (mtp85) cc_final: 0.7894 (mtp85) REVERT: B 362 ASP cc_start: 0.9056 (m-30) cc_final: 0.8078 (m-30) REVERT: B 375 LYS cc_start: 0.9199 (mmtm) cc_final: 0.8836 (mmtm) REVERT: B 390 GLN cc_start: 0.9359 (mt0) cc_final: 0.9157 (mm-40) REVERT: B 393 SER cc_start: 0.9583 (t) cc_final: 0.9048 (t) REVERT: B 402 GLU cc_start: 0.8749 (mp0) cc_final: 0.8343 (mp0) REVERT: B 403 ILE cc_start: 0.9121 (mm) cc_final: 0.8810 (tp) REVERT: B 413 SER cc_start: 0.9571 (m) cc_final: 0.9152 (t) REVERT: B 447 ASN cc_start: 0.8850 (m-40) cc_final: 0.7924 (m-40) REVERT: B 459 LYS cc_start: 0.9121 (mppt) cc_final: 0.8275 (mptt) REVERT: B 494 MET cc_start: 0.9366 (mtt) cc_final: 0.8899 (mtt) REVERT: B 501 GLN cc_start: 0.9559 (mt0) cc_final: 0.9349 (mp10) REVERT: B 561 LEU cc_start: 0.9637 (tp) cc_final: 0.9418 (tp) REVERT: B 585 SER cc_start: 0.9239 (p) cc_final: 0.8874 (t) REVERT: B 588 GLN cc_start: 0.9356 (mm-40) cc_final: 0.8973 (mm-40) REVERT: B 591 THR cc_start: 0.9208 (p) cc_final: 0.8873 (p) REVERT: B 604 ARG cc_start: 0.8795 (mmp80) cc_final: 0.8422 (mmp-170) REVERT: B 615 MET cc_start: 0.9026 (mmp) cc_final: 0.8779 (mmp) REVERT: B 631 ASP cc_start: 0.9624 (m-30) cc_final: 0.9377 (m-30) REVERT: B 636 LYS cc_start: 0.9724 (mmtm) cc_final: 0.9341 (mmmt) REVERT: B 639 ASP cc_start: 0.9311 (m-30) cc_final: 0.8922 (m-30) REVERT: B 645 GLN cc_start: 0.9460 (tp40) cc_final: 0.9112 (tp-100) REVERT: B 648 ILE cc_start: 0.9569 (mm) cc_final: 0.9295 (mm) REVERT: B 658 LEU cc_start: 0.9142 (mm) cc_final: 0.8812 (mm) REVERT: B 667 LEU cc_start: 0.9543 (tt) cc_final: 0.9321 (tt) REVERT: B 668 ASN cc_start: 0.9364 (m-40) cc_final: 0.8924 (m-40) REVERT: B 677 ARG cc_start: 0.9571 (mmm160) cc_final: 0.9303 (mmm-85) REVERT: C 101 HIS cc_start: 0.7729 (m90) cc_final: 0.7461 (m90) REVERT: D 69 GLN cc_start: 0.9549 (tp40) cc_final: 0.9106 (tm-30) REVERT: D 100 VAL cc_start: 0.4500 (t) cc_final: 0.3766 (p) REVERT: D 201 HIS cc_start: 0.7814 (m170) cc_final: 0.7347 (m170) REVERT: D 204 TYR cc_start: 0.9133 (t80) cc_final: 0.8923 (t80) outliers start: 0 outliers final: 0 residues processed: 630 average time/residue: 0.1300 time to fit residues: 123.2817 Evaluate side-chains 561 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 561 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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: 5.9990 chunk 62 optimal weight: 2.9990 chunk 33 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 189 optimal weight: 20.0000 chunk 181 optimal weight: 5.9990 chunk 165 optimal weight: 8.9990 chunk 16 optimal weight: 8.9990 chunk 54 optimal weight: 0.0870 chunk 132 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 overall best weight: 3.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 158 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.128038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.085603 restraints weight = 47674.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.088482 restraints weight = 28340.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.090367 restraints weight = 19059.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.091733 restraints weight = 14130.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.092642 restraints weight = 11186.642| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.7719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 16386 Z= 0.222 Angle : 0.676 8.261 22134 Z= 0.363 Chirality : 0.045 0.254 2360 Planarity : 0.004 0.056 2818 Dihedral : 8.603 132.917 2290 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.06 % Allowed : 0.47 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.19), residues: 1932 helix: 0.95 (0.15), residues: 1148 sheet: -0.15 (0.44), residues: 112 loop : -0.27 (0.23), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 161 TYR 0.042 0.002 TYR A 683 PHE 0.038 0.002 PHE C 227 TRP 0.027 0.003 TRP C 44 HIS 0.014 0.002 HIS D 201 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.22 (16386) covalent geometry : angle 0.67618 / 0.36 (22134) hydrogen bonds : bond 0.03881 / 2.44 ( 871) hydrogen bonds : angle 5.13508 / 3.69 ( 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 617 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 616 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 PHE cc_start: 0.9568 (m-80) cc_final: 0.9022 (m-80) REVERT: A 139 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8973 (pt0) REVERT: A 143 LEU cc_start: 0.9597 (tp) cc_final: 0.9199 (tp) REVERT: A 148 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8667 (mt-10) REVERT: A 176 ASN cc_start: 0.9096 (t0) cc_final: 0.8708 (m-40) REVERT: A 204 SER cc_start: 0.9458 (m) cc_final: 0.8992 (p) REVERT: A 251 LEU cc_start: 0.9652 (tp) cc_final: 0.9401 (tp) REVERT: A 252 ASN cc_start: 0.9441 (t0) cc_final: 0.9026 (t0) REVERT: A 255 HIS cc_start: 0.8824 (t-90) cc_final: 0.8493 (t-90) REVERT: A 307 TYR cc_start: 0.9608 (t80) cc_final: 0.9074 (t80) REVERT: A 322 MET cc_start: 0.9143 (mmp) cc_final: 0.8734 (mmm) REVERT: A 350 ARG cc_start: 0.9061 (mmm-85) cc_final: 0.8551 (mmm-85) REVERT: A 370 ASN cc_start: 0.9605 (m-40) cc_final: 0.9235 (m110) REVERT: A 377 LYS cc_start: 0.8802 (mttt) cc_final: 0.8571 (mtmt) REVERT: A 387 GLN cc_start: 0.9090 (mt0) cc_final: 0.8485 (mp10) REVERT: A 394 TYR cc_start: 0.9329 (m-80) cc_final: 0.8731 (m-80) REVERT: A 421 GLU cc_start: 0.9205 (tm-30) cc_final: 0.8942 (tm-30) REVERT: A 425 ILE cc_start: 0.9469 (mp) cc_final: 0.9256 (mp) REVERT: A 468 LEU cc_start: 0.9737 (tp) cc_final: 0.9505 (tp) REVERT: A 472 LEU cc_start: 0.9784 (mt) cc_final: 0.9574 (mt) REVERT: A 496 ASN cc_start: 0.9653 (t0) cc_final: 0.9047 (t0) REVERT: A 499 SER cc_start: 0.9932 (t) cc_final: 0.9713 (p) REVERT: A 500 ILE cc_start: 0.9803 (mt) cc_final: 0.9460 (mt) REVERT: A 515 ASP cc_start: 0.9345 (m-30) cc_final: 0.9079 (m-30) REVERT: A 522 TYR cc_start: 0.9197 (m-80) cc_final: 0.8859 (m-10) REVERT: A 558 TRP cc_start: 0.9251 (m100) cc_final: 0.8681 (m100) REVERT: A 575 ARG cc_start: 0.9458 (mtm110) cc_final: 0.8938 (ptp90) REVERT: A 599 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8698 (tm-30) REVERT: A 601 ILE cc_start: 0.9485 (tt) cc_final: 0.9251 (tt) REVERT: A 602 GLU cc_start: 0.8667 (pm20) cc_final: 0.7786 (pm20) REVERT: A 615 MET cc_start: 0.9141 (mmp) cc_final: 0.8444 (mmp) REVERT: A 639 ASP cc_start: 0.9284 (m-30) cc_final: 0.8953 (m-30) REVERT: A 645 GLN cc_start: 0.9162 (tp40) cc_final: 0.8898 (tp-100) REVERT: A 650 GLN cc_start: 0.8873 (mt0) cc_final: 0.7537 (mt0) REVERT: A 682 ILE cc_start: 0.9492 (mp) cc_final: 0.9202 (mp) REVERT: B 15 GLU cc_start: 0.9005 (tp30) cc_final: 0.8647 (tp30) REVERT: B 17 MET cc_start: 0.8906 (mpp) cc_final: 0.8226 (mpp) REVERT: B 31 GLU cc_start: 0.9448 (mt-10) cc_final: 0.9143 (mt-10) REVERT: B 51 LEU cc_start: 0.9528 (tp) cc_final: 0.9313 (tp) REVERT: B 99 LYS cc_start: 0.9640 (mmmt) cc_final: 0.8943 (mmmt) REVERT: B 136 LYS cc_start: 0.9699 (mmtp) cc_final: 0.9310 (mmmm) REVERT: B 144 MET cc_start: 0.9052 (mtm) cc_final: 0.8774 (mtm) REVERT: B 147 GLN cc_start: 0.9209 (mt0) cc_final: 0.8711 (mt0) REVERT: B 157 LEU cc_start: 0.9644 (tp) cc_final: 0.9366 (tp) REVERT: B 158 ASN cc_start: 0.8680 (p0) cc_final: 0.8457 (p0) REVERT: B 161 ARG cc_start: 0.8888 (ttm110) cc_final: 0.8253 (mtp85) REVERT: B 209 LYS cc_start: 0.9132 (tptp) cc_final: 0.8897 (tptp) REVERT: B 211 GLU cc_start: 0.8238 (mm-30) cc_final: 0.7274 (mm-30) REVERT: B 227 MET cc_start: 0.9283 (mtm) cc_final: 0.9059 (mtm) REVERT: B 251 LEU cc_start: 0.9464 (tp) cc_final: 0.9187 (tp) REVERT: B 286 ASP cc_start: 0.8703 (m-30) cc_final: 0.8314 (m-30) REVERT: B 290 GLU cc_start: 0.9224 (pp20) cc_final: 0.8681 (pp20) REVERT: B 291 LEU cc_start: 0.9598 (mt) cc_final: 0.9294 (mt) REVERT: B 296 LYS cc_start: 0.9121 (mmpt) cc_final: 0.8835 (mtmm) REVERT: B 322 MET cc_start: 0.8725 (mmm) cc_final: 0.8444 (mmm) REVERT: B 333 LYS cc_start: 0.9466 (ttmm) cc_final: 0.9190 (ttmm) REVERT: B 335 GLU cc_start: 0.9047 (pt0) cc_final: 0.8721 (pp20) REVERT: B 337 ILE cc_start: 0.9487 (mp) cc_final: 0.8828 (mp) REVERT: B 342 LEU cc_start: 0.9759 (tp) cc_final: 0.9475 (tp) REVERT: B 344 GLU cc_start: 0.9271 (mm-30) cc_final: 0.8855 (mm-30) REVERT: B 345 LYS cc_start: 0.9698 (tttt) cc_final: 0.9471 (tttt) REVERT: B 346 LEU cc_start: 0.9702 (mt) cc_final: 0.9499 (mt) REVERT: B 348 MET cc_start: 0.9497 (tpp) cc_final: 0.9034 (tpp) REVERT: B 350 ARG cc_start: 0.8815 (mtp85) cc_final: 0.7998 (mtp85) REVERT: B 362 ASP cc_start: 0.9041 (m-30) cc_final: 0.8044 (m-30) REVERT: B 375 LYS cc_start: 0.9186 (mmtm) cc_final: 0.8794 (mmtm) REVERT: B 402 GLU cc_start: 0.8701 (mp0) cc_final: 0.8471 (mp0) REVERT: B 403 ILE cc_start: 0.9161 (mm) cc_final: 0.8820 (tp) REVERT: B 413 SER cc_start: 0.9527 (m) cc_final: 0.9169 (t) REVERT: B 459 LYS cc_start: 0.9113 (mppt) cc_final: 0.8676 (mmmt) REVERT: B 494 MET cc_start: 0.9429 (mtt) cc_final: 0.8809 (mtt) REVERT: B 585 SER cc_start: 0.9189 (p) cc_final: 0.8806 (t) REVERT: B 591 THR cc_start: 0.9358 (p) cc_final: 0.9017 (p) REVERT: B 604 ARG cc_start: 0.8858 (mmp80) cc_final: 0.8335 (mmp-170) REVERT: B 606 TYR cc_start: 0.8466 (m-80) cc_final: 0.8206 (m-80) REVERT: B 615 MET cc_start: 0.9103 (mmp) cc_final: 0.8835 (mmp) REVERT: B 631 ASP cc_start: 0.9604 (m-30) cc_final: 0.9271 (m-30) REVERT: B 636 LYS cc_start: 0.9719 (mmtm) cc_final: 0.9369 (mmmt) REVERT: B 639 ASP cc_start: 0.9367 (m-30) cc_final: 0.8987 (m-30) REVERT: B 645 GLN cc_start: 0.9475 (tp40) cc_final: 0.9239 (tp-100) REVERT: B 648 ILE cc_start: 0.9572 (mm) cc_final: 0.9343 (mm) REVERT: B 658 LEU cc_start: 0.9175 (mm) cc_final: 0.8894 (mm) REVERT: B 668 ASN cc_start: 0.9410 (m-40) cc_final: 0.8988 (m-40) REVERT: B 677 ARG cc_start: 0.9592 (mmm160) cc_final: 0.9299 (mmm-85) REVERT: B 683 TYR cc_start: 0.8938 (t80) cc_final: 0.8554 (t80) REVERT: C 62 LEU cc_start: 0.8066 (mt) cc_final: 0.7820 (mt) REVERT: C 95 MET cc_start: 0.9244 (tmm) cc_final: 0.8993 (tmm) REVERT: C 100 VAL cc_start: 0.8855 (t) cc_final: 0.8526 (p) REVERT: D 25 ASN cc_start: 0.8250 (m-40) cc_final: 0.7847 (m-40) REVERT: D 69 GLN cc_start: 0.9575 (tp40) cc_final: 0.9207 (tm-30) REVERT: D 91 ASN cc_start: 0.8094 (m-40) cc_final: 0.7786 (m-40) REVERT: D 211 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8634 (pt0) outliers start: 1 outliers final: 0 residues processed: 616 average time/residue: 0.1284 time to fit residues: 118.7519 Evaluate side-chains 542 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 542 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 67.8393 > 50: distance: 6 - 26: 33.121 distance: 22 - 26: 30.919 distance: 26 - 27: 21.949 distance: 27 - 28: 29.739 distance: 27 - 30: 28.914 distance: 28 - 29: 48.109 distance: 28 - 35: 23.185 distance: 30 - 31: 27.845 distance: 31 - 32: 40.311 distance: 32 - 33: 43.025 distance: 32 - 34: 14.016 distance: 35 - 36: 24.548 distance: 36 - 37: 4.737 distance: 36 - 39: 19.875 distance: 37 - 38: 24.407 distance: 37 - 43: 28.572 distance: 39 - 40: 45.778 distance: 39 - 41: 23.491 distance: 40 - 42: 26.378 distance: 43 - 44: 40.483 distance: 44 - 45: 14.074 distance: 44 - 47: 49.362 distance: 45 - 46: 44.962 distance: 45 - 51: 9.891 distance: 47 - 48: 45.067 distance: 48 - 49: 29.266 distance: 49 - 50: 42.604 distance: 51 - 52: 16.427 distance: 52 - 53: 14.175 distance: 52 - 55: 31.475 distance: 53 - 54: 36.002 distance: 53 - 59: 46.511 distance: 55 - 56: 31.316 distance: 55 - 57: 26.854 distance: 56 - 58: 11.929 distance: 59 - 60: 29.770 distance: 60 - 61: 15.510 distance: 60 - 63: 19.822 distance: 61 - 62: 26.000 distance: 61 - 68: 18.378 distance: 63 - 64: 23.108 distance: 64 - 65: 20.175 distance: 65 - 66: 10.747 distance: 65 - 67: 9.838 distance: 68 - 69: 4.038 distance: 68 - 92: 11.723 distance: 69 - 70: 7.742 distance: 69 - 72: 32.792 distance: 70 - 71: 25.944 distance: 71 - 89: 33.326 distance: 72 - 73: 11.246 distance: 73 - 74: 45.510 distance: 74 - 75: 29.115 distance: 75 - 76: 9.156 distance: 77 - 78: 14.284 distance: 78 - 79: 19.791 distance: 78 - 81: 6.663 distance: 79 - 80: 6.739 distance: 79 - 85: 31.464 distance: 81 - 82: 12.699 distance: 82 - 83: 17.708 distance: 82 - 84: 47.055 distance: 85 - 86: 37.949 distance: 86 - 87: 53.009 distance: 87 - 88: 28.137 distance: 87 - 89: 37.107 distance: 89 - 90: 26.096 distance: 90 - 91: 46.402 distance: 90 - 93: 17.824 distance: 91 - 92: 20.519 distance: 91 - 98: 23.964 distance: 93 - 94: 9.372 distance: 94 - 95: 26.674 distance: 95 - 96: 44.855 distance: 96 - 97: 6.192 distance: 98 - 99: 18.779 distance: 99 - 100: 13.904 distance: 99 - 102: 12.010 distance: 100 - 101: 21.207 distance: 100 - 109: 18.395 distance: 102 - 103: 11.473 distance: 103 - 104: 34.928 distance: 103 - 105: 18.304 distance: 104 - 106: 23.773 distance: 105 - 107: 21.603 distance: 106 - 108: 13.177 distance: 107 - 108: 31.689