Starting phenix.real_space_refine on Sat Jun 14 07:36:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzd_45064/06_2025/9bzd_45064_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzd_45064/06_2025/9bzd_45064.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bzd_45064/06_2025/9bzd_45064.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzd_45064/06_2025/9bzd_45064.map" model { file = "/net/cci-nas-00/data/ceres_data/9bzd_45064/06_2025/9bzd_45064_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzd_45064/06_2025/9bzd_45064_neut.cif" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 82 5.16 5 C 10228 2.51 5 N 2614 2.21 5 O 3092 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 10.17, per 1000 atoms: 0.63 Number of scatterers: 16038 At special positions: 0 Unit cell: (93.288, 128.778, 129.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.33 Conformation dependent library (CDL) restraints added in 2.1 seconds 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... Secondary structure from input PDB file: 98 helices and 11 sheets defined 64.0% alpha, 6.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.984A 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: 4.128A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.694A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.394A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.627A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A 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: 3.677A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.878A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.645A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.027A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.068A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.544A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.934A 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: 3.668A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.359A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.902A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.716A 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: 7.228A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.049A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.345A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.12 Time building geometry restraints manager: 5.09 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: 4892 1.34 - 1.46: 3091 1.46 - 1.58: 8222 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.060 1.25e-02 6.40e+03 2.34e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.579 -0.039 1.20e-02 6.94e+03 1.07e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.033 1.08e-02 8.57e+03 9.08e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.568 -0.031 1.17e-02 7.31e+03 7.11e+00 bond pdb=" CA ILE C 35 " pdb=" CB ILE C 35 " ideal model delta sigma weight residual 1.537 1.568 -0.031 1.21e-02 6.83e+03 6.69e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 21579 2.10 - 4.19: 513 4.19 - 6.29: 37 6.29 - 8.38: 1 8.38 - 10.48: 4 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.60 -6.06 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 111.71 116.14 -4.43 1.15e+00 7.56e-01 1.48e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.22 -3.94 1.09e+00 8.42e-01 1.31e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.82 -4.32 1.23e+00 6.61e-01 1.23e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.73 -4.02 1.15e+00 7.56e-01 1.22e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 9470 35.80 - 71.60: 337 71.60 - 107.40: 37 107.40 - 143.20: 3 143.20 - 178.99: 3 Dihedral angle restraints: 9850 sinusoidal: 4092 harmonic: 5758 Sorted by residual: dihedral pdb=" C2 TTP A 803 " pdb=" C1' TTP A 803 " pdb=" N1 TTP A 803 " pdb=" O4' TTP A 803 " ideal model delta sinusoidal sigma weight residual -58.32 120.68 -178.99 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual 301.68 151.21 150.47 1 2.00e+01 2.50e-03 4.49e+01 dihedral pdb=" C5' TTP A 803 " pdb=" O5' TTP A 803 " pdb=" PA TTP A 803 " pdb=" O3A TTP A 803 " ideal model delta sinusoidal sigma weight residual 179.97 31.93 148.04 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 9847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2147 0.093 - 0.187: 180 0.187 - 0.280: 28 0.280 - 0.373: 3 0.373 - 0.467: 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 4.58e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO D 75 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.017 2.00e-02 2.50e+03 1.10e-02 2.13e+00 pdb=" CG PHE D 92 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 169 " 0.017 2.00e-02 2.50e+03 1.01e-02 2.04e+00 pdb=" CG TYR C 169 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 169 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 169 " 0.008 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 131 2.51 - 3.11: 11547 3.11 - 3.70: 27037 3.70 - 4.30: 41565 4.30 - 4.90: 65447 Nonbonded interactions: 145727 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.911 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.962 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.012 3.040 ... (remaining 145722 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.730 Check model and map are aligned: 0.140 Set scattering table: 0.180 Process input model: 38.930 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6807 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 16386 Z= 0.316 Angle : 0.740 10.479 22134 Z= 0.463 Chirality : 0.058 0.467 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.948 178.994 6154 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.18), residues: 1932 helix: 0.59 (0.14), residues: 1149 sheet: 0.46 (0.42), residues: 124 loop : 0.24 (0.23), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE C 168 TYR 0.021 0.002 TYR D 179 ARG 0.003 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.15424 ( 871) hydrogen bonds : angle 6.51733 ( 2571) covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74031 (22134) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 1075 time to evaluate : 2.011 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLN cc_start: 0.8048 (mt0) cc_final: 0.7537 (mt0) REVERT: A 12 LEU cc_start: 0.7978 (mt) cc_final: 0.7763 (mp) REVERT: A 28 LYS cc_start: 0.8502 (mmtm) cc_final: 0.8297 (tppp) REVERT: A 76 ASP cc_start: 0.7984 (m-30) cc_final: 0.7332 (m-30) REVERT: A 127 LEU cc_start: 0.8536 (mt) cc_final: 0.8214 (mt) REVERT: A 179 LEU cc_start: 0.8732 (tp) cc_final: 0.8488 (tp) REVERT: A 181 ASP cc_start: 0.7596 (m-30) cc_final: 0.7209 (m-30) REVERT: A 204 SER cc_start: 0.8470 (m) cc_final: 0.8033 (t) REVERT: A 265 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8596 (mmmt) REVERT: A 280 ILE cc_start: 0.8960 (pt) cc_final: 0.8676 (pt) REVERT: A 348 MET cc_start: 0.7366 (tmm) cc_final: 0.6796 (tmm) REVERT: A 352 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6377 (mt-10) REVERT: A 362 ASP cc_start: 0.5957 (m-30) cc_final: 0.5567 (m-30) REVERT: A 598 MET cc_start: 0.7520 (mtm) cc_final: 0.6921 (mtp) REVERT: A 604 ARG cc_start: 0.7657 (mmp80) cc_final: 0.6301 (mmt90) REVERT: A 606 TYR cc_start: 0.6419 (m-80) cc_final: 0.5933 (m-80) REVERT: A 645 GLN cc_start: 0.8195 (tp40) cc_final: 0.7656 (tp40) REVERT: B 11 GLN cc_start: 0.7881 (mt0) cc_final: 0.7486 (mt0) REVERT: B 12 LEU cc_start: 0.8243 (mt) cc_final: 0.7947 (mt) REVERT: B 109 ASN cc_start: 0.8024 (m-40) cc_final: 0.7571 (p0) REVERT: B 121 ARG cc_start: 0.8401 (tpm170) cc_final: 0.7995 (tpp-160) REVERT: B 187 ASP cc_start: 0.6443 (t70) cc_final: 0.6214 (t0) REVERT: B 286 ASP cc_start: 0.6756 (OUTLIER) cc_final: 0.6118 (m-30) REVERT: B 295 ASP cc_start: 0.8038 (t0) cc_final: 0.7827 (t0) REVERT: B 350 ARG cc_start: 0.7566 (mtp85) cc_final: 0.7293 (mtp85) REVERT: B 362 ASP cc_start: 0.6613 (m-30) cc_final: 0.6365 (m-30) REVERT: B 366 LYS cc_start: 0.8398 (ptpp) cc_final: 0.8182 (ttmt) REVERT: B 381 LEU cc_start: 0.8713 (tp) cc_final: 0.8396 (tp) REVERT: B 387 GLN cc_start: 0.7785 (mt0) cc_final: 0.7580 (mt0) REVERT: B 458 MET cc_start: 0.8485 (mmm) cc_final: 0.8245 (mmm) REVERT: B 460 SER cc_start: 0.8996 (t) cc_final: 0.8747 (p) REVERT: B 471 TYR cc_start: 0.8414 (t80) cc_final: 0.7952 (t80) REVERT: B 485 ARG cc_start: 0.7856 (mtm-85) cc_final: 0.7324 (mtm-85) REVERT: B 493 MET cc_start: 0.8356 (tmm) cc_final: 0.8142 (tmm) REVERT: B 496 ASN cc_start: 0.8372 (t0) cc_final: 0.8095 (t0) REVERT: B 500 ILE cc_start: 0.8730 (mt) cc_final: 0.8376 (mt) REVERT: B 546 LEU cc_start: 0.9032 (mt) cc_final: 0.8740 (mt) REVERT: B 550 MET cc_start: 0.7893 (mtm) cc_final: 0.7341 (mtm) REVERT: B 601 ILE cc_start: 0.8458 (mt) cc_final: 0.8133 (mt) REVERT: B 604 ARG cc_start: 0.7109 (mmp80) cc_final: 0.6761 (tpp80) REVERT: B 612 TYR cc_start: 0.7795 (m-80) cc_final: 0.7494 (m-80) REVERT: B 664 THR cc_start: 0.8952 (p) cc_final: 0.8738 (p) REVERT: C 106 SER cc_start: 0.7759 (m) cc_final: 0.6427 (m) REVERT: C 212 ILE cc_start: 0.6000 (mt) cc_final: 0.5755 (mt) REVERT: D 178 PHE cc_start: 0.5471 (m-80) cc_final: 0.5101 (m-80) REVERT: D 193 LEU cc_start: 0.7895 (mt) cc_final: 0.7621 (mt) REVERT: D 256 VAL cc_start: 0.6964 (t) cc_final: 0.6762 (p) REVERT: D 260 ILE cc_start: 0.7126 (mt) cc_final: 0.6805 (mt) REVERT: D 315 LEU cc_start: 0.7098 (mt) cc_final: 0.6830 (mt) outliers start: 23 outliers final: 7 residues processed: 1082 average time/residue: 0.3073 time to fit residues: 471.8428 Evaluate side-chains 722 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 714 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 4.9990 chunk 145 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 174 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 11 GLN ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN B 329 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 361 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN ** B 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 474 GLN B 501 GLN B 646 GLN B 676 HIS C 24 GLN C 28 GLN C 80 HIS C 85 GLN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 263 ASN C 270 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 71 ASN D 80 HIS D 91 ASN D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.124964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.088768 restraints weight = 34871.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.092369 restraints weight = 16243.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.094724 restraints weight = 9654.081| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16386 Z= 0.190 Angle : 0.729 15.294 22134 Z= 0.378 Chirality : 0.046 0.215 2360 Planarity : 0.004 0.043 2818 Dihedral : 11.595 179.876 2256 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 4.02 % Allowed : 22.55 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.19), residues: 1932 helix: 1.39 (0.15), residues: 1129 sheet: 0.21 (0.44), residues: 130 loop : 0.42 (0.23), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP D 30 HIS 0.010 0.001 HIS C 201 PHE 0.031 0.002 PHE C 168 TYR 0.020 0.002 TYR B 72 ARG 0.007 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04914 ( 871) hydrogen bonds : angle 5.14877 ( 2571) covalent geometry : bond 0.00413 (16386) covalent geometry : angle 0.72933 (22134) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 771 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.8624 (mm-30) cc_final: 0.8375 (mm-30) REVERT: A 66 GLU cc_start: 0.8658 (tp30) cc_final: 0.8453 (tp30) REVERT: A 144 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8778 (mtm) REVERT: A 181 ASP cc_start: 0.8743 (m-30) cc_final: 0.8361 (m-30) REVERT: A 220 THR cc_start: 0.8893 (m) cc_final: 0.8643 (p) REVERT: A 221 LYS cc_start: 0.8901 (mmtp) cc_final: 0.8648 (mttp) REVERT: A 243 ARG cc_start: 0.7659 (ttp80) cc_final: 0.7380 (tmm-80) REVERT: A 257 ASP cc_start: 0.9311 (m-30) cc_final: 0.8748 (m-30) REVERT: A 335 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8690 (mm-30) REVERT: A 348 MET cc_start: 0.8175 (OUTLIER) cc_final: 0.7293 (tmm) REVERT: A 352 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7108 (mt-10) REVERT: A 359 MET cc_start: 0.8884 (OUTLIER) cc_final: 0.8196 (ttp) REVERT: A 384 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8112 (pm20) REVERT: A 415 ASN cc_start: 0.9362 (t0) cc_final: 0.9119 (t0) REVERT: A 420 MET cc_start: 0.9323 (mmm) cc_final: 0.8924 (mmm) REVERT: A 492 PHE cc_start: 0.9251 (m-80) cc_final: 0.8968 (m-10) REVERT: A 493 MET cc_start: 0.9068 (tmm) cc_final: 0.8621 (tmm) REVERT: A 494 MET cc_start: 0.9382 (OUTLIER) cc_final: 0.9000 (mtt) REVERT: A 505 GLU cc_start: 0.9088 (mt-10) cc_final: 0.8608 (mt-10) REVERT: A 527 TYR cc_start: 0.8869 (t80) cc_final: 0.8570 (t80) REVERT: A 586 TYR cc_start: 0.8731 (m-80) cc_final: 0.8442 (m-10) REVERT: A 598 MET cc_start: 0.8714 (mtm) cc_final: 0.8243 (mtp) REVERT: A 602 GLU cc_start: 0.7879 (pt0) cc_final: 0.6869 (pt0) REVERT: A 604 ARG cc_start: 0.8878 (mmp80) cc_final: 0.8243 (mmt90) REVERT: A 615 MET cc_start: 0.9399 (mmm) cc_final: 0.9184 (mmm) REVERT: A 630 TYR cc_start: 0.8615 (m-80) cc_final: 0.8372 (m-80) REVERT: A 640 MET cc_start: 0.9490 (tpp) cc_final: 0.9181 (tpp) REVERT: A 645 GLN cc_start: 0.8872 (tp40) cc_final: 0.8613 (tp-100) REVERT: A 667 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8980 (tt) REVERT: B 41 ILE cc_start: 0.9561 (mm) cc_final: 0.9360 (mm) REVERT: B 65 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8132 (mp0) REVERT: B 99 LYS cc_start: 0.9545 (mmmm) cc_final: 0.9292 (mmmm) REVERT: B 106 LEU cc_start: 0.9166 (tp) cc_final: 0.8739 (tt) REVERT: B 109 ASN cc_start: 0.9129 (m-40) cc_final: 0.8446 (p0) REVERT: B 147 GLN cc_start: 0.8873 (mt0) cc_final: 0.8100 (mm-40) REVERT: B 184 ARG cc_start: 0.9240 (mmm-85) cc_final: 0.8951 (tpp80) REVERT: B 202 ASN cc_start: 0.9277 (t0) cc_final: 0.8730 (t0) REVERT: B 246 SER cc_start: 0.7811 (m) cc_final: 0.7565 (p) REVERT: B 257 ASP cc_start: 0.8899 (m-30) cc_final: 0.8505 (m-30) REVERT: B 286 ASP cc_start: 0.8308 (OUTLIER) cc_final: 0.7384 (m-30) REVERT: B 288 PHE cc_start: 0.9425 (t80) cc_final: 0.9215 (t80) REVERT: B 290 GLU cc_start: 0.8866 (tm-30) cc_final: 0.7776 (tm-30) REVERT: B 312 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8517 (pm20) REVERT: B 317 MET cc_start: 0.8689 (ptp) cc_final: 0.8354 (pmm) REVERT: B 322 MET cc_start: 0.9327 (mmm) cc_final: 0.8962 (mmm) REVERT: B 348 MET cc_start: 0.9000 (ttp) cc_final: 0.8526 (ttp) REVERT: B 362 ASP cc_start: 0.8600 (m-30) cc_final: 0.7450 (m-30) REVERT: B 366 LYS cc_start: 0.9242 (ptpp) cc_final: 0.9014 (ptpp) REVERT: B 374 SER cc_start: 0.9037 (t) cc_final: 0.8661 (t) REVERT: B 447 ASN cc_start: 0.8542 (m-40) cc_final: 0.7874 (t0) REVERT: B 471 TYR cc_start: 0.9442 (t80) cc_final: 0.9158 (t80) REVERT: B 477 ILE cc_start: 0.9299 (mp) cc_final: 0.9066 (pt) REVERT: B 480 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8635 (mt-10) REVERT: B 492 PHE cc_start: 0.9526 (m-80) cc_final: 0.9080 (m-10) REVERT: B 493 MET cc_start: 0.9689 (tmm) cc_final: 0.9083 (tmm) REVERT: B 515 ASP cc_start: 0.9226 (m-30) cc_final: 0.8790 (m-30) REVERT: B 526 GLU cc_start: 0.9043 (tt0) cc_final: 0.8838 (tt0) REVERT: B 558 TRP cc_start: 0.9367 (m100) cc_final: 0.8856 (m100) REVERT: B 588 GLN cc_start: 0.9448 (mm-40) cc_final: 0.8960 (mm110) REVERT: B 610 LYS cc_start: 0.8694 (mmmt) cc_final: 0.8387 (mmmt) REVERT: B 612 TYR cc_start: 0.8742 (m-80) cc_final: 0.8205 (m-80) REVERT: B 640 MET cc_start: 0.9355 (tpp) cc_final: 0.9113 (tpp) REVERT: B 664 THR cc_start: 0.9332 (p) cc_final: 0.9013 (p) REVERT: B 668 ASN cc_start: 0.9249 (m-40) cc_final: 0.8884 (m110) REVERT: C 41 LEU cc_start: 0.8499 (mm) cc_final: 0.8262 (mm) REVERT: C 47 LEU cc_start: 0.8162 (mt) cc_final: 0.7822 (tp) REVERT: C 55 TYR cc_start: 0.8212 (t80) cc_final: 0.7506 (t80) REVERT: C 56 MET cc_start: 0.5637 (ttt) cc_final: 0.5408 (ttt) REVERT: C 93 MET cc_start: 0.9352 (mtt) cc_final: 0.9027 (mtt) REVERT: C 96 MET cc_start: 0.9003 (OUTLIER) cc_final: 0.8598 (mmm) REVERT: C 97 GLU cc_start: 0.6983 (mm-30) cc_final: 0.6309 (mm-30) REVERT: C 111 THR cc_start: 0.8299 (m) cc_final: 0.8020 (p) REVERT: C 130 TYR cc_start: 0.9434 (m-10) cc_final: 0.9233 (m-10) REVERT: C 164 GLU cc_start: 0.9432 (mm-30) cc_final: 0.8724 (mm-30) REVERT: C 178 PHE cc_start: 0.9038 (m-80) cc_final: 0.7913 (m-80) REVERT: C 185 MET cc_start: 0.8276 (pmm) cc_final: 0.6957 (pmm) REVERT: C 186 GLN cc_start: 0.9443 (mm110) cc_final: 0.8968 (mp10) REVERT: C 198 GLU cc_start: 0.9494 (mm-30) cc_final: 0.9027 (mm-30) REVERT: C 259 PHE cc_start: 0.8995 (t80) cc_final: 0.8715 (t80) REVERT: C 270 ASN cc_start: 0.7880 (m110) cc_final: 0.7511 (m110) REVERT: D 46 TYR cc_start: 0.9211 (m-80) cc_final: 0.8860 (m-80) REVERT: D 96 MET cc_start: 0.8555 (mmt) cc_final: 0.8325 (mmt) REVERT: D 105 TYR cc_start: 0.7618 (m-10) cc_final: 0.7412 (m-10) REVERT: D 178 PHE cc_start: 0.9128 (m-10) cc_final: 0.8270 (m-80) REVERT: D 186 GLN cc_start: 0.9102 (mm-40) cc_final: 0.8862 (mm110) REVERT: D 200 ILE cc_start: 0.8027 (tt) cc_final: 0.7498 (tt) REVERT: D 212 ILE cc_start: 0.9064 (mt) cc_final: 0.8474 (tp) REVERT: D 247 TYR cc_start: 0.8708 (m-10) cc_final: 0.8465 (m-10) REVERT: D 282 ILE cc_start: 0.4664 (OUTLIER) cc_final: 0.4254 (pt) outliers start: 69 outliers final: 34 residues processed: 798 average time/residue: 0.2749 time to fit residues: 325.8349 Evaluate side-chains 741 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 697 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 239 GLN Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 455 ASN Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 461 ILE Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 41 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 281 ASP Chi-restraints excluded: chain D residue 282 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 6.9990 chunk 168 optimal weight: 0.8980 chunk 175 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 191 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 171 optimal weight: 0.9980 chunk 189 optimal weight: 0.9980 chunk 141 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN B 232 ASN B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 GLN C 91 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** D 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.123311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.087407 restraints weight = 35370.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.090861 restraints weight = 16639.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.093256 restraints weight = 9929.412| |-----------------------------------------------------------------------------| r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3063 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3063 r_free = 0.3063 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3063 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16386 Z= 0.163 Angle : 0.687 14.439 22134 Z= 0.353 Chirality : 0.045 0.245 2360 Planarity : 0.004 0.042 2818 Dihedral : 11.107 172.295 2253 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.61 % Allowed : 25.82 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.19), residues: 1932 helix: 1.33 (0.15), residues: 1141 sheet: 0.84 (0.48), residues: 104 loop : 0.16 (0.22), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 44 HIS 0.006 0.001 HIS B 438 PHE 0.046 0.002 PHE C 168 TYR 0.023 0.001 TYR D 242 ARG 0.006 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04411 ( 871) hydrogen bonds : angle 5.06975 ( 2571) covalent geometry : bond 0.00364 (16386) covalent geometry : angle 0.68655 (22134) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 748 time to evaluate : 1.768 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 64 TYR cc_start: 0.9122 (m-10) cc_final: 0.8462 (m-10) REVERT: A 65 GLU cc_start: 0.8614 (mm-30) cc_final: 0.7924 (mp0) REVERT: A 82 LYS cc_start: 0.9645 (mmmm) cc_final: 0.9307 (mmmm) REVERT: A 144 MET cc_start: 0.9140 (OUTLIER) cc_final: 0.8662 (mtm) REVERT: A 163 ARG cc_start: 0.8415 (mmp80) cc_final: 0.8189 (mmm-85) REVERT: A 181 ASP cc_start: 0.8815 (m-30) cc_final: 0.8478 (m-30) REVERT: A 187 ASP cc_start: 0.9045 (t70) cc_final: 0.8738 (t70) REVERT: A 202 ASN cc_start: 0.9479 (t0) cc_final: 0.9090 (t0) REVERT: A 218 ASN cc_start: 0.9050 (t0) cc_final: 0.8705 (t0) REVERT: A 220 THR cc_start: 0.8960 (m) cc_final: 0.8667 (p) REVERT: A 221 LYS cc_start: 0.8870 (mmtp) cc_final: 0.8656 (mttp) REVERT: A 243 ARG cc_start: 0.7760 (ttp80) cc_final: 0.7532 (tmm-80) REVERT: A 257 ASP cc_start: 0.9362 (m-30) cc_final: 0.8763 (m-30) REVERT: A 274 ARG cc_start: 0.7820 (ttp80) cc_final: 0.6826 (ptp90) REVERT: A 286 ASP cc_start: 0.8505 (m-30) cc_final: 0.8228 (m-30) REVERT: A 321 GLU cc_start: 0.8768 (tp30) cc_final: 0.8368 (tp30) REVERT: A 335 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8634 (mm-30) REVERT: A 341 LYS cc_start: 0.9253 (mmmm) cc_final: 0.9049 (mmtt) REVERT: A 344 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8575 (mt-10) REVERT: A 348 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7541 (tmm) REVERT: A 352 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7352 (mt-10) REVERT: A 362 ASP cc_start: 0.8605 (m-30) cc_final: 0.8068 (m-30) REVERT: A 370 ASN cc_start: 0.9103 (m-40) cc_final: 0.8771 (m-40) REVERT: A 384 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.7323 (pm20) REVERT: A 415 ASN cc_start: 0.9276 (t0) cc_final: 0.9009 (t0) REVERT: A 420 MET cc_start: 0.9366 (mmm) cc_final: 0.9092 (mmm) REVERT: A 447 ASN cc_start: 0.8413 (m-40) cc_final: 0.7909 (t0) REVERT: A 493 MET cc_start: 0.9055 (tmm) cc_final: 0.8582 (tmm) REVERT: A 505 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8594 (mt-10) REVERT: A 510 LYS cc_start: 0.9100 (mtpt) cc_final: 0.8598 (mtpt) REVERT: A 512 GLU cc_start: 0.8483 (pt0) cc_final: 0.8125 (pm20) REVERT: A 527 TYR cc_start: 0.8867 (t80) cc_final: 0.8616 (t80) REVERT: A 571 TYR cc_start: 0.8435 (t80) cc_final: 0.8235 (t80) REVERT: A 598 MET cc_start: 0.8797 (mtm) cc_final: 0.8535 (mtp) REVERT: A 599 GLU cc_start: 0.8405 (mp0) cc_final: 0.8004 (mp0) REVERT: A 602 GLU cc_start: 0.7559 (pt0) cc_final: 0.7174 (pt0) REVERT: A 604 ARG cc_start: 0.8894 (mmp80) cc_final: 0.8429 (mmt-90) REVERT: A 615 MET cc_start: 0.9462 (mmm) cc_final: 0.9204 (mmm) REVERT: A 640 MET cc_start: 0.9525 (tpp) cc_final: 0.8993 (tpp) REVERT: A 667 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9058 (tt) REVERT: A 686 ARG cc_start: 0.8606 (mmm-85) cc_final: 0.8269 (ttm-80) REVERT: B 8 LYS cc_start: 0.8966 (tppt) cc_final: 0.8709 (tppt) REVERT: B 15 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8555 (tm-30) REVERT: B 17 MET cc_start: 0.8658 (mmm) cc_final: 0.8221 (mmm) REVERT: B 27 ASP cc_start: 0.9091 (p0) cc_final: 0.8670 (p0) REVERT: B 65 GLU cc_start: 0.8739 (mm-30) cc_final: 0.8016 (mp0) REVERT: B 99 LYS cc_start: 0.9595 (mmmm) cc_final: 0.9361 (mmmm) REVERT: B 106 LEU cc_start: 0.9274 (tp) cc_final: 0.8985 (tt) REVERT: B 109 ASN cc_start: 0.9094 (m-40) cc_final: 0.8550 (p0) REVERT: B 184 ARG cc_start: 0.9281 (mmm-85) cc_final: 0.8960 (tpp80) REVERT: B 202 ASN cc_start: 0.9233 (t0) cc_final: 0.8124 (t0) REVERT: B 246 SER cc_start: 0.7847 (m) cc_final: 0.7553 (p) REVERT: B 257 ASP cc_start: 0.9101 (m-30) cc_final: 0.8551 (m-30) REVERT: B 271 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8593 (mm-30) REVERT: B 276 LYS cc_start: 0.8841 (mmtm) cc_final: 0.8636 (mmtt) REVERT: B 286 ASP cc_start: 0.8384 (OUTLIER) cc_final: 0.7514 (m-30) REVERT: B 290 GLU cc_start: 0.8663 (tm-30) cc_final: 0.8341 (tm-30) REVERT: B 312 GLN cc_start: 0.8951 (OUTLIER) cc_final: 0.8749 (pm20) REVERT: B 317 MET cc_start: 0.8655 (ptp) cc_final: 0.8182 (pmm) REVERT: B 321 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8401 (tm-30) REVERT: B 322 MET cc_start: 0.9338 (mmm) cc_final: 0.9135 (mmm) REVERT: B 335 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7858 (mt-10) REVERT: B 359 MET cc_start: 0.8902 (ttp) cc_final: 0.8665 (tmm) REVERT: B 362 ASP cc_start: 0.8671 (m-30) cc_final: 0.7576 (m-30) REVERT: B 366 LYS cc_start: 0.9271 (ptpp) cc_final: 0.8999 (ptpp) REVERT: B 374 SER cc_start: 0.9129 (t) cc_final: 0.8743 (t) REVERT: B 399 GLU cc_start: 0.8196 (mp0) cc_final: 0.7927 (mp0) REVERT: B 434 ASP cc_start: 0.8928 (m-30) cc_final: 0.8438 (m-30) REVERT: B 447 ASN cc_start: 0.8512 (m-40) cc_final: 0.8243 (m-40) REVERT: B 467 ASN cc_start: 0.9419 (t0) cc_final: 0.9207 (m-40) REVERT: B 471 TYR cc_start: 0.9405 (t80) cc_final: 0.9070 (t80) REVERT: B 477 ILE cc_start: 0.9317 (mp) cc_final: 0.9109 (pt) REVERT: B 493 MET cc_start: 0.9685 (tmm) cc_final: 0.9084 (tmm) REVERT: B 515 ASP cc_start: 0.9204 (m-30) cc_final: 0.8844 (m-30) REVERT: B 558 TRP cc_start: 0.9565 (m100) cc_final: 0.8938 (m100) REVERT: B 602 GLU cc_start: 0.8723 (tt0) cc_final: 0.8478 (tt0) REVERT: B 610 LYS cc_start: 0.8589 (mmmt) cc_final: 0.8293 (mmmt) REVERT: B 612 TYR cc_start: 0.8740 (m-80) cc_final: 0.8287 (m-80) REVERT: B 640 MET cc_start: 0.9298 (tpp) cc_final: 0.8975 (tpp) REVERT: C 19 GLN cc_start: 0.7812 (mp10) cc_final: 0.7469 (pm20) REVERT: C 20 MET cc_start: 0.9095 (tpp) cc_final: 0.8883 (tpp) REVERT: C 55 TYR cc_start: 0.8304 (t80) cc_final: 0.7990 (t80) REVERT: C 56 MET cc_start: 0.5781 (ttt) cc_final: 0.5284 (ttt) REVERT: C 86 ARG cc_start: 0.6598 (mpt180) cc_final: 0.6377 (mmt-90) REVERT: C 91 ASN cc_start: 0.9061 (m110) cc_final: 0.8849 (m110) REVERT: C 93 MET cc_start: 0.9344 (mtt) cc_final: 0.9019 (mtt) REVERT: C 130 TYR cc_start: 0.9445 (m-10) cc_final: 0.9224 (m-10) REVERT: C 131 LEU cc_start: 0.9478 (mt) cc_final: 0.9161 (mt) REVERT: C 164 GLU cc_start: 0.9499 (mm-30) cc_final: 0.8919 (mm-30) REVERT: C 166 PHE cc_start: 0.7899 (t80) cc_final: 0.7512 (t80) REVERT: C 169 TYR cc_start: 0.8035 (m-80) cc_final: 0.7806 (m-80) REVERT: C 178 PHE cc_start: 0.9136 (m-80) cc_final: 0.8830 (m-10) REVERT: C 185 MET cc_start: 0.8429 (pmm) cc_final: 0.7405 (pmm) REVERT: C 186 GLN cc_start: 0.9389 (mm110) cc_final: 0.8931 (mp10) REVERT: C 198 GLU cc_start: 0.9409 (mm-30) cc_final: 0.9046 (mm-30) REVERT: C 220 LYS cc_start: 0.9164 (tppt) cc_final: 0.8740 (ptpt) REVERT: C 259 PHE cc_start: 0.8882 (t80) cc_final: 0.8500 (t80) REVERT: C 268 LEU cc_start: 0.9034 (tp) cc_final: 0.8486 (pp) REVERT: C 270 ASN cc_start: 0.7869 (m110) cc_final: 0.7596 (m110) REVERT: C 274 ASP cc_start: 0.7453 (p0) cc_final: 0.7225 (p0) REVERT: C 313 GLU cc_start: 0.8864 (tt0) cc_final: 0.8590 (tt0) REVERT: D 30 TRP cc_start: 0.8723 (p-90) cc_final: 0.8431 (p-90) REVERT: D 46 TYR cc_start: 0.9238 (m-80) cc_final: 0.8794 (m-80) REVERT: D 56 MET cc_start: 0.7441 (mmm) cc_final: 0.6888 (ptp) REVERT: D 59 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7899 (mm) REVERT: D 96 MET cc_start: 0.8477 (mmt) cc_final: 0.8264 (mmt) REVERT: D 105 TYR cc_start: 0.7748 (m-10) cc_final: 0.7469 (m-10) REVERT: D 178 PHE cc_start: 0.9008 (m-10) cc_final: 0.8159 (m-80) REVERT: D 186 GLN cc_start: 0.9215 (mm-40) cc_final: 0.8813 (mp10) REVERT: D 212 ILE cc_start: 0.9261 (mt) cc_final: 0.8978 (mm) REVERT: D 227 PHE cc_start: 0.8142 (OUTLIER) cc_final: 0.7655 (m-80) REVERT: D 287 LEU cc_start: 0.7011 (OUTLIER) cc_final: 0.6724 (mt) outliers start: 62 outliers final: 40 residues processed: 772 average time/residue: 0.2632 time to fit residues: 302.3455 Evaluate side-chains 748 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 699 time to evaluate : 1.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 314 MET Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 584 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 312 GLN Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 595 MET Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 59 LEU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 246 LEU Chi-restraints excluded: chain D residue 287 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 180 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 1 optimal weight: 0.0870 chunk 39 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 71 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 148 optimal weight: 8.9990 chunk 90 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 overall best weight: 1.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS A 645 GLN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN B 320 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.121203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.086261 restraints weight = 36083.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.089669 restraints weight = 16743.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.091909 restraints weight = 10028.456| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3008 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3008 r_free = 0.3008 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3008 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.5916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16386 Z= 0.201 Angle : 0.696 15.306 22134 Z= 0.356 Chirality : 0.045 0.220 2360 Planarity : 0.004 0.049 2818 Dihedral : 10.954 169.804 2247 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.84 % Allowed : 27.33 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.19), residues: 1932 helix: 1.24 (0.15), residues: 1152 sheet: 0.54 (0.47), residues: 110 loop : 0.12 (0.23), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 44 HIS 0.006 0.001 HIS A 438 PHE 0.038 0.002 PHE C 168 TYR 0.023 0.002 TYR D 242 ARG 0.006 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04205 ( 871) hydrogen bonds : angle 5.05853 ( 2571) covalent geometry : bond 0.00442 (16386) covalent geometry : angle 0.69629 (22134) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 813 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 730 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 27 ASP cc_start: 0.9192 (p0) cc_final: 0.8987 (p0) REVERT: A 64 TYR cc_start: 0.9195 (m-10) cc_final: 0.8606 (m-10) REVERT: A 65 GLU cc_start: 0.8678 (mm-30) cc_final: 0.8054 (mp0) REVERT: A 66 GLU cc_start: 0.8542 (tp30) cc_final: 0.8255 (tp30) REVERT: A 82 LYS cc_start: 0.9652 (mmmm) cc_final: 0.9340 (mmmm) REVERT: A 144 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8725 (mtm) REVERT: A 149 TYR cc_start: 0.9320 (t80) cc_final: 0.8697 (t80) REVERT: A 181 ASP cc_start: 0.8847 (m-30) cc_final: 0.8545 (m-30) REVERT: A 187 ASP cc_start: 0.9074 (t70) cc_final: 0.8731 (t70) REVERT: A 218 ASN cc_start: 0.9256 (t0) cc_final: 0.8883 (t0) REVERT: A 221 LYS cc_start: 0.8870 (mmtp) cc_final: 0.8651 (mttp) REVERT: A 228 LYS cc_start: 0.9484 (mmmm) cc_final: 0.8853 (mmtt) REVERT: A 257 ASP cc_start: 0.9453 (m-30) cc_final: 0.8911 (m-30) REVERT: A 274 ARG cc_start: 0.7640 (ttp80) cc_final: 0.6990 (ptp90) REVERT: A 321 GLU cc_start: 0.8887 (tp30) cc_final: 0.8470 (tp30) REVERT: A 348 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7672 (tmm) REVERT: A 352 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7684 (mt-10) REVERT: A 359 MET cc_start: 0.9115 (OUTLIER) cc_final: 0.8366 (ttp) REVERT: A 370 ASN cc_start: 0.9230 (m-40) cc_final: 0.8955 (m110) REVERT: A 384 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.7621 (pm20) REVERT: A 389 SER cc_start: 0.9388 (OUTLIER) cc_final: 0.9066 (p) REVERT: A 415 ASN cc_start: 0.9324 (t0) cc_final: 0.9100 (t0) REVERT: A 420 MET cc_start: 0.9356 (mmm) cc_final: 0.9143 (mmm) REVERT: A 447 ASN cc_start: 0.8547 (m-40) cc_final: 0.8339 (m-40) REVERT: A 493 MET cc_start: 0.9059 (tmm) cc_final: 0.8469 (tmm) REVERT: A 505 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8783 (mt-10) REVERT: A 527 TYR cc_start: 0.9026 (t80) cc_final: 0.8819 (t80) REVERT: A 598 MET cc_start: 0.8746 (mtm) cc_final: 0.7866 (mtp) REVERT: A 602 GLU cc_start: 0.7756 (pt0) cc_final: 0.7438 (pt0) REVERT: A 604 ARG cc_start: 0.8863 (mmp80) cc_final: 0.8505 (mmt-90) REVERT: A 610 LYS cc_start: 0.8196 (tppt) cc_final: 0.7701 (tppt) REVERT: A 640 MET cc_start: 0.9662 (tpp) cc_final: 0.8840 (tpp) REVERT: A 643 THR cc_start: 0.9607 (m) cc_final: 0.9402 (t) REVERT: A 659 LYS cc_start: 0.9104 (mmmt) cc_final: 0.8761 (mmmt) REVERT: A 667 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9207 (tt) REVERT: A 686 ARG cc_start: 0.8826 (mmm-85) cc_final: 0.8115 (mmm-85) REVERT: B 15 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8663 (tm-30) REVERT: B 27 ASP cc_start: 0.8941 (p0) cc_final: 0.8657 (p0) REVERT: B 65 GLU cc_start: 0.8784 (mm-30) cc_final: 0.8089 (mp0) REVERT: B 106 LEU cc_start: 0.9257 (tp) cc_final: 0.9003 (tt) REVERT: B 109 ASN cc_start: 0.9188 (m-40) cc_final: 0.8782 (p0) REVERT: B 174 GLU cc_start: 0.8671 (mm-30) cc_final: 0.8365 (mm-30) REVERT: B 181 ASP cc_start: 0.9017 (m-30) cc_final: 0.8801 (t0) REVERT: B 184 ARG cc_start: 0.9255 (mmm-85) cc_final: 0.9052 (ttm-80) REVERT: B 202 ASN cc_start: 0.9507 (t0) cc_final: 0.9054 (t0) REVERT: B 217 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7266 (tm-30) REVERT: B 218 ASN cc_start: 0.9294 (OUTLIER) cc_final: 0.8392 (m-40) REVERT: B 257 ASP cc_start: 0.8967 (m-30) cc_final: 0.8476 (m-30) REVERT: B 261 PHE cc_start: 0.9508 (t80) cc_final: 0.9299 (t80) REVERT: B 286 ASP cc_start: 0.8506 (OUTLIER) cc_final: 0.7637 (m-30) REVERT: B 290 GLU cc_start: 0.8657 (tm-30) cc_final: 0.8444 (tm-30) REVERT: B 314 MET cc_start: 0.9229 (OUTLIER) cc_final: 0.8995 (ttt) REVERT: B 316 GLU cc_start: 0.8642 (tm-30) cc_final: 0.7920 (tm-30) REVERT: B 317 MET cc_start: 0.8756 (ptp) cc_final: 0.8173 (pmm) REVERT: B 335 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7893 (mt-10) REVERT: B 362 ASP cc_start: 0.8766 (m-30) cc_final: 0.7572 (m-30) REVERT: B 366 LYS cc_start: 0.9360 (ptpp) cc_final: 0.9030 (ptpp) REVERT: B 374 SER cc_start: 0.9275 (t) cc_final: 0.8931 (t) REVERT: B 393 SER cc_start: 0.9379 (m) cc_final: 0.9029 (p) REVERT: B 415 ASN cc_start: 0.9254 (t0) cc_final: 0.8951 (t0) REVERT: B 434 ASP cc_start: 0.9029 (m-30) cc_final: 0.8475 (m-30) REVERT: B 467 ASN cc_start: 0.9439 (t0) cc_final: 0.9225 (m-40) REVERT: B 471 TYR cc_start: 0.9436 (t80) cc_final: 0.9092 (t80) REVERT: B 493 MET cc_start: 0.9691 (tmm) cc_final: 0.8884 (tmm) REVERT: B 515 ASP cc_start: 0.9175 (m-30) cc_final: 0.8869 (m-30) REVERT: B 574 TYR cc_start: 0.9195 (m-80) cc_final: 0.8722 (m-80) REVERT: B 602 GLU cc_start: 0.8685 (tt0) cc_final: 0.8334 (tt0) REVERT: B 610 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8522 (mmmt) REVERT: B 612 TYR cc_start: 0.8736 (m-80) cc_final: 0.8121 (m-80) REVERT: C 19 GLN cc_start: 0.7757 (mp10) cc_final: 0.7411 (pm20) REVERT: C 20 MET cc_start: 0.9076 (tpp) cc_final: 0.8776 (tmm) REVERT: C 55 TYR cc_start: 0.8390 (t80) cc_final: 0.7921 (t80) REVERT: C 56 MET cc_start: 0.5966 (ttt) cc_final: 0.5444 (ttt) REVERT: C 80 HIS cc_start: 0.8681 (m90) cc_final: 0.8475 (m90) REVERT: C 91 ASN cc_start: 0.9146 (m-40) cc_final: 0.8930 (m-40) REVERT: C 93 MET cc_start: 0.9447 (mtt) cc_final: 0.9150 (mtt) REVERT: C 130 TYR cc_start: 0.9304 (m-10) cc_final: 0.9064 (m-10) REVERT: C 178 PHE cc_start: 0.9453 (m-80) cc_final: 0.8645 (m-10) REVERT: C 185 MET cc_start: 0.8508 (pmm) cc_final: 0.7390 (pmm) REVERT: C 186 GLN cc_start: 0.9397 (mm110) cc_final: 0.8897 (mp10) REVERT: C 242 TYR cc_start: 0.9472 (t80) cc_final: 0.8988 (t80) REVERT: C 259 PHE cc_start: 0.8851 (t80) cc_final: 0.8454 (t80) REVERT: C 263 ASN cc_start: 0.8391 (m-40) cc_final: 0.8028 (m-40) REVERT: C 270 ASN cc_start: 0.8108 (m110) cc_final: 0.7839 (m110) REVERT: D 28 GLN cc_start: 0.9158 (tt0) cc_final: 0.8633 (tt0) REVERT: D 30 TRP cc_start: 0.8767 (p-90) cc_final: 0.8014 (p-90) REVERT: D 46 TYR cc_start: 0.9201 (m-80) cc_final: 0.8880 (m-10) REVERT: D 136 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8251 (mt0) REVERT: D 153 LEU cc_start: 0.9149 (pp) cc_final: 0.8921 (pp) REVERT: D 178 PHE cc_start: 0.9219 (m-10) cc_final: 0.8395 (m-80) REVERT: D 186 GLN cc_start: 0.9115 (mm-40) cc_final: 0.8679 (mp10) REVERT: D 207 LEU cc_start: 0.9141 (mm) cc_final: 0.8810 (mm) outliers start: 83 outliers final: 52 residues processed: 760 average time/residue: 0.2647 time to fit residues: 298.4613 Evaluate side-chains 747 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 685 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 VAL Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 667 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 232 ASN Chi-restraints excluded: chain B residue 239 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 289 VAL Chi-restraints excluded: chain B residue 314 MET Chi-restraints excluded: chain B residue 343 LEU Chi-restraints excluded: chain B residue 348 MET Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 67 optimal weight: 5.9990 chunk 41 optimal weight: 0.9990 chunk 57 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 182 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN ** A 239 GLN ** 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 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 234 GLN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN D 128 ASN ** D 216 GLN ** 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 = 0.3586 r_free = 0.3586 target = 0.121798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.086275 restraints weight = 36258.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.089727 restraints weight = 16986.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.091926 restraints weight = 10196.205| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3059 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3059 r_free = 0.3059 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3059 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.6312 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 : 0.720 15.817 22134 Z= 0.358 Chirality : 0.045 0.253 2360 Planarity : 0.003 0.048 2818 Dihedral : 10.736 166.507 2247 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 4.20 % Allowed : 30.24 % Favored : 65.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.19), residues: 1932 helix: 1.21 (0.15), residues: 1149 sheet: -0.33 (0.42), residues: 148 loop : 0.17 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 44 HIS 0.005 0.001 HIS A 255 PHE 0.033 0.002 PHE D 172 TYR 0.021 0.001 TYR D 242 ARG 0.007 0.001 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.04061 ( 871) hydrogen bonds : angle 5.02100 ( 2571) covalent geometry : bond 0.00381 (16386) covalent geometry : angle 0.71953 (22134) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 791 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 719 time to evaluate : 2.032 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.9188 (m-10) cc_final: 0.8643 (m-10) REVERT: A 65 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8124 (mp0) REVERT: A 66 GLU cc_start: 0.8515 (tp30) cc_final: 0.8213 (tp30) REVERT: A 82 LYS cc_start: 0.9652 (mmmm) cc_final: 0.9426 (mmmm) REVERT: A 127 LEU cc_start: 0.9409 (mt) cc_final: 0.9179 (mm) REVERT: A 144 MET cc_start: 0.9178 (OUTLIER) cc_final: 0.8672 (mtm) REVERT: A 181 ASP cc_start: 0.8834 (m-30) cc_final: 0.8575 (m-30) REVERT: A 187 ASP cc_start: 0.9038 (t70) cc_final: 0.8735 (t70) REVERT: A 202 ASN cc_start: 0.9520 (t0) cc_final: 0.9238 (t0) REVERT: A 218 ASN cc_start: 0.9296 (t0) cc_final: 0.8953 (t0) REVERT: A 221 LYS cc_start: 0.8889 (mmtp) cc_final: 0.8630 (mttp) REVERT: A 228 LYS cc_start: 0.9465 (mmmm) cc_final: 0.8846 (mmtt) REVERT: A 239 GLN cc_start: 0.8153 (mm-40) cc_final: 0.7708 (mm-40) REVERT: A 243 ARG cc_start: 0.7285 (ttp80) cc_final: 0.7047 (ttp80) REVERT: A 257 ASP cc_start: 0.9443 (m-30) cc_final: 0.8966 (m-30) REVERT: A 286 ASP cc_start: 0.8529 (m-30) cc_final: 0.8214 (m-30) REVERT: A 321 GLU cc_start: 0.8863 (tp30) cc_final: 0.8459 (tp30) REVERT: A 359 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8305 (ttp) REVERT: A 362 ASP cc_start: 0.8626 (m-30) cc_final: 0.8046 (m-30) REVERT: A 370 ASN cc_start: 0.9262 (m-40) cc_final: 0.9013 (m110) REVERT: A 384 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.7715 (pm20) REVERT: A 415 ASN cc_start: 0.9308 (t0) cc_final: 0.9099 (t0) REVERT: A 447 ASN cc_start: 0.8517 (m-40) cc_final: 0.7993 (t0) REVERT: A 493 MET cc_start: 0.9000 (tmm) cc_final: 0.8278 (tmm) REVERT: A 505 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8767 (mt-10) REVERT: A 512 GLU cc_start: 0.8665 (pt0) cc_final: 0.8199 (pt0) REVERT: A 527 TYR cc_start: 0.9048 (t80) cc_final: 0.8806 (t80) REVERT: A 539 LYS cc_start: 0.9339 (mmmm) cc_final: 0.9053 (mmmt) REVERT: A 583 SER cc_start: 0.9451 (m) cc_final: 0.8842 (t) REVERT: A 602 GLU cc_start: 0.7809 (pt0) cc_final: 0.6111 (pt0) REVERT: A 604 ARG cc_start: 0.8796 (mmp80) cc_final: 0.7949 (mmt90) REVERT: A 640 MET cc_start: 0.9665 (tpp) cc_final: 0.8702 (tpp) REVERT: A 686 ARG cc_start: 0.8931 (mmm-85) cc_final: 0.8351 (ttm-80) REVERT: B 15 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8701 (tm-30) REVERT: B 17 MET cc_start: 0.8788 (mmm) cc_final: 0.8299 (mmm) REVERT: B 27 ASP cc_start: 0.8925 (p0) cc_final: 0.8600 (p0) REVERT: B 31 GLU cc_start: 0.8429 (mt-10) cc_final: 0.7932 (mt-10) REVERT: B 65 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8110 (mp0) REVERT: B 106 LEU cc_start: 0.9322 (tp) cc_final: 0.9052 (tp) REVERT: B 109 ASN cc_start: 0.9292 (m-40) cc_final: 0.8604 (p0) REVERT: B 174 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8294 (mm-30) REVERT: B 184 ARG cc_start: 0.9214 (mmm-85) cc_final: 0.8920 (tpp80) REVERT: B 202 ASN cc_start: 0.9489 (t0) cc_final: 0.8947 (t0) REVERT: B 257 ASP cc_start: 0.8892 (m-30) cc_final: 0.8400 (m-30) REVERT: B 276 LYS cc_start: 0.9160 (mmtm) cc_final: 0.8876 (mmtt) REVERT: B 286 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.7627 (m-30) REVERT: B 290 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8462 (tm-30) REVERT: B 335 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7870 (mt-10) REVERT: B 362 ASP cc_start: 0.8762 (m-30) cc_final: 0.7539 (m-30) REVERT: B 366 LYS cc_start: 0.9400 (ptpp) cc_final: 0.9110 (ptpp) REVERT: B 374 SER cc_start: 0.9217 (t) cc_final: 0.8965 (t) REVERT: B 393 SER cc_start: 0.9400 (m) cc_final: 0.8999 (p) REVERT: B 447 ASN cc_start: 0.8262 (m-40) cc_final: 0.7801 (t0) REVERT: B 471 TYR cc_start: 0.9448 (t80) cc_final: 0.9136 (t80) REVERT: B 483 GLU cc_start: 0.9481 (mp0) cc_final: 0.9265 (mp0) REVERT: B 493 MET cc_start: 0.9686 (tmm) cc_final: 0.8902 (tmm) REVERT: B 515 ASP cc_start: 0.9125 (m-30) cc_final: 0.8825 (m-30) REVERT: B 610 LYS cc_start: 0.8860 (mmmt) cc_final: 0.8547 (mmmt) REVERT: B 612 TYR cc_start: 0.8680 (m-80) cc_final: 0.8215 (m-80) REVERT: C 19 GLN cc_start: 0.7689 (mp10) cc_final: 0.7306 (pm20) REVERT: C 20 MET cc_start: 0.9042 (tpp) cc_final: 0.8740 (tmm) REVERT: C 55 TYR cc_start: 0.8416 (t80) cc_final: 0.7891 (t80) REVERT: C 56 MET cc_start: 0.5837 (ttt) cc_final: 0.5437 (ttt) REVERT: C 80 HIS cc_start: 0.8589 (m90) cc_final: 0.7920 (m90) REVERT: C 164 GLU cc_start: 0.9339 (mm-30) cc_final: 0.8908 (mm-30) REVERT: C 177 TYR cc_start: 0.8990 (t80) cc_final: 0.8747 (t80) REVERT: C 178 PHE cc_start: 0.9390 (m-80) cc_final: 0.8517 (m-10) REVERT: C 181 GLN cc_start: 0.9190 (mt0) cc_final: 0.8862 (mt0) REVERT: C 185 MET cc_start: 0.8540 (pmm) cc_final: 0.7398 (pmm) REVERT: C 186 GLN cc_start: 0.9400 (mm110) cc_final: 0.8870 (mp10) REVERT: C 242 TYR cc_start: 0.9392 (t80) cc_final: 0.9064 (t80) REVERT: C 259 PHE cc_start: 0.8831 (t80) cc_final: 0.8362 (t80) REVERT: C 270 ASN cc_start: 0.8148 (m110) cc_final: 0.7763 (m110) REVERT: C 313 GLU cc_start: 0.9021 (tt0) cc_final: 0.8779 (tt0) REVERT: D 17 PHE cc_start: 0.7398 (m-80) cc_final: 0.7079 (t80) REVERT: D 28 GLN cc_start: 0.9134 (tt0) cc_final: 0.8810 (tp40) REVERT: D 30 TRP cc_start: 0.8551 (p-90) cc_final: 0.8124 (p-90) REVERT: D 46 TYR cc_start: 0.9113 (m-80) cc_final: 0.8813 (m-10) REVERT: D 136 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8312 (mt0) REVERT: D 178 PHE cc_start: 0.9246 (m-10) cc_final: 0.8536 (m-80) REVERT: D 186 GLN cc_start: 0.9097 (mm-40) cc_final: 0.8625 (mp10) REVERT: D 227 PHE cc_start: 0.8019 (OUTLIER) cc_final: 0.7545 (m-80) REVERT: D 252 LEU cc_start: 0.6237 (mt) cc_final: 0.5693 (mm) REVERT: D 269 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.8220 (ppp) outliers start: 72 outliers final: 48 residues processed: 744 average time/residue: 0.2759 time to fit residues: 305.6174 Evaluate side-chains 725 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 670 time to evaluate : 1.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 585 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 598 MET Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 96 MET Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 31 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 62 optimal weight: 0.0670 chunk 69 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 21 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 169 optimal weight: 2.9990 chunk 113 optimal weight: 7.9990 chunk 177 optimal weight: 7.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN B 232 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.122256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.086939 restraints weight = 35729.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.090417 restraints weight = 17097.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.092658 restraints weight = 10243.232| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3067 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3067 r_free = 0.3067 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3067 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.6619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 16386 Z= 0.160 Angle : 0.755 16.442 22134 Z= 0.373 Chirality : 0.047 0.380 2360 Planarity : 0.004 0.048 2818 Dihedral : 10.601 163.416 2247 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.02 % Allowed : 30.54 % Favored : 65.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.19), residues: 1932 helix: 1.13 (0.15), residues: 1157 sheet: -0.52 (0.41), residues: 148 loop : 0.11 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 44 HIS 0.006 0.001 HIS B 438 PHE 0.047 0.002 PHE B 261 TYR 0.020 0.001 TYR D 242 ARG 0.008 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.04121 ( 871) hydrogen bonds : angle 5.10298 ( 2571) covalent geometry : bond 0.00365 (16386) covalent geometry : angle 0.75451 (22134) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 688 time to evaluate : 1.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9249 (mtpp) cc_final: 0.9012 (ttpp) REVERT: A 64 TYR cc_start: 0.9206 (m-10) cc_final: 0.8787 (m-10) REVERT: A 65 GLU cc_start: 0.8602 (mm-30) cc_final: 0.8116 (mp0) REVERT: A 66 GLU cc_start: 0.8547 (tp30) cc_final: 0.8238 (tp30) REVERT: A 82 LYS cc_start: 0.9653 (mmmm) cc_final: 0.9347 (mmmm) REVERT: A 127 LEU cc_start: 0.9387 (mt) cc_final: 0.9178 (mm) REVERT: A 144 MET cc_start: 0.9166 (OUTLIER) cc_final: 0.8585 (mtm) REVERT: A 149 TYR cc_start: 0.9270 (t80) cc_final: 0.8775 (t80) REVERT: A 163 ARG cc_start: 0.8374 (mmm-85) cc_final: 0.8090 (mmm160) REVERT: A 181 ASP cc_start: 0.8781 (m-30) cc_final: 0.8540 (m-30) REVERT: A 187 ASP cc_start: 0.8991 (t70) cc_final: 0.8651 (t70) REVERT: A 202 ASN cc_start: 0.9518 (t0) cc_final: 0.9178 (t0) REVERT: A 218 ASN cc_start: 0.9338 (t0) cc_final: 0.8959 (t0) REVERT: A 221 LYS cc_start: 0.8854 (mmtp) cc_final: 0.8611 (mttp) REVERT: A 228 LYS cc_start: 0.9430 (mmmm) cc_final: 0.8860 (mmtt) REVERT: A 232 ASN cc_start: 0.9384 (OUTLIER) cc_final: 0.9006 (m-40) REVERT: A 257 ASP cc_start: 0.9415 (m-30) cc_final: 0.8978 (m-30) REVERT: A 286 ASP cc_start: 0.8517 (m-30) cc_final: 0.8267 (m-30) REVERT: A 321 GLU cc_start: 0.8883 (tp30) cc_final: 0.8400 (tp30) REVERT: A 348 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8044 (tmm) REVERT: A 359 MET cc_start: 0.9064 (OUTLIER) cc_final: 0.8293 (ttp) REVERT: A 362 ASP cc_start: 0.8635 (m-30) cc_final: 0.7970 (m-30) REVERT: A 370 ASN cc_start: 0.9258 (m-40) cc_final: 0.9012 (m110) REVERT: A 384 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.7707 (pm20) REVERT: A 415 ASN cc_start: 0.9274 (t0) cc_final: 0.9026 (t0) REVERT: A 447 ASN cc_start: 0.8446 (m-40) cc_final: 0.7948 (t0) REVERT: A 453 ARG cc_start: 0.9222 (OUTLIER) cc_final: 0.9016 (ttp80) REVERT: A 493 MET cc_start: 0.8956 (tmm) cc_final: 0.8245 (tmm) REVERT: A 505 GLU cc_start: 0.9048 (mt-10) cc_final: 0.8768 (mt-10) REVERT: A 512 GLU cc_start: 0.8708 (pt0) cc_final: 0.8378 (pt0) REVERT: A 539 LYS cc_start: 0.9344 (mmmm) cc_final: 0.9011 (mmmt) REVERT: A 583 SER cc_start: 0.9453 (m) cc_final: 0.8849 (t) REVERT: A 595 MET cc_start: 0.8845 (mmp) cc_final: 0.8499 (mmp) REVERT: A 598 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.8409 (mtp) REVERT: A 602 GLU cc_start: 0.7765 (pt0) cc_final: 0.6735 (pt0) REVERT: A 604 ARG cc_start: 0.8788 (mmp80) cc_final: 0.8151 (mmt-90) REVERT: A 640 MET cc_start: 0.9658 (tpp) cc_final: 0.8862 (tpp) REVERT: A 686 ARG cc_start: 0.8823 (mmm-85) cc_final: 0.8364 (ttm-80) REVERT: B 17 MET cc_start: 0.8737 (mmm) cc_final: 0.8295 (mmm) REVERT: B 31 GLU cc_start: 0.8421 (mt-10) cc_final: 0.8135 (mt-10) REVERT: B 65 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8131 (mp0) REVERT: B 109 ASN cc_start: 0.9282 (m-40) cc_final: 0.8748 (p0) REVERT: B 174 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8249 (mm-30) REVERT: B 181 ASP cc_start: 0.8933 (m-30) cc_final: 0.8663 (t0) REVERT: B 184 ARG cc_start: 0.9214 (mmm-85) cc_final: 0.8901 (tpp80) REVERT: B 202 ASN cc_start: 0.9503 (t0) cc_final: 0.8888 (t0) REVERT: B 252 ASN cc_start: 0.9110 (t0) cc_final: 0.8709 (t0) REVERT: B 257 ASP cc_start: 0.8930 (m-30) cc_final: 0.8455 (m-30) REVERT: B 263 ASP cc_start: 0.9166 (m-30) cc_final: 0.8750 (p0) REVERT: B 276 LYS cc_start: 0.9115 (mmtm) cc_final: 0.8856 (mmtt) REVERT: B 286 ASP cc_start: 0.8436 (OUTLIER) cc_final: 0.7617 (m-30) REVERT: B 290 GLU cc_start: 0.8705 (tm-30) cc_final: 0.8306 (tm-30) REVERT: B 335 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7851 (mt-10) REVERT: B 362 ASP cc_start: 0.8766 (m-30) cc_final: 0.7532 (m-30) REVERT: B 366 LYS cc_start: 0.9421 (ptpp) cc_final: 0.9090 (ptpp) REVERT: B 393 SER cc_start: 0.9374 (m) cc_final: 0.8984 (p) REVERT: B 415 ASN cc_start: 0.9204 (t0) cc_final: 0.8910 (t0) REVERT: B 440 SER cc_start: 0.9582 (OUTLIER) cc_final: 0.9243 (p) REVERT: B 447 ASN cc_start: 0.8303 (m-40) cc_final: 0.7897 (t0) REVERT: B 467 ASN cc_start: 0.9327 (m-40) cc_final: 0.9093 (m-40) REVERT: B 471 TYR cc_start: 0.9462 (t80) cc_final: 0.9195 (t80) REVERT: B 483 GLU cc_start: 0.9465 (mp0) cc_final: 0.9246 (mp0) REVERT: B 493 MET cc_start: 0.9687 (tmm) cc_final: 0.8896 (tmm) REVERT: B 515 ASP cc_start: 0.9102 (m-30) cc_final: 0.8815 (m-30) REVERT: B 610 LYS cc_start: 0.8965 (mmmt) cc_final: 0.8733 (mmmt) REVERT: B 612 TYR cc_start: 0.8623 (m-80) cc_final: 0.8160 (m-80) REVERT: C 20 MET cc_start: 0.9038 (tpp) cc_final: 0.8531 (tmm) REVERT: C 55 TYR cc_start: 0.8341 (t80) cc_final: 0.7621 (t80) REVERT: C 56 MET cc_start: 0.5898 (ttt) cc_final: 0.5507 (ttt) REVERT: C 80 HIS cc_start: 0.8520 (m90) cc_final: 0.8062 (m90) REVERT: C 150 GLU cc_start: 0.9212 (OUTLIER) cc_final: 0.8925 (tp30) REVERT: C 164 GLU cc_start: 0.9192 (mm-30) cc_final: 0.8889 (mm-30) REVERT: C 178 PHE cc_start: 0.9369 (m-80) cc_final: 0.8226 (m-10) REVERT: C 185 MET cc_start: 0.8579 (pmm) cc_final: 0.7463 (pmm) REVERT: C 186 GLN cc_start: 0.9393 (mm110) cc_final: 0.8876 (mp10) REVERT: C 274 ASP cc_start: 0.7327 (p0) cc_final: 0.6929 (p0) REVERT: C 316 LYS cc_start: 0.9184 (mmtt) cc_final: 0.8871 (mmtt) REVERT: D 28 GLN cc_start: 0.9155 (tt0) cc_final: 0.8795 (tp40) REVERT: D 30 TRP cc_start: 0.8512 (p-90) cc_final: 0.8107 (p-90) REVERT: D 46 TYR cc_start: 0.9023 (m-80) cc_final: 0.8766 (m-10) REVERT: D 96 MET cc_start: 0.8436 (mmt) cc_final: 0.8019 (mmm) REVERT: D 136 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8356 (mt0) REVERT: D 178 PHE cc_start: 0.9263 (m-10) cc_final: 0.8612 (m-80) REVERT: D 186 GLN cc_start: 0.9127 (mm-40) cc_final: 0.8645 (mp10) REVERT: D 207 LEU cc_start: 0.9167 (mm) cc_final: 0.8915 (mm) REVERT: D 210 GLN cc_start: 0.9346 (tm-30) cc_final: 0.9067 (pt0) REVERT: D 227 PHE cc_start: 0.8042 (OUTLIER) cc_final: 0.7506 (m-80) REVERT: D 240 LEU cc_start: 0.8590 (mt) cc_final: 0.7954 (pp) REVERT: D 252 LEU cc_start: 0.6136 (mt) cc_final: 0.5650 (mm) REVERT: D 269 MET cc_start: 0.8536 (OUTLIER) cc_final: 0.8171 (ppp) outliers start: 69 outliers final: 48 residues processed: 712 average time/residue: 0.2697 time to fit residues: 285.6335 Evaluate side-chains 733 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 672 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 413 SER Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 605 THR Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 446 ARG Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 50 ASN Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 269 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 39 optimal weight: 3.9990 chunk 85 optimal weight: 4.9990 chunk 161 optimal weight: 20.0000 chunk 23 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 175 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN B 218 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN C 91 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 ASN D 127 GLN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.119318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.084151 restraints weight = 36172.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.087551 restraints weight = 17443.505| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.089824 restraints weight = 10565.623| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.6875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 16386 Z= 0.213 Angle : 0.755 15.819 22134 Z= 0.380 Chirality : 0.046 0.200 2360 Planarity : 0.004 0.049 2818 Dihedral : 10.675 163.517 2246 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 4.55 % Allowed : 31.00 % Favored : 64.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.19), residues: 1932 helix: 1.08 (0.15), residues: 1156 sheet: -0.65 (0.40), residues: 148 loop : -0.04 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 44 HIS 0.006 0.001 HIS A 255 PHE 0.028 0.002 PHE C 172 TYR 0.019 0.002 TYR C 262 ARG 0.011 0.001 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 871) hydrogen bonds : angle 5.14900 ( 2571) covalent geometry : bond 0.00475 (16386) covalent geometry : angle 0.75496 (22134) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 682 time to evaluate : 2.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.9249 (m-10) cc_final: 0.8699 (m-10) REVERT: A 65 GLU cc_start: 0.8617 (mm-30) cc_final: 0.8164 (mp0) REVERT: A 66 GLU cc_start: 0.8548 (tp30) cc_final: 0.8255 (tp30) REVERT: A 82 LYS cc_start: 0.9653 (mmmm) cc_final: 0.9361 (mmmm) REVERT: A 144 MET cc_start: 0.9176 (OUTLIER) cc_final: 0.8682 (mtm) REVERT: A 149 TYR cc_start: 0.9278 (t80) cc_final: 0.8910 (t80) REVERT: A 181 ASP cc_start: 0.8758 (m-30) cc_final: 0.8512 (m-30) REVERT: A 187 ASP cc_start: 0.9026 (t70) cc_final: 0.8707 (t70) REVERT: A 202 ASN cc_start: 0.9616 (t0) cc_final: 0.9338 (t0) REVERT: A 218 ASN cc_start: 0.9381 (t0) cc_final: 0.9034 (t0) REVERT: A 221 LYS cc_start: 0.8874 (mmtp) cc_final: 0.8504 (mttp) REVERT: A 227 MET cc_start: 0.9226 (mtp) cc_final: 0.8916 (mtp) REVERT: A 228 LYS cc_start: 0.9509 (mmmm) cc_final: 0.8873 (mmtt) REVERT: A 232 ASN cc_start: 0.9451 (OUTLIER) cc_final: 0.8751 (m-40) REVERT: A 257 ASP cc_start: 0.9410 (m-30) cc_final: 0.8975 (m-30) REVERT: A 321 GLU cc_start: 0.8923 (tp30) cc_final: 0.8502 (tp30) REVERT: A 322 MET cc_start: 0.9206 (mmp) cc_final: 0.8997 (mmm) REVERT: A 348 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.8079 (tmm) REVERT: A 359 MET cc_start: 0.9133 (OUTLIER) cc_final: 0.8656 (ttp) REVERT: A 362 ASP cc_start: 0.8718 (m-30) cc_final: 0.7950 (m-30) REVERT: A 384 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.7791 (pm20) REVERT: A 389 SER cc_start: 0.9460 (OUTLIER) cc_final: 0.9146 (p) REVERT: A 435 SER cc_start: 0.9532 (OUTLIER) cc_final: 0.9275 (t) REVERT: A 447 ASN cc_start: 0.8486 (m-40) cc_final: 0.7934 (t0) REVERT: A 493 MET cc_start: 0.8942 (tmm) cc_final: 0.8180 (tmm) REVERT: A 494 MET cc_start: 0.9227 (mtm) cc_final: 0.8849 (mtt) REVERT: A 505 GLU cc_start: 0.9012 (mt-10) cc_final: 0.8531 (mt-10) REVERT: A 512 GLU cc_start: 0.8710 (pt0) cc_final: 0.8413 (pt0) REVERT: A 527 TYR cc_start: 0.9061 (t80) cc_final: 0.8804 (t80) REVERT: A 539 LYS cc_start: 0.9352 (mmmm) cc_final: 0.9038 (mmmt) REVERT: A 583 SER cc_start: 0.9483 (m) cc_final: 0.8901 (t) REVERT: A 598 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8400 (mtp) REVERT: A 640 MET cc_start: 0.9648 (tpp) cc_final: 0.8832 (tpp) REVERT: A 686 ARG cc_start: 0.8882 (mmm-85) cc_final: 0.8650 (mmm-85) REVERT: B 17 MET cc_start: 0.8946 (mmm) cc_final: 0.8523 (mmm) REVERT: B 31 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8085 (mt-10) REVERT: B 65 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8473 (mm-30) REVERT: B 109 ASN cc_start: 0.9261 (m-40) cc_final: 0.8740 (p0) REVERT: B 174 GLU cc_start: 0.8626 (mm-30) cc_final: 0.8199 (mm-30) REVERT: B 202 ASN cc_start: 0.9459 (t0) cc_final: 0.8867 (t0) REVERT: B 232 ASN cc_start: 0.9434 (t0) cc_final: 0.8950 (m-40) REVERT: B 257 ASP cc_start: 0.8853 (m-30) cc_final: 0.8412 (m-30) REVERT: B 286 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.7689 (m-30) REVERT: B 290 GLU cc_start: 0.8704 (tm-30) cc_final: 0.8399 (tm-30) REVERT: B 335 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7872 (mt-10) REVERT: B 362 ASP cc_start: 0.8814 (m-30) cc_final: 0.7551 (m-30) REVERT: B 366 LYS cc_start: 0.9455 (ptpp) cc_final: 0.9083 (ptpp) REVERT: B 393 SER cc_start: 0.9355 (m) cc_final: 0.9077 (p) REVERT: B 415 ASN cc_start: 0.9250 (t0) cc_final: 0.8939 (t0) REVERT: B 447 ASN cc_start: 0.8338 (m-40) cc_final: 0.7860 (t0) REVERT: B 471 TYR cc_start: 0.9462 (t80) cc_final: 0.8844 (t80) REVERT: B 483 GLU cc_start: 0.9480 (mp0) cc_final: 0.9242 (mp0) REVERT: B 493 MET cc_start: 0.9694 (tmm) cc_final: 0.8895 (tmm) REVERT: B 515 ASP cc_start: 0.9148 (m-30) cc_final: 0.8872 (m-30) REVERT: B 546 LEU cc_start: 0.9706 (mt) cc_final: 0.9439 (mt) REVERT: B 595 MET cc_start: 0.8969 (mmm) cc_final: 0.8143 (mmm) REVERT: B 606 TYR cc_start: 0.8642 (m-80) cc_final: 0.8266 (m-80) REVERT: B 610 LYS cc_start: 0.9025 (mmmt) cc_final: 0.8742 (mmmt) REVERT: B 612 TYR cc_start: 0.8602 (m-80) cc_final: 0.8207 (m-80) REVERT: C 19 GLN cc_start: 0.7664 (mp10) cc_final: 0.7276 (pm20) REVERT: C 20 MET cc_start: 0.9016 (tpp) cc_final: 0.8722 (tmm) REVERT: C 25 ASN cc_start: 0.9231 (t0) cc_final: 0.8780 (p0) REVERT: C 29 PHE cc_start: 0.8408 (t80) cc_final: 0.7937 (t80) REVERT: C 47 LEU cc_start: 0.8560 (tp) cc_final: 0.8095 (tp) REVERT: C 55 TYR cc_start: 0.8410 (t80) cc_final: 0.7774 (t80) REVERT: C 56 MET cc_start: 0.5855 (ttt) cc_final: 0.5515 (ttt) REVERT: C 80 HIS cc_start: 0.8725 (m90) cc_final: 0.8285 (m90) REVERT: C 96 MET cc_start: 0.8938 (mmt) cc_final: 0.7994 (mmt) REVERT: C 134 LYS cc_start: 0.9609 (pttm) cc_final: 0.9226 (pttm) REVERT: C 150 GLU cc_start: 0.9231 (OUTLIER) cc_final: 0.8932 (mm-30) REVERT: C 153 LEU cc_start: 0.9384 (pp) cc_final: 0.9176 (pp) REVERT: C 164 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8899 (tp30) REVERT: C 169 TYR cc_start: 0.8345 (m-80) cc_final: 0.8038 (m-80) REVERT: C 174 TYR cc_start: 0.9315 (OUTLIER) cc_final: 0.8653 (t80) REVERT: C 185 MET cc_start: 0.8553 (pmm) cc_final: 0.7398 (pmm) REVERT: C 186 GLN cc_start: 0.9395 (mm110) cc_final: 0.8877 (mp10) REVERT: C 205 VAL cc_start: 0.9393 (t) cc_final: 0.9166 (p) REVERT: C 242 TYR cc_start: 0.9407 (t80) cc_final: 0.9164 (t80) REVERT: C 259 PHE cc_start: 0.8859 (t80) cc_final: 0.8439 (t80) REVERT: D 17 PHE cc_start: 0.7038 (OUTLIER) cc_final: 0.6472 (t80) REVERT: D 30 TRP cc_start: 0.8630 (p-90) cc_final: 0.7650 (p-90) REVERT: D 34 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8161 (mm-30) REVERT: D 46 TYR cc_start: 0.9049 (m-80) cc_final: 0.8774 (m-10) REVERT: D 96 MET cc_start: 0.8776 (mmt) cc_final: 0.8304 (mmm) REVERT: D 136 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8416 (mt0) REVERT: D 178 PHE cc_start: 0.9352 (m-10) cc_final: 0.8791 (m-80) REVERT: D 186 GLN cc_start: 0.9140 (mm-40) cc_final: 0.8639 (mp10) REVERT: D 207 LEU cc_start: 0.9140 (mm) cc_final: 0.8799 (mm) REVERT: D 210 GLN cc_start: 0.9337 (tm-30) cc_final: 0.9031 (pt0) REVERT: D 227 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7499 (m-80) REVERT: D 240 LEU cc_start: 0.8694 (mt) cc_final: 0.8027 (pp) REVERT: D 252 LEU cc_start: 0.6167 (mt) cc_final: 0.5779 (mm) REVERT: D 269 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8116 (ppp) outliers start: 78 outliers final: 53 residues processed: 710 average time/residue: 0.2981 time to fit residues: 316.8893 Evaluate side-chains 729 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 661 time to evaluate : 3.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 232 ASN Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 218 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 31 LEU Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 108 ILE Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 218 GLU Chi-restraints excluded: chain D residue 227 PHE Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 287 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 159 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 183 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.122136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.086086 restraints weight = 35602.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.089539 restraints weight = 17223.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.091781 restraints weight = 10409.540| |-----------------------------------------------------------------------------| r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.7096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16386 Z= 0.165 Angle : 0.776 17.096 22134 Z= 0.382 Chirality : 0.046 0.244 2360 Planarity : 0.004 0.047 2818 Dihedral : 10.507 160.835 2246 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 4.08 % Allowed : 33.04 % Favored : 62.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.19), residues: 1932 helix: 1.03 (0.15), residues: 1153 sheet: -0.66 (0.41), residues: 148 loop : -0.12 (0.23), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 44 HIS 0.006 0.001 HIS A 255 PHE 0.029 0.002 PHE C 172 TYR 0.032 0.001 TYR B 574 ARG 0.010 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.04115 ( 871) hydrogen bonds : angle 5.16169 ( 2571) covalent geometry : bond 0.00374 (16386) covalent geometry : angle 0.77565 (22134) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 753 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 683 time to evaluate : 1.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 TYR cc_start: 0.9269 (m-10) cc_final: 0.8825 (m-10) REVERT: A 65 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8206 (mp0) REVERT: A 66 GLU cc_start: 0.8571 (tp30) cc_final: 0.8226 (tp30) REVERT: A 82 LYS cc_start: 0.9666 (mmmm) cc_final: 0.9335 (mmmm) REVERT: A 149 TYR cc_start: 0.9343 (t80) cc_final: 0.8903 (t80) REVERT: A 181 ASP cc_start: 0.8760 (m-30) cc_final: 0.8503 (m-30) REVERT: A 187 ASP cc_start: 0.8988 (t70) cc_final: 0.8673 (t70) REVERT: A 202 ASN cc_start: 0.9572 (t0) cc_final: 0.9246 (t0) REVERT: A 218 ASN cc_start: 0.9395 (t0) cc_final: 0.9030 (t0) REVERT: A 221 LYS cc_start: 0.8807 (mmtp) cc_final: 0.8454 (mttp) REVERT: A 227 MET cc_start: 0.9180 (mtp) cc_final: 0.8877 (mtp) REVERT: A 228 LYS cc_start: 0.9465 (mmmm) cc_final: 0.8966 (mmtt) REVERT: A 257 ASP cc_start: 0.9440 (m-30) cc_final: 0.8985 (m-30) REVERT: A 321 GLU cc_start: 0.8937 (tp30) cc_final: 0.8202 (tp30) REVERT: A 348 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7610 (tmm) REVERT: A 352 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7656 (mt-10) REVERT: A 359 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8352 (ttp) REVERT: A 384 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.7725 (pm20) REVERT: A 389 SER cc_start: 0.9448 (OUTLIER) cc_final: 0.9152 (p) REVERT: A 435 SER cc_start: 0.9517 (OUTLIER) cc_final: 0.9265 (t) REVERT: A 447 ASN cc_start: 0.8444 (m-40) cc_final: 0.7892 (t0) REVERT: A 493 MET cc_start: 0.8877 (tmm) cc_final: 0.8123 (tmm) REVERT: A 494 MET cc_start: 0.9228 (mtm) cc_final: 0.8797 (mtt) REVERT: A 505 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8773 (mt-10) REVERT: A 512 GLU cc_start: 0.8692 (pt0) cc_final: 0.8385 (pt0) REVERT: A 539 LYS cc_start: 0.9376 (mmmm) cc_final: 0.9043 (mmmt) REVERT: A 583 SER cc_start: 0.9450 (m) cc_final: 0.8865 (t) REVERT: A 598 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8159 (mtp) REVERT: A 602 GLU cc_start: 0.7980 (pt0) cc_final: 0.7487 (pt0) REVERT: A 604 ARG cc_start: 0.8883 (mmp80) cc_final: 0.8607 (mmt-90) REVERT: A 610 LYS cc_start: 0.8454 (tppt) cc_final: 0.8170 (tppt) REVERT: A 640 MET cc_start: 0.9675 (tpp) cc_final: 0.8868 (tpp) REVERT: A 686 ARG cc_start: 0.8890 (mmm-85) cc_final: 0.8527 (mmm-85) REVERT: B 17 MET cc_start: 0.8975 (mmm) cc_final: 0.8608 (mmm) REVERT: B 28 LYS cc_start: 0.9260 (mmtt) cc_final: 0.8940 (mmmm) REVERT: B 31 GLU cc_start: 0.8347 (mt-10) cc_final: 0.8091 (mt-10) REVERT: B 65 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8457 (mm-30) REVERT: B 109 ASN cc_start: 0.9301 (m-40) cc_final: 0.8628 (p0) REVERT: B 174 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8210 (mm-30) REVERT: B 184 ARG cc_start: 0.9199 (tpp80) cc_final: 0.8874 (tpp80) REVERT: B 202 ASN cc_start: 0.9452 (t0) cc_final: 0.8843 (t0) REVERT: B 257 ASP cc_start: 0.8879 (m-30) cc_final: 0.8382 (m-30) REVERT: B 263 ASP cc_start: 0.9159 (m-30) cc_final: 0.8723 (p0) REVERT: B 276 LYS cc_start: 0.9276 (mptt) cc_final: 0.9013 (mmtt) REVERT: B 286 ASP cc_start: 0.8538 (OUTLIER) cc_final: 0.7782 (m-30) REVERT: B 290 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8338 (tm-30) REVERT: B 319 MET cc_start: 0.8836 (tpp) cc_final: 0.8553 (tmm) REVERT: B 335 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7839 (mt-10) REVERT: B 348 MET cc_start: 0.9021 (ttp) cc_final: 0.8795 (ttp) REVERT: B 362 ASP cc_start: 0.8835 (m-30) cc_final: 0.7584 (m-30) REVERT: B 366 LYS cc_start: 0.9443 (ptpp) cc_final: 0.9093 (ptpp) REVERT: B 415 ASN cc_start: 0.9223 (t0) cc_final: 0.8875 (t0) REVERT: B 447 ASN cc_start: 0.8291 (m-40) cc_final: 0.7902 (t0) REVERT: B 452 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8310 (ttt-90) REVERT: B 471 TYR cc_start: 0.9452 (t80) cc_final: 0.8760 (t80) REVERT: B 483 GLU cc_start: 0.9492 (mp0) cc_final: 0.9263 (mp0) REVERT: B 493 MET cc_start: 0.9694 (tmm) cc_final: 0.8913 (tmm) REVERT: B 515 ASP cc_start: 0.9135 (m-30) cc_final: 0.8852 (m-30) REVERT: B 546 LEU cc_start: 0.9677 (mt) cc_final: 0.9358 (mt) REVERT: B 595 MET cc_start: 0.8950 (mmm) cc_final: 0.8187 (mmm) REVERT: B 610 LYS cc_start: 0.9058 (mmmt) cc_final: 0.8762 (mmmt) REVERT: B 612 TYR cc_start: 0.8618 (m-80) cc_final: 0.8285 (m-80) REVERT: C 20 MET cc_start: 0.9042 (tpp) cc_final: 0.8552 (tmm) REVERT: C 29 PHE cc_start: 0.8372 (t80) cc_final: 0.7866 (t80) REVERT: C 56 MET cc_start: 0.5843 (ttt) cc_final: 0.5545 (ttt) REVERT: C 80 HIS cc_start: 0.8725 (m90) cc_final: 0.8297 (m90) REVERT: C 96 MET cc_start: 0.8895 (mmt) cc_final: 0.7949 (mmt) REVERT: C 134 LYS cc_start: 0.9579 (pttm) cc_final: 0.9178 (pttm) REVERT: C 150 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.8977 (mm-30) REVERT: C 153 LEU cc_start: 0.9399 (pp) cc_final: 0.9196 (pp) REVERT: C 164 GLU cc_start: 0.9212 (mm-30) cc_final: 0.8973 (tp30) REVERT: C 169 TYR cc_start: 0.8419 (m-80) cc_final: 0.8191 (m-80) REVERT: C 178 PHE cc_start: 0.9422 (m-80) cc_final: 0.8771 (m-10) REVERT: C 185 MET cc_start: 0.8643 (pmm) cc_final: 0.7532 (pmm) REVERT: C 186 GLN cc_start: 0.9376 (mm110) cc_final: 0.8831 (mp10) REVERT: C 205 VAL cc_start: 0.9436 (t) cc_final: 0.9236 (p) REVERT: C 259 PHE cc_start: 0.8892 (t80) cc_final: 0.8428 (t80) REVERT: C 274 ASP cc_start: 0.7286 (p0) cc_final: 0.6883 (p0) REVERT: D 30 TRP cc_start: 0.8600 (p-90) cc_final: 0.7746 (p-90) REVERT: D 34 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8320 (mm-30) REVERT: D 41 LEU cc_start: 0.8971 (pp) cc_final: 0.8561 (mm) REVERT: D 42 LEU cc_start: 0.9450 (mp) cc_final: 0.9025 (mm) REVERT: D 46 TYR cc_start: 0.9071 (m-80) cc_final: 0.8753 (m-10) REVERT: D 178 PHE cc_start: 0.9349 (m-10) cc_final: 0.8814 (m-80) REVERT: D 186 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8584 (mp10) REVERT: D 207 LEU cc_start: 0.9154 (mm) cc_final: 0.8845 (mm) REVERT: D 210 GLN cc_start: 0.9326 (tm-30) cc_final: 0.9003 (pt0) REVERT: D 252 LEU cc_start: 0.6133 (mt) cc_final: 0.5754 (mm) REVERT: D 269 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8038 (ppp) outliers start: 70 outliers final: 50 residues processed: 711 average time/residue: 0.2704 time to fit residues: 286.8463 Evaluate side-chains 721 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 661 time to evaluate : 1.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 226 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 598 MET Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 413 SER Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 PHE Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 684 TYR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 287 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 111 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 182 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 chunk 127 optimal weight: 0.5980 chunk 188 optimal weight: 5.9990 chunk 27 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.121635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.087491 restraints weight = 35735.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.090971 restraints weight = 17067.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.093167 restraints weight = 10225.967| |-----------------------------------------------------------------------------| r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.7315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16386 Z= 0.163 Angle : 0.800 17.155 22134 Z= 0.395 Chirality : 0.047 0.255 2360 Planarity : 0.004 0.046 2818 Dihedral : 10.371 157.739 2246 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.67 % Allowed : 34.03 % Favored : 62.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.19), residues: 1932 helix: 0.97 (0.15), residues: 1146 sheet: -0.82 (0.41), residues: 148 loop : -0.19 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 44 HIS 0.006 0.001 HIS A 255 PHE 0.029 0.002 PHE B 261 TYR 0.036 0.002 TYR C 242 ARG 0.026 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.04174 ( 871) hydrogen bonds : angle 5.20634 ( 2571) covalent geometry : bond 0.00371 (16386) covalent geometry : angle 0.80020 (22134) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 675 time to evaluate : 1.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.9684 (tttt) cc_final: 0.9473 (ttmm) REVERT: A 64 TYR cc_start: 0.9201 (m-10) cc_final: 0.8856 (m-10) REVERT: A 65 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8251 (mp0) REVERT: A 66 GLU cc_start: 0.8482 (tp30) cc_final: 0.8152 (tp30) REVERT: A 82 LYS cc_start: 0.9627 (mmmm) cc_final: 0.9303 (mmmm) REVERT: A 102 ASN cc_start: 0.9263 (m110) cc_final: 0.8709 (m110) REVERT: A 181 ASP cc_start: 0.8758 (m-30) cc_final: 0.8466 (m-30) REVERT: A 187 ASP cc_start: 0.8951 (t70) cc_final: 0.8606 (t70) REVERT: A 202 ASN cc_start: 0.9547 (t0) cc_final: 0.9213 (t0) REVERT: A 218 ASN cc_start: 0.9277 (t0) cc_final: 0.8958 (t0) REVERT: A 221 LYS cc_start: 0.8842 (mmtp) cc_final: 0.8562 (mttp) REVERT: A 227 MET cc_start: 0.9105 (mtp) cc_final: 0.8787 (mtp) REVERT: A 228 LYS cc_start: 0.9484 (mmmm) cc_final: 0.8814 (mmtt) REVERT: A 232 ASN cc_start: 0.9169 (m-40) cc_final: 0.8939 (m-40) REVERT: A 257 ASP cc_start: 0.9379 (m-30) cc_final: 0.8995 (m-30) REVERT: A 290 GLU cc_start: 0.8735 (tp30) cc_final: 0.8453 (tm-30) REVERT: A 321 GLU cc_start: 0.8864 (tp30) cc_final: 0.8151 (tp30) REVERT: A 348 MET cc_start: 0.8554 (OUTLIER) cc_final: 0.7597 (tmm) REVERT: A 350 ARG cc_start: 0.9264 (mtp180) cc_final: 0.8989 (mtp180) REVERT: A 352 GLU cc_start: 0.8301 (mt-10) cc_final: 0.7611 (mt-10) REVERT: A 359 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8312 (ttp) REVERT: A 384 GLU cc_start: 0.9059 (OUTLIER) cc_final: 0.7742 (pm20) REVERT: A 389 SER cc_start: 0.9393 (OUTLIER) cc_final: 0.9084 (p) REVERT: A 394 TYR cc_start: 0.9191 (m-80) cc_final: 0.8842 (m-80) REVERT: A 435 SER cc_start: 0.9538 (OUTLIER) cc_final: 0.9281 (t) REVERT: A 447 ASN cc_start: 0.8394 (m-40) cc_final: 0.7879 (t0) REVERT: A 479 TYR cc_start: 0.9040 (t80) cc_final: 0.8434 (t80) REVERT: A 493 MET cc_start: 0.8901 (tmm) cc_final: 0.8148 (tmm) REVERT: A 494 MET cc_start: 0.9143 (mtm) cc_final: 0.8640 (mtt) REVERT: A 505 GLU cc_start: 0.9016 (mt-10) cc_final: 0.8758 (mt-10) REVERT: A 512 GLU cc_start: 0.8622 (pt0) cc_final: 0.8324 (pt0) REVERT: A 539 LYS cc_start: 0.9342 (mmmm) cc_final: 0.9006 (mmmt) REVERT: A 583 SER cc_start: 0.9427 (m) cc_final: 0.8860 (t) REVERT: A 598 MET cc_start: 0.8710 (mtp) cc_final: 0.8152 (mtp) REVERT: A 602 GLU cc_start: 0.7900 (pt0) cc_final: 0.7310 (pt0) REVERT: A 604 ARG cc_start: 0.8856 (mmp80) cc_final: 0.8540 (mmt-90) REVERT: A 610 LYS cc_start: 0.8572 (tppt) cc_final: 0.8303 (tppt) REVERT: A 640 MET cc_start: 0.9642 (tpp) cc_final: 0.8894 (tpp) REVERT: A 686 ARG cc_start: 0.8834 (mmm-85) cc_final: 0.8475 (mmm-85) REVERT: B 17 MET cc_start: 0.8975 (mmm) cc_final: 0.8588 (mmm) REVERT: B 28 LYS cc_start: 0.9254 (mmtt) cc_final: 0.8943 (mmmm) REVERT: B 31 GLU cc_start: 0.8352 (mt-10) cc_final: 0.8089 (mt-10) REVERT: B 65 GLU cc_start: 0.8756 (mm-30) cc_final: 0.8474 (mm-30) REVERT: B 109 ASN cc_start: 0.9194 (m-40) cc_final: 0.8648 (p0) REVERT: B 119 GLU cc_start: 0.8760 (mp0) cc_final: 0.8396 (mp0) REVERT: B 184 ARG cc_start: 0.9237 (tpp80) cc_final: 0.8928 (tpp80) REVERT: B 202 ASN cc_start: 0.9448 (t0) cc_final: 0.8977 (t0) REVERT: B 232 ASN cc_start: 0.9206 (m-40) cc_final: 0.8806 (m-40) REVERT: B 257 ASP cc_start: 0.8867 (m-30) cc_final: 0.8399 (m-30) REVERT: B 263 ASP cc_start: 0.9147 (m-30) cc_final: 0.8689 (p0) REVERT: B 286 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.7793 (m-30) REVERT: B 290 GLU cc_start: 0.8677 (tm-30) cc_final: 0.8354 (tm-30) REVERT: B 319 MET cc_start: 0.8789 (tpp) cc_final: 0.8560 (tmm) REVERT: B 335 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7812 (mt-10) REVERT: B 362 ASP cc_start: 0.8811 (m-30) cc_final: 0.7533 (m-30) REVERT: B 366 LYS cc_start: 0.9454 (ptpp) cc_final: 0.9113 (ptpp) REVERT: B 415 ASN cc_start: 0.9110 (t0) cc_final: 0.8904 (t0) REVERT: B 447 ASN cc_start: 0.8241 (m-40) cc_final: 0.7866 (t0) REVERT: B 452 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8244 (ttt-90) REVERT: B 471 TYR cc_start: 0.9428 (t80) cc_final: 0.8708 (t80) REVERT: B 483 GLU cc_start: 0.9478 (mp0) cc_final: 0.9253 (mp0) REVERT: B 493 MET cc_start: 0.9672 (tmm) cc_final: 0.8880 (tmm) REVERT: B 515 ASP cc_start: 0.9071 (m-30) cc_final: 0.8802 (m-30) REVERT: B 546 LEU cc_start: 0.9647 (mt) cc_final: 0.9338 (mt) REVERT: B 606 TYR cc_start: 0.8611 (m-80) cc_final: 0.8281 (m-80) REVERT: B 610 LYS cc_start: 0.9073 (mmmt) cc_final: 0.8826 (mmmt) REVERT: B 612 TYR cc_start: 0.8563 (m-80) cc_final: 0.8187 (m-80) REVERT: C 20 MET cc_start: 0.9016 (tpp) cc_final: 0.8482 (tmm) REVERT: C 25 ASN cc_start: 0.9110 (t0) cc_final: 0.8622 (p0) REVERT: C 29 PHE cc_start: 0.8293 (t80) cc_final: 0.7664 (t80) REVERT: C 56 MET cc_start: 0.5786 (ttt) cc_final: 0.5494 (ttt) REVERT: C 80 HIS cc_start: 0.8724 (m90) cc_final: 0.8293 (m90) REVERT: C 96 MET cc_start: 0.8869 (mmt) cc_final: 0.7885 (mmt) REVERT: C 130 TYR cc_start: 0.9344 (m-10) cc_final: 0.9122 (m-10) REVERT: C 134 LYS cc_start: 0.9471 (pttm) cc_final: 0.8834 (pttm) REVERT: C 150 GLU cc_start: 0.9179 (OUTLIER) cc_final: 0.8900 (mm-30) REVERT: C 164 GLU cc_start: 0.9275 (mm-30) cc_final: 0.8961 (tp30) REVERT: C 178 PHE cc_start: 0.9509 (m-80) cc_final: 0.8816 (m-10) REVERT: C 185 MET cc_start: 0.8663 (pmm) cc_final: 0.7559 (pmm) REVERT: C 186 GLN cc_start: 0.9417 (mm110) cc_final: 0.8920 (mp10) REVERT: C 229 ILE cc_start: 0.8600 (mm) cc_final: 0.8253 (mm) REVERT: C 242 TYR cc_start: 0.9216 (t80) cc_final: 0.8684 (m-80) REVERT: C 259 PHE cc_start: 0.8877 (t80) cc_final: 0.8394 (t80) REVERT: D 30 TRP cc_start: 0.8527 (p-90) cc_final: 0.7668 (p-90) REVERT: D 34 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8302 (mm-30) REVERT: D 41 LEU cc_start: 0.9012 (pp) cc_final: 0.8572 (mm) REVERT: D 47 LEU cc_start: 0.8712 (tt) cc_final: 0.8428 (tt) REVERT: D 96 MET cc_start: 0.8874 (mmt) cc_final: 0.8432 (mmm) REVERT: D 154 PHE cc_start: 0.9116 (t80) cc_final: 0.8654 (m-80) REVERT: D 186 GLN cc_start: 0.9165 (mm110) cc_final: 0.8619 (mp10) REVERT: D 207 LEU cc_start: 0.9145 (mm) cc_final: 0.8766 (mm) REVERT: D 210 GLN cc_start: 0.9321 (tm-30) cc_final: 0.9027 (pt0) REVERT: D 240 LEU cc_start: 0.8852 (mt) cc_final: 0.8194 (pp) REVERT: D 252 LEU cc_start: 0.5966 (mt) cc_final: 0.5624 (mm) REVERT: D 269 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8050 (ppp) outliers start: 63 outliers final: 51 residues processed: 700 average time/residue: 0.2985 time to fit residues: 314.1433 Evaluate side-chains 716 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 656 time to evaluate : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 199 VAL Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 359 MET Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 515 ASP Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 583 SER Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 PHE Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 21 PHE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 137 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 106 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 135 optimal weight: 0.0670 chunk 148 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 668 ASN ** C 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 ASN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.124311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.089335 restraints weight = 36116.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.092902 restraints weight = 16781.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.095177 restraints weight = 10046.014| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.7526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16386 Z= 0.154 Angle : 0.844 15.864 22134 Z= 0.409 Chirality : 0.047 0.245 2360 Planarity : 0.004 0.044 2818 Dihedral : 10.185 150.737 2246 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.38 % Allowed : 35.31 % Favored : 61.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.19), residues: 1932 helix: 0.92 (0.15), residues: 1144 sheet: -0.74 (0.42), residues: 144 loop : -0.24 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 44 HIS 0.006 0.001 HIS B 438 PHE 0.036 0.002 PHE C 172 TYR 0.033 0.001 TYR C 242 ARG 0.018 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.04142 ( 871) hydrogen bonds : angle 5.19929 ( 2571) covalent geometry : bond 0.00352 (16386) covalent geometry : angle 0.84377 (22134) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3864 Ramachandran restraints generated. 1932 Oldfield, 0 Emsley, 1932 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 686 time to evaluate : 1.779 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.9686 (tttt) cc_final: 0.9484 (ttmm) REVERT: A 55 LEU cc_start: 0.9734 (mt) cc_final: 0.9414 (pp) REVERT: A 64 TYR cc_start: 0.9205 (m-10) cc_final: 0.8931 (m-10) REVERT: A 65 GLU cc_start: 0.8630 (mm-30) cc_final: 0.8271 (mp0) REVERT: A 66 GLU cc_start: 0.8478 (tp30) cc_final: 0.8151 (tp30) REVERT: A 82 LYS cc_start: 0.9620 (mmmm) cc_final: 0.9270 (mmmm) REVERT: A 102 ASN cc_start: 0.9253 (m110) cc_final: 0.8877 (m-40) REVERT: A 144 MET cc_start: 0.9119 (mtm) cc_final: 0.8663 (mtm) REVERT: A 187 ASP cc_start: 0.8923 (t70) cc_final: 0.8569 (t70) REVERT: A 202 ASN cc_start: 0.9494 (t0) cc_final: 0.9141 (t0) REVERT: A 218 ASN cc_start: 0.9274 (t0) cc_final: 0.8944 (t0) REVERT: A 227 MET cc_start: 0.9095 (mtp) cc_final: 0.8778 (mtp) REVERT: A 228 LYS cc_start: 0.9469 (mmmm) cc_final: 0.8789 (mmtt) REVERT: A 232 ASN cc_start: 0.9144 (m-40) cc_final: 0.8932 (m-40) REVERT: A 257 ASP cc_start: 0.9382 (m-30) cc_final: 0.9057 (m-30) REVERT: A 290 GLU cc_start: 0.8798 (tp30) cc_final: 0.8476 (tm-30) REVERT: A 321 GLU cc_start: 0.8839 (tp30) cc_final: 0.8160 (tp30) REVERT: A 348 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.7558 (tmm) REVERT: A 350 ARG cc_start: 0.9237 (mtp180) cc_final: 0.8964 (mtp180) REVERT: A 352 GLU cc_start: 0.8347 (mt-10) cc_final: 0.7613 (mt-10) REVERT: A 370 ASN cc_start: 0.9277 (m-40) cc_final: 0.8879 (m110) REVERT: A 384 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.7671 (pm20) REVERT: A 389 SER cc_start: 0.9389 (OUTLIER) cc_final: 0.9047 (p) REVERT: A 435 SER cc_start: 0.9522 (OUTLIER) cc_final: 0.9272 (t) REVERT: A 447 ASN cc_start: 0.8306 (m-40) cc_final: 0.7878 (t0) REVERT: A 479 TYR cc_start: 0.9092 (t80) cc_final: 0.8503 (t80) REVERT: A 493 MET cc_start: 0.8846 (tmm) cc_final: 0.8538 (tmm) REVERT: A 505 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8792 (mt-10) REVERT: A 539 LYS cc_start: 0.9355 (mmmm) cc_final: 0.9004 (mmmt) REVERT: A 583 SER cc_start: 0.9365 (m) cc_final: 0.8860 (t) REVERT: A 598 MET cc_start: 0.8728 (mtp) cc_final: 0.8205 (mtp) REVERT: A 602 GLU cc_start: 0.7860 (pt0) cc_final: 0.7147 (pt0) REVERT: A 604 ARG cc_start: 0.8840 (mmp80) cc_final: 0.8560 (mmt-90) REVERT: A 610 LYS cc_start: 0.8525 (tppt) cc_final: 0.8299 (tppt) REVERT: A 640 MET cc_start: 0.9655 (tpp) cc_final: 0.8898 (tpp) REVERT: A 645 GLN cc_start: 0.8808 (tp40) cc_final: 0.8345 (tp-100) REVERT: A 686 ARG cc_start: 0.8893 (mmm-85) cc_final: 0.8540 (mmm-85) REVERT: B 17 MET cc_start: 0.8969 (mmm) cc_final: 0.8702 (mmm) REVERT: B 28 LYS cc_start: 0.9214 (mmtt) cc_final: 0.8595 (mmmm) REVERT: B 31 GLU cc_start: 0.8352 (mt-10) cc_final: 0.7908 (mt-10) REVERT: B 65 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8149 (mp0) REVERT: B 119 GLU cc_start: 0.8587 (mp0) cc_final: 0.8342 (mp0) REVERT: B 184 ARG cc_start: 0.9213 (tpp80) cc_final: 0.8996 (mmm-85) REVERT: B 202 ASN cc_start: 0.9431 (t0) cc_final: 0.8991 (t0) REVERT: B 232 ASN cc_start: 0.9081 (m-40) cc_final: 0.8794 (m-40) REVERT: B 257 ASP cc_start: 0.8875 (m-30) cc_final: 0.8418 (m-30) REVERT: B 274 ARG cc_start: 0.8965 (ttt180) cc_final: 0.8706 (ttt90) REVERT: B 286 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.7839 (m-30) REVERT: B 290 GLU cc_start: 0.8675 (tm-30) cc_final: 0.8321 (tm-30) REVERT: B 319 MET cc_start: 0.8763 (tpp) cc_final: 0.8441 (tmm) REVERT: B 335 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7828 (mt-10) REVERT: B 362 ASP cc_start: 0.8819 (m-30) cc_final: 0.7594 (m-30) REVERT: B 366 LYS cc_start: 0.9439 (ptpp) cc_final: 0.9117 (ptpp) REVERT: B 406 ASP cc_start: 0.8304 (m-30) cc_final: 0.8098 (m-30) REVERT: B 447 ASN cc_start: 0.8204 (m-40) cc_final: 0.7855 (t0) REVERT: B 452 ARG cc_start: 0.9076 (OUTLIER) cc_final: 0.8234 (ttt-90) REVERT: B 471 TYR cc_start: 0.9389 (t80) cc_final: 0.8974 (t80) REVERT: B 483 GLU cc_start: 0.9466 (mp0) cc_final: 0.9247 (mp0) REVERT: B 493 MET cc_start: 0.9654 (tmm) cc_final: 0.8874 (tmm) REVERT: B 515 ASP cc_start: 0.9052 (m-30) cc_final: 0.8772 (m-30) REVERT: B 548 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8120 (mm-30) REVERT: B 606 TYR cc_start: 0.8551 (m-80) cc_final: 0.8222 (m-80) REVERT: B 610 LYS cc_start: 0.9097 (mmmt) cc_final: 0.8834 (mmmt) REVERT: C 20 MET cc_start: 0.8914 (tpp) cc_final: 0.8419 (tmm) REVERT: C 54 THR cc_start: 0.8172 (p) cc_final: 0.7889 (t) REVERT: C 56 MET cc_start: 0.5661 (ttt) cc_final: 0.5435 (ttt) REVERT: C 80 HIS cc_start: 0.8723 (m90) cc_final: 0.8324 (m90) REVERT: C 96 MET cc_start: 0.8771 (mmt) cc_final: 0.7795 (mmt) REVERT: C 134 LYS cc_start: 0.9476 (pttm) cc_final: 0.9066 (pttm) REVERT: C 150 GLU cc_start: 0.9126 (OUTLIER) cc_final: 0.8824 (mm-30) REVERT: C 164 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8788 (tp30) REVERT: C 178 PHE cc_start: 0.9501 (m-80) cc_final: 0.8380 (m-10) REVERT: C 183 LYS cc_start: 0.8352 (pttm) cc_final: 0.7106 (ptmm) REVERT: C 185 MET cc_start: 0.8768 (pmm) cc_final: 0.7675 (pmm) REVERT: C 186 GLN cc_start: 0.9441 (mm110) cc_final: 0.9030 (mp10) REVERT: C 229 ILE cc_start: 0.8533 (mm) cc_final: 0.8172 (mm) REVERT: C 242 TYR cc_start: 0.9264 (t80) cc_final: 0.8707 (m-80) REVERT: C 259 PHE cc_start: 0.9008 (t80) cc_final: 0.8489 (t80) REVERT: D 28 GLN cc_start: 0.9252 (tt0) cc_final: 0.8747 (tm-30) REVERT: D 41 LEU cc_start: 0.9077 (pp) cc_final: 0.8596 (mm) REVERT: D 96 MET cc_start: 0.8921 (mmt) cc_final: 0.8613 (mmm) REVERT: D 154 PHE cc_start: 0.9142 (t80) cc_final: 0.8657 (m-80) REVERT: D 178 PHE cc_start: 0.9351 (m-10) cc_final: 0.8833 (m-80) REVERT: D 186 GLN cc_start: 0.9286 (mm110) cc_final: 0.8708 (mp10) REVERT: D 196 ARG cc_start: 0.9119 (ttp80) cc_final: 0.8882 (ttp80) REVERT: D 207 LEU cc_start: 0.9134 (mm) cc_final: 0.8775 (mm) REVERT: D 210 GLN cc_start: 0.9271 (tm-30) cc_final: 0.8992 (pt0) REVERT: D 252 LEU cc_start: 0.6040 (mt) cc_final: 0.5756 (mm) REVERT: D 269 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.8060 (ppp) outliers start: 58 outliers final: 48 residues processed: 712 average time/residue: 0.2909 time to fit residues: 308.7748 Evaluate side-chains 714 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 658 time to evaluate : 2.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 141 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 178 SER Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 277 THR Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 384 GLU Chi-restraints excluded: chain A residue 389 SER Chi-restraints excluded: chain A residue 409 CYS Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 435 SER Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain A residue 684 TYR Chi-restraints excluded: chain B residue 93 SER Chi-restraints excluded: chain B residue 144 MET Chi-restraints excluded: chain B residue 155 THR Chi-restraints excluded: chain B residue 180 ASN Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 376 VAL Chi-restraints excluded: chain B residue 410 ASN Chi-restraints excluded: chain B residue 411 LEU Chi-restraints excluded: chain B residue 440 SER Chi-restraints excluded: chain B residue 441 GLU Chi-restraints excluded: chain B residue 443 THR Chi-restraints excluded: chain B residue 452 ARG Chi-restraints excluded: chain B residue 587 VAL Chi-restraints excluded: chain B residue 604 ARG Chi-restraints excluded: chain B residue 620 SER Chi-restraints excluded: chain B residue 624 PHE Chi-restraints excluded: chain B residue 660 ASP Chi-restraints excluded: chain B residue 661 THR Chi-restraints excluded: chain B residue 687 THR Chi-restraints excluded: chain C residue 46 TYR Chi-restraints excluded: chain C residue 69 GLN Chi-restraints excluded: chain C residue 150 GLU Chi-restraints excluded: chain C residue 174 TYR Chi-restraints excluded: chain C residue 216 GLN Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 17 PHE Chi-restraints excluded: chain D residue 21 PHE Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain D residue 136 GLN Chi-restraints excluded: chain D residue 200 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 231 LEU Chi-restraints excluded: chain D residue 269 MET Chi-restraints excluded: chain D residue 286 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 81 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 2 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 105 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** 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 = 0.3610 r_free = 0.3610 target = 0.122627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.088671 restraints weight = 35835.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.092137 restraints weight = 17010.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.094319 restraints weight = 10134.915| |-----------------------------------------------------------------------------| r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 moved from start: 0.7674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 16386 Z= 0.177 Angle : 0.864 16.846 22134 Z= 0.422 Chirality : 0.047 0.214 2360 Planarity : 0.004 0.064 2818 Dihedral : 10.082 140.389 2246 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 18.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.32 % Allowed : 35.96 % Favored : 60.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.19), residues: 1932 helix: 0.85 (0.15), residues: 1142 sheet: -0.76 (0.42), residues: 154 loop : -0.27 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 44 HIS 0.006 0.001 HIS A 469 PHE 0.038 0.002 PHE B 74 TYR 0.031 0.002 TYR C 242 ARG 0.016 0.001 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.04222 ( 871) hydrogen bonds : angle 5.23241 ( 2571) covalent geometry : bond 0.00409 (16386) covalent geometry : angle 0.86397 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7172.72 seconds wall clock time: 125 minutes 40.82 seconds (7540.82 seconds total)