Starting phenix.real_space_refine on Sat May 17 16:36:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzk_45070/05_2025/9bzk_45070_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzk_45070/05_2025/9bzk_45070.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bzk_45070/05_2025/9bzk_45070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzk_45070/05_2025/9bzk_45070.map" model { file = "/net/cci-nas-00/data/ceres_data/9bzk_45070/05_2025/9bzk_45070_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzk_45070/05_2025/9bzk_45070_neut.cif" } resolution = 4.19 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-5687/modules/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 9.78, per 1000 atoms: 0.61 Number of scatterers: 16038 At special positions: 0 Unit cell: (94.302, 132.834, 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: 4.39 Conformation dependent library (CDL) restraints added in 2.0 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: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.104A 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: 3.985A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.954A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.664A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.949A 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: 3.575A 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: 3.693A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.393A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.627A 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: 4.018A 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: 3.730A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.027A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.068A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.936A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.567A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.668A 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: 4.876A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.359A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.501A 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: 6.064A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.049A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.515A 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: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.94 Time building geometry restraints manager: 4.99 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: 4852 1.34 - 1.46: 3050 1.46 - 1.58: 8303 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.25e-02 6.40e+03 2.35e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.039 1.20e-02 6.94e+03 1.03e+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 9.06e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.569 -0.032 1.17e-02 7.31e+03 7.29e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.573 -0.033 1.25e-02 6.40e+03 6.76e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 21576 2.09 - 4.18: 515 4.18 - 6.27: 37 6.27 - 8.36: 2 8.36 - 10.45: 4 Bond angle restraints: 22134 Sorted by residual: angle pdb=" N VAL C 125 " pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 110.54 116.65 -6.11 1.36e+00 5.41e-01 2.02e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.17 -4.46 1.15e+00 7.56e-01 1.50e+01 angle pdb=" N SER D 253 " pdb=" CA SER D 253 " pdb=" C SER D 253 " ideal model delta sigma weight residual 111.28 115.24 -3.96 1.09e+00 8.42e-01 1.32e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.86 -4.36 1.23e+00 6.61e-01 1.25e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.71 -4.00 1.15e+00 7.56e-01 1.21e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 9469 35.80 - 71.61: 338 71.61 - 107.41: 37 107.41 - 143.22: 3 143.22 - 179.02: 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 -58.32 120.71 -179.02 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 301.68 151.19 150.50 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 31.94 148.04 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 9847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 2146 0.094 - 0.187: 181 0.187 - 0.281: 28 0.281 - 0.375: 3 0.375 - 0.468: 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 5.48e+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 4.63e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.97e+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 1.12e-02 2.21e+00 pdb=" CG PHE D 92 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 169 " 0.017 2.00e-02 2.50e+03 9.72e-03 1.89e+00 pdb=" CG TYR C 169 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR C 169 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 169 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 169 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR C 169 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR C 169 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 169 " 0.008 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 128 2.51 - 3.11: 11559 3.11 - 3.70: 27043 3.70 - 4.30: 41517 4.30 - 4.90: 65395 Nonbonded interactions: 145642 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.965 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.013 3.040 ... (remaining 145637 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.650 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 37.120 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6254 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16386 Z= 0.315 Angle : 0.741 10.450 22134 Z= 0.463 Chirality : 0.058 0.468 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.952 179.023 6154 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.40 % Allowed : 15.21 % Favored : 83.39 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.18), residues: 1932 helix: 0.58 (0.14), residues: 1151 sheet: 0.47 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE D 92 TYR 0.020 0.002 TYR D 179 ARG 0.004 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.15423 ( 871) hydrogen bonds : angle 6.51778 ( 2571) covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74064 (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 937 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 913 time to evaluate : 1.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 37 PHE cc_start: 0.7508 (m-80) cc_final: 0.7149 (m-80) REVERT: A 41 ILE cc_start: 0.8408 (mm) cc_final: 0.8159 (mm) REVERT: A 99 LYS cc_start: 0.8803 (mmtt) cc_final: 0.8386 (mmtm) REVERT: A 106 LEU cc_start: 0.8446 (tp) cc_final: 0.8068 (tp) REVERT: A 118 TYR cc_start: 0.7505 (t80) cc_final: 0.7188 (t80) REVERT: A 119 GLU cc_start: 0.7086 (mp0) cc_final: 0.6849 (mp0) REVERT: A 144 MET cc_start: 0.6928 (mtm) cc_final: 0.6683 (mtm) REVERT: A 166 GLU cc_start: 0.8144 (mm-30) cc_final: 0.7938 (mm-30) REVERT: A 172 LEU cc_start: 0.9353 (mp) cc_final: 0.9137 (mp) REVERT: A 179 LEU cc_start: 0.8735 (tp) cc_final: 0.8511 (tp) REVERT: A 188 ILE cc_start: 0.9062 (mt) cc_final: 0.8738 (mt) REVERT: A 192 LEU cc_start: 0.9304 (mt) cc_final: 0.8865 (mt) REVERT: A 202 ASN cc_start: 0.9213 (t0) cc_final: 0.8916 (t0) REVERT: A 232 ASN cc_start: 0.8042 (OUTLIER) cc_final: 0.7815 (m-40) REVERT: A 236 TYR cc_start: 0.8422 (t80) cc_final: 0.8002 (t80) REVERT: A 264 THR cc_start: 0.8918 (p) cc_final: 0.8554 (m) REVERT: A 275 VAL cc_start: 0.8957 (m) cc_final: 0.8595 (m) REVERT: A 278 LEU cc_start: 0.8110 (tp) cc_final: 0.7819 (tp) REVERT: A 322 MET cc_start: 0.7414 (mmp) cc_final: 0.6519 (mmm) REVERT: A 326 PHE cc_start: 0.8335 (m-10) cc_final: 0.7964 (m-80) REVERT: A 407 ILE cc_start: 0.8739 (mt) cc_final: 0.8087 (mt) REVERT: A 441 GLU cc_start: 0.6812 (mt-10) cc_final: 0.6597 (mt-10) REVERT: A 493 MET cc_start: 0.8030 (tmm) cc_final: 0.7750 (tmm) REVERT: A 521 THR cc_start: 0.8394 (p) cc_final: 0.8121 (t) REVERT: A 550 MET cc_start: 0.6605 (mtm) cc_final: 0.5854 (mtp) REVERT: A 587 VAL cc_start: 0.8823 (t) cc_final: 0.8593 (t) REVERT: A 594 VAL cc_start: 0.9069 (m) cc_final: 0.8861 (m) REVERT: A 644 ILE cc_start: 0.8778 (mt) cc_final: 0.8325 (mt) REVERT: A 652 ILE cc_start: 0.8933 (mt) cc_final: 0.8618 (mt) REVERT: B 58 LEU cc_start: 0.8920 (mt) cc_final: 0.8679 (mt) REVERT: B 119 GLU cc_start: 0.7782 (mp0) cc_final: 0.7496 (mp0) REVERT: B 190 MET cc_start: 0.8079 (mtm) cc_final: 0.7822 (mtm) REVERT: B 191 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8092 (mm-40) REVERT: B 205 LYS cc_start: 0.8288 (mttp) cc_final: 0.7889 (mtmm) REVERT: B 211 GLU cc_start: 0.7363 (mt-10) cc_final: 0.6930 (mm-30) REVERT: B 265 LYS cc_start: 0.8841 (mmtt) cc_final: 0.7977 (mmmt) REVERT: B 278 LEU cc_start: 0.8720 (tp) cc_final: 0.8351 (tp) REVERT: B 322 MET cc_start: 0.7656 (mmm) cc_final: 0.6065 (mmm) REVERT: B 345 LYS cc_start: 0.8415 (tttt) cc_final: 0.8114 (ttpt) REVERT: B 355 TYR cc_start: 0.7499 (m-80) cc_final: 0.7158 (m-80) REVERT: B 362 ASP cc_start: 0.6438 (m-30) cc_final: 0.6060 (m-30) REVERT: B 387 GLN cc_start: 0.7521 (mt0) cc_final: 0.7290 (mt0) REVERT: B 430 LYS cc_start: 0.8025 (mttt) cc_final: 0.7721 (mtmm) REVERT: B 492 PHE cc_start: 0.7730 (m-80) cc_final: 0.7477 (m-80) REVERT: B 561 LEU cc_start: 0.8223 (tp) cc_final: 0.8014 (tp) REVERT: B 570 MET cc_start: 0.6973 (mtm) cc_final: 0.6032 (mtm) REVERT: B 574 TYR cc_start: 0.7964 (m-80) cc_final: 0.7562 (m-80) REVERT: B 585 SER cc_start: 0.8561 (p) cc_final: 0.8009 (p) REVERT: B 644 ILE cc_start: 0.8728 (mt) cc_final: 0.8488 (mt) REVERT: C 89 VAL cc_start: 0.5211 (t) cc_final: 0.3769 (t) REVERT: C 90 LEU cc_start: 0.5607 (mt) cc_final: 0.5113 (mt) REVERT: D 112 LEU cc_start: 0.7301 (mt) cc_final: 0.6415 (mt) REVERT: D 256 VAL cc_start: 0.5192 (t) cc_final: 0.4859 (t) REVERT: D 282 ILE cc_start: 0.3776 (OUTLIER) cc_final: 0.3418 (tp) REVERT: D 286 VAL cc_start: 0.5978 (t) cc_final: 0.5602 (p) outliers start: 24 outliers final: 7 residues processed: 928 average time/residue: 0.2999 time to fit residues: 396.3318 Evaluate side-chains 660 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 651 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 162 optimal weight: 5.9990 chunk 145 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 98 optimal weight: 5.9990 chunk 77 optimal weight: 0.0770 chunk 150 optimal weight: 5.9990 chunk 58 optimal weight: 0.1980 chunk 91 optimal weight: 9.9990 chunk 112 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 overall best weight: 1.6142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 232 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS B 19 GLN B 61 ASN ** B 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN C 23 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN D 71 ASN D 80 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.147444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.104629 restraints weight = 37278.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.108623 restraints weight = 21391.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.111297 restraints weight = 13900.101| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3273 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16386 Z= 0.178 Angle : 0.637 12.478 22134 Z= 0.339 Chirality : 0.044 0.272 2360 Planarity : 0.004 0.074 2818 Dihedral : 11.223 176.211 2242 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.12 % Allowed : 2.51 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.34 (0.19), residues: 1932 helix: 1.31 (0.15), residues: 1128 sheet: -0.05 (0.41), residues: 134 loop : 0.58 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 558 HIS 0.007 0.001 HIS A 438 PHE 0.032 0.002 PHE D 259 TYR 0.027 0.002 TYR A 498 ARG 0.008 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.04525 ( 871) hydrogen bonds : angle 5.03070 ( 2571) covalent geometry : bond 0.00379 (16386) covalent geometry : angle 0.63704 (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 747 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 745 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 12 LEU cc_start: 0.9458 (mp) cc_final: 0.9245 (mt) REVERT: A 29 ASP cc_start: 0.9302 (t0) cc_final: 0.8797 (t70) REVERT: A 82 LYS cc_start: 0.9693 (mtpp) cc_final: 0.9486 (mmtp) REVERT: A 118 TYR cc_start: 0.8945 (t80) cc_final: 0.8531 (t80) REVERT: A 119 GLU cc_start: 0.8887 (mp0) cc_final: 0.8350 (mp0) REVERT: A 142 ASN cc_start: 0.9187 (m-40) cc_final: 0.8933 (m110) REVERT: A 143 LEU cc_start: 0.9240 (tp) cc_final: 0.8973 (tp) REVERT: A 147 GLN cc_start: 0.9091 (mt0) cc_final: 0.7423 (mt0) REVERT: A 148 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8566 (mt-10) REVERT: A 150 GLN cc_start: 0.9300 (tp40) cc_final: 0.9036 (tp40) REVERT: A 172 LEU cc_start: 0.9507 (mp) cc_final: 0.8894 (mp) REVERT: A 173 LEU cc_start: 0.9529 (mt) cc_final: 0.9110 (mt) REVERT: A 176 ASN cc_start: 0.8718 (t0) cc_final: 0.8407 (t0) REVERT: A 181 ASP cc_start: 0.9029 (m-30) cc_final: 0.8758 (m-30) REVERT: A 187 ASP cc_start: 0.9416 (t70) cc_final: 0.8784 (t0) REVERT: A 188 ILE cc_start: 0.9705 (mt) cc_final: 0.9413 (mt) REVERT: A 191 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8286 (mp10) REVERT: A 195 LEU cc_start: 0.9545 (mt) cc_final: 0.9271 (mt) REVERT: A 202 ASN cc_start: 0.9299 (t0) cc_final: 0.8930 (t0) REVERT: A 214 LYS cc_start: 0.9109 (tppt) cc_final: 0.8832 (mmtt) REVERT: A 221 LYS cc_start: 0.8906 (mmtp) cc_final: 0.8496 (mmtp) REVERT: A 223 VAL cc_start: 0.9606 (m) cc_final: 0.9158 (p) REVERT: A 243 ARG cc_start: 0.6843 (tmt-80) cc_final: 0.6606 (tpt-90) REVERT: A 257 ASP cc_start: 0.9263 (m-30) cc_final: 0.8968 (m-30) REVERT: A 270 ASP cc_start: 0.7998 (t70) cc_final: 0.7472 (t70) REVERT: A 314 MET cc_start: 0.9326 (ttt) cc_final: 0.9085 (ttt) REVERT: A 317 MET cc_start: 0.8116 (mtp) cc_final: 0.7755 (mtp) REVERT: A 319 MET cc_start: 0.9138 (tpp) cc_final: 0.8892 (tpp) REVERT: A 322 MET cc_start: 0.8490 (mmp) cc_final: 0.7773 (mmm) REVERT: A 326 PHE cc_start: 0.9591 (m-10) cc_final: 0.8844 (m-80) REVERT: A 335 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8544 (mm-30) REVERT: A 348 MET cc_start: 0.8801 (tpt) cc_final: 0.8434 (tpp) REVERT: A 355 TYR cc_start: 0.9016 (m-10) cc_final: 0.8770 (m-10) REVERT: A 357 TYR cc_start: 0.8982 (m-10) cc_final: 0.8566 (m-10) REVERT: A 366 LYS cc_start: 0.9392 (mtmt) cc_final: 0.9155 (mtmm) REVERT: A 377 LYS cc_start: 0.9018 (mttt) cc_final: 0.8766 (mtmm) REVERT: A 406 ASP cc_start: 0.8130 (m-30) cc_final: 0.7465 (m-30) REVERT: A 407 ILE cc_start: 0.9063 (mt) cc_final: 0.8832 (mt) REVERT: A 421 GLU cc_start: 0.8746 (pp20) cc_final: 0.8454 (pp20) REVERT: A 444 ASP cc_start: 0.8307 (t0) cc_final: 0.7918 (t0) REVERT: A 493 MET cc_start: 0.8976 (tmm) cc_final: 0.8580 (tmm) REVERT: A 515 ASP cc_start: 0.9038 (m-30) cc_final: 0.8829 (m-30) REVERT: A 521 THR cc_start: 0.8434 (p) cc_final: 0.7841 (t) REVERT: A 550 MET cc_start: 0.7242 (mtm) cc_final: 0.6813 (mtp) REVERT: A 583 SER cc_start: 0.9455 (m) cc_final: 0.8878 (p) REVERT: A 588 GLN cc_start: 0.9017 (mm-40) cc_final: 0.8038 (mm-40) REVERT: A 595 MET cc_start: 0.9304 (mmp) cc_final: 0.9090 (mmp) REVERT: A 615 MET cc_start: 0.8859 (mmp) cc_final: 0.8318 (mmp) REVERT: A 645 GLN cc_start: 0.8492 (tp40) cc_final: 0.7923 (tp40) REVERT: A 668 ASN cc_start: 0.9163 (m110) cc_final: 0.8828 (m110) REVERT: A 680 LYS cc_start: 0.9257 (mttt) cc_final: 0.8871 (mttt) REVERT: A 684 TYR cc_start: 0.7800 (m-10) cc_final: 0.7020 (m-80) REVERT: B 12 LEU cc_start: 0.9351 (mp) cc_final: 0.8967 (mt) REVERT: B 51 LEU cc_start: 0.9039 (tp) cc_final: 0.8707 (tp) REVERT: B 87 LYS cc_start: 0.9336 (tptp) cc_final: 0.9049 (tptp) REVERT: B 99 LYS cc_start: 0.9548 (mmmt) cc_final: 0.9214 (mmmt) REVERT: B 133 ASP cc_start: 0.8715 (t0) cc_final: 0.8467 (t0) REVERT: B 211 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8138 (mm-30) REVERT: B 236 TYR cc_start: 0.9058 (t80) cc_final: 0.8569 (t80) REVERT: B 250 TYR cc_start: 0.9224 (m-80) cc_final: 0.8801 (m-80) REVERT: B 286 ASP cc_start: 0.8248 (m-30) cc_final: 0.7793 (m-30) REVERT: B 308 LYS cc_start: 0.9483 (mtmt) cc_final: 0.9261 (ptpp) REVERT: B 312 GLN cc_start: 0.8713 (pm20) cc_final: 0.8297 (pm20) REVERT: B 322 MET cc_start: 0.9026 (mmm) cc_final: 0.8152 (mmm) REVERT: B 326 PHE cc_start: 0.9132 (m-80) cc_final: 0.8519 (m-80) REVERT: B 348 MET cc_start: 0.9022 (ptp) cc_final: 0.8513 (ptt) REVERT: B 352 GLU cc_start: 0.9123 (mt-10) cc_final: 0.8718 (mt-10) REVERT: B 355 TYR cc_start: 0.9001 (m-80) cc_final: 0.8496 (m-80) REVERT: B 362 ASP cc_start: 0.8618 (m-30) cc_final: 0.7884 (m-30) REVERT: B 403 ILE cc_start: 0.9476 (mp) cc_final: 0.9212 (tp) REVERT: B 410 ASN cc_start: 0.8784 (m110) cc_final: 0.8575 (m110) REVERT: B 415 ASN cc_start: 0.9568 (t0) cc_final: 0.9297 (t0) REVERT: B 459 LYS cc_start: 0.9146 (mmmm) cc_final: 0.8790 (mmtm) REVERT: B 460 SER cc_start: 0.8721 (t) cc_final: 0.8507 (t) REVERT: B 493 MET cc_start: 0.9647 (tmm) cc_final: 0.9396 (tmm) REVERT: B 494 MET cc_start: 0.9577 (mtp) cc_final: 0.9335 (mtp) REVERT: B 515 ASP cc_start: 0.9311 (m-30) cc_final: 0.8882 (m-30) REVERT: B 522 TYR cc_start: 0.8928 (m-10) cc_final: 0.8419 (m-10) REVERT: B 558 TRP cc_start: 0.9184 (m100) cc_final: 0.8415 (m100) REVERT: B 599 GLU cc_start: 0.8589 (pt0) cc_final: 0.8247 (pt0) REVERT: B 601 ILE cc_start: 0.9518 (mm) cc_final: 0.9138 (tp) REVERT: B 603 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8681 (tp30) REVERT: B 615 MET cc_start: 0.9247 (mmp) cc_final: 0.8748 (mmp) REVERT: B 640 MET cc_start: 0.9180 (tpp) cc_final: 0.8943 (tpp) REVERT: B 657 PHE cc_start: 0.8855 (m-80) cc_final: 0.8651 (m-80) REVERT: B 664 THR cc_start: 0.9138 (p) cc_final: 0.8871 (p) REVERT: B 667 LEU cc_start: 0.9257 (tp) cc_final: 0.8950 (tp) REVERT: B 684 TYR cc_start: 0.7669 (m-10) cc_final: 0.6546 (m-10) REVERT: C 17 PHE cc_start: 0.7156 (p90) cc_final: 0.6018 (p90) REVERT: C 21 PHE cc_start: 0.8962 (m-10) cc_final: 0.8121 (m-10) REVERT: C 87 LYS cc_start: 0.8912 (mtmm) cc_final: 0.8650 (mtmt) REVERT: C 283 ASN cc_start: 0.2282 (p0) cc_final: 0.1991 (p0) REVERT: D 46 TYR cc_start: 0.8521 (m-80) cc_final: 0.8058 (m-80) REVERT: D 105 TYR cc_start: 0.8924 (m-10) cc_final: 0.8405 (m-10) REVERT: D 169 TYR cc_start: 0.8840 (m-80) cc_final: 0.8361 (m-80) REVERT: D 194 ILE cc_start: 0.9834 (mt) cc_final: 0.9597 (mm) REVERT: D 197 ASP cc_start: 0.9107 (m-30) cc_final: 0.8825 (m-30) REVERT: D 204 TYR cc_start: 0.9557 (t80) cc_final: 0.9248 (t80) outliers start: 2 outliers final: 0 residues processed: 745 average time/residue: 0.2836 time to fit residues: 307.8084 Evaluate side-chains 613 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 613 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 8 optimal weight: 5.9990 chunk 168 optimal weight: 4.9990 chunk 175 optimal weight: 9.9990 chunk 34 optimal weight: 0.9980 chunk 47 optimal weight: 0.6980 chunk 191 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 141 optimal weight: 9.9990 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 ASN A 232 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 HIS ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN ** B 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 676 HIS C 25 ASN C 201 HIS ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.133871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.093536 restraints weight = 40478.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.097170 restraints weight = 22616.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.099600 restraints weight = 14524.376| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3161 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3161 r_free = 0.3161 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 16386 Z= 0.265 Angle : 0.675 13.396 22134 Z= 0.352 Chirality : 0.043 0.177 2360 Planarity : 0.004 0.056 2818 Dihedral : 11.088 179.124 2242 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.06 % Allowed : 2.51 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.08 (0.19), residues: 1932 helix: 1.18 (0.15), residues: 1141 sheet: -0.06 (0.42), residues: 134 loop : 0.27 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP D 124 HIS 0.007 0.001 HIS A 568 PHE 0.030 0.002 PHE A 171 TYR 0.035 0.002 TYR B 574 ARG 0.009 0.001 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.04266 ( 871) hydrogen bonds : angle 4.92198 ( 2571) covalent geometry : bond 0.00556 (16386) covalent geometry : angle 0.67452 (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 667 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 666 time to evaluate : 2.418 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 29 ASP cc_start: 0.9232 (t0) cc_final: 0.8842 (t70) REVERT: A 54 LYS cc_start: 0.9659 (ttmt) cc_final: 0.9453 (ttmt) REVERT: A 118 TYR cc_start: 0.8974 (t80) cc_final: 0.8710 (t80) REVERT: A 119 GLU cc_start: 0.9027 (mp0) cc_final: 0.8573 (mp0) REVERT: A 125 VAL cc_start: 0.9510 (t) cc_final: 0.9271 (t) REVERT: A 150 GLN cc_start: 0.9354 (tp40) cc_final: 0.9033 (tp40) REVERT: A 158 ASN cc_start: 0.9191 (m-40) cc_final: 0.8693 (m-40) REVERT: A 172 LEU cc_start: 0.9524 (mp) cc_final: 0.9011 (mp) REVERT: A 173 LEU cc_start: 0.9615 (mt) cc_final: 0.9391 (mt) REVERT: A 181 ASP cc_start: 0.9171 (m-30) cc_final: 0.8920 (m-30) REVERT: A 191 GLN cc_start: 0.8951 (mm-40) cc_final: 0.8362 (mp10) REVERT: A 214 LYS cc_start: 0.9156 (tppt) cc_final: 0.8838 (mmtt) REVERT: A 223 VAL cc_start: 0.9527 (m) cc_final: 0.9262 (p) REVERT: A 228 LYS cc_start: 0.9394 (mmmt) cc_final: 0.9192 (mmmm) REVERT: A 257 ASP cc_start: 0.9226 (m-30) cc_final: 0.8838 (m-30) REVERT: A 270 ASP cc_start: 0.8280 (t70) cc_final: 0.7716 (t70) REVERT: A 277 THR cc_start: 0.8893 (p) cc_final: 0.8546 (p) REVERT: A 295 ASP cc_start: 0.8674 (t70) cc_final: 0.8378 (t70) REVERT: A 317 MET cc_start: 0.8137 (mtp) cc_final: 0.7781 (mtp) REVERT: A 335 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8719 (mm-30) REVERT: A 355 TYR cc_start: 0.8971 (m-10) cc_final: 0.8763 (m-10) REVERT: A 366 LYS cc_start: 0.9357 (mtmt) cc_final: 0.9087 (mtmm) REVERT: A 377 LYS cc_start: 0.9127 (mttt) cc_final: 0.8846 (mtmm) REVERT: A 396 ASP cc_start: 0.8859 (m-30) cc_final: 0.8449 (m-30) REVERT: A 407 ILE cc_start: 0.9244 (mt) cc_final: 0.9022 (mt) REVERT: A 421 GLU cc_start: 0.8872 (pp20) cc_final: 0.8597 (pp20) REVERT: A 444 ASP cc_start: 0.8365 (t0) cc_final: 0.7748 (t0) REVERT: A 446 ARG cc_start: 0.7965 (mmt90) cc_final: 0.7478 (mmm-85) REVERT: A 483 GLU cc_start: 0.9492 (mp0) cc_final: 0.9178 (pm20) REVERT: A 493 MET cc_start: 0.8867 (tmm) cc_final: 0.8420 (tmm) REVERT: A 515 ASP cc_start: 0.9117 (m-30) cc_final: 0.8894 (m-30) REVERT: A 550 MET cc_start: 0.7341 (mtm) cc_final: 0.7027 (mtp) REVERT: A 583 SER cc_start: 0.9470 (m) cc_final: 0.9129 (p) REVERT: A 595 MET cc_start: 0.9381 (mmp) cc_final: 0.9157 (mmp) REVERT: A 598 MET cc_start: 0.8385 (mtp) cc_final: 0.7962 (mtp) REVERT: A 615 MET cc_start: 0.9196 (mmp) cc_final: 0.8788 (mmp) REVERT: A 639 ASP cc_start: 0.9259 (m-30) cc_final: 0.9050 (m-30) REVERT: A 641 ILE cc_start: 0.9714 (mm) cc_final: 0.9510 (mm) REVERT: A 645 GLN cc_start: 0.8896 (tp40) cc_final: 0.8665 (tp-100) REVERT: A 657 PHE cc_start: 0.9010 (m-80) cc_final: 0.8787 (m-80) REVERT: A 672 LEU cc_start: 0.9275 (mt) cc_final: 0.9028 (mt) REVERT: B 51 LEU cc_start: 0.9316 (tp) cc_final: 0.9113 (tp) REVERT: B 52 LYS cc_start: 0.9398 (tptp) cc_final: 0.9138 (tppt) REVERT: B 54 LYS cc_start: 0.9717 (ttmt) cc_final: 0.9492 (ttmm) REVERT: B 87 LYS cc_start: 0.9330 (tptp) cc_final: 0.9071 (tptp) REVERT: B 99 LYS cc_start: 0.9567 (mmmt) cc_final: 0.9243 (mmmt) REVERT: B 119 GLU cc_start: 0.9308 (mp0) cc_final: 0.8861 (mp0) REVERT: B 120 ASP cc_start: 0.9052 (m-30) cc_final: 0.8836 (m-30) REVERT: B 158 ASN cc_start: 0.9332 (m110) cc_final: 0.8794 (t0) REVERT: B 179 LEU cc_start: 0.9787 (tp) cc_final: 0.9586 (tp) REVERT: B 250 TYR cc_start: 0.9215 (m-80) cc_final: 0.8854 (m-80) REVERT: B 290 GLU cc_start: 0.9023 (tm-30) cc_final: 0.8262 (tm-30) REVERT: B 291 LEU cc_start: 0.9602 (mt) cc_final: 0.9401 (mt) REVERT: B 322 MET cc_start: 0.9164 (mmm) cc_final: 0.8051 (mmm) REVERT: B 326 PHE cc_start: 0.9221 (m-80) cc_final: 0.8487 (m-80) REVERT: B 355 TYR cc_start: 0.8996 (m-80) cc_final: 0.8557 (m-80) REVERT: B 362 ASP cc_start: 0.8744 (m-30) cc_final: 0.8028 (m-30) REVERT: B 393 SER cc_start: 0.9621 (m) cc_final: 0.8901 (p) REVERT: B 410 ASN cc_start: 0.9031 (m110) cc_final: 0.8668 (m110) REVERT: B 415 ASN cc_start: 0.9595 (t0) cc_final: 0.9372 (t0) REVERT: B 459 LYS cc_start: 0.9129 (mmtp) cc_final: 0.8824 (mptt) REVERT: B 480 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8046 (pp20) REVERT: B 515 ASP cc_start: 0.9346 (m-30) cc_final: 0.8899 (m-30) REVERT: B 522 TYR cc_start: 0.9007 (m-10) cc_final: 0.8693 (m-10) REVERT: B 588 GLN cc_start: 0.9258 (mm-40) cc_final: 0.8857 (mm-40) REVERT: B 599 GLU cc_start: 0.8619 (pt0) cc_final: 0.8267 (pt0) REVERT: B 615 MET cc_start: 0.9275 (mmp) cc_final: 0.8970 (mmp) REVERT: B 632 MET cc_start: 0.8702 (mpp) cc_final: 0.7952 (mpp) REVERT: B 645 GLN cc_start: 0.9330 (tp40) cc_final: 0.8844 (tp-100) REVERT: B 667 LEU cc_start: 0.9299 (tp) cc_final: 0.9013 (tp) REVERT: B 668 ASN cc_start: 0.9300 (m110) cc_final: 0.9022 (m-40) REVERT: C 17 PHE cc_start: 0.7284 (p90) cc_final: 0.6330 (p90) REVERT: C 21 PHE cc_start: 0.8907 (m-10) cc_final: 0.8062 (m-80) REVERT: C 97 GLU cc_start: 0.7824 (tp30) cc_final: 0.7527 (tp30) REVERT: C 204 TYR cc_start: 0.9219 (t80) cc_final: 0.8973 (t80) REVERT: D 20 MET cc_start: 0.8200 (ttp) cc_final: 0.7956 (ptm) REVERT: D 46 TYR cc_start: 0.8575 (m-80) cc_final: 0.8064 (m-80) REVERT: D 96 MET cc_start: 0.8749 (tpt) cc_final: 0.8479 (tpp) REVERT: D 105 TYR cc_start: 0.9212 (m-10) cc_final: 0.8484 (m-10) REVERT: D 119 ASN cc_start: 0.8895 (t0) cc_final: 0.8692 (t0) REVERT: D 169 TYR cc_start: 0.9091 (m-80) cc_final: 0.8615 (m-80) REVERT: D 172 PHE cc_start: 0.8964 (m-80) cc_final: 0.8669 (m-80) REVERT: D 177 TYR cc_start: 0.8983 (t80) cc_final: 0.8769 (t80) REVERT: D 204 TYR cc_start: 0.9628 (t80) cc_final: 0.9204 (t80) outliers start: 1 outliers final: 0 residues processed: 666 average time/residue: 0.2749 time to fit residues: 268.5740 Evaluate side-chains 584 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 584 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 180 optimal weight: 0.9990 chunk 99 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 50 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 71 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 148 optimal weight: 5.9990 chunk 90 optimal weight: 0.7980 chunk 94 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 232 ASN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN C 25 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.136552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.095984 restraints weight = 40032.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.099716 restraints weight = 22251.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.102221 restraints weight = 14256.895| |-----------------------------------------------------------------------------| r_work (final): 0.3187 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.5859 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= 0.178 Angle : 0.603 10.537 22134 Z= 0.314 Chirality : 0.043 0.211 2360 Planarity : 0.004 0.059 2818 Dihedral : 10.862 178.803 2242 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.12 % Allowed : 1.98 % Favored : 97.90 % 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: 1.19 (0.15), residues: 1128 sheet: -0.09 (0.43), residues: 130 loop : 0.19 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 30 HIS 0.021 0.002 HIS C 201 PHE 0.022 0.002 PHE D 109 TYR 0.024 0.001 TYR B 574 ARG 0.007 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03919 ( 871) hydrogen bonds : angle 4.85667 ( 2571) covalent geometry : bond 0.00385 (16386) covalent geometry : angle 0.60277 (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 658 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 656 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.9080 (mp0) cc_final: 0.8734 (mp0) REVERT: A 65 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8547 (mm-30) REVERT: A 106 LEU cc_start: 0.9498 (tp) cc_final: 0.9213 (tp) REVERT: A 118 TYR cc_start: 0.8908 (t80) cc_final: 0.8559 (t80) REVERT: A 119 GLU cc_start: 0.8914 (mp0) cc_final: 0.8453 (mp0) REVERT: A 136 LYS cc_start: 0.9383 (tttp) cc_final: 0.9096 (tptt) REVERT: A 143 LEU cc_start: 0.9273 (tp) cc_final: 0.9011 (tp) REVERT: A 148 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8582 (mt-10) REVERT: A 164 ARG cc_start: 0.8780 (ptt90) cc_final: 0.8500 (ptt90) REVERT: A 172 LEU cc_start: 0.9526 (mp) cc_final: 0.9050 (mp) REVERT: A 173 LEU cc_start: 0.9628 (mt) cc_final: 0.9390 (mt) REVERT: A 214 LYS cc_start: 0.9077 (tppt) cc_final: 0.8676 (mmtt) REVERT: A 223 VAL cc_start: 0.9577 (m) cc_final: 0.9283 (p) REVERT: A 228 LYS cc_start: 0.9413 (mmmt) cc_final: 0.9202 (mmmm) REVERT: A 255 HIS cc_start: 0.8877 (t-90) cc_final: 0.8034 (t-90) REVERT: A 257 ASP cc_start: 0.9272 (m-30) cc_final: 0.8698 (m-30) REVERT: A 270 ASP cc_start: 0.8157 (t70) cc_final: 0.7582 (t70) REVERT: A 277 THR cc_start: 0.8761 (p) cc_final: 0.8534 (p) REVERT: A 295 ASP cc_start: 0.8688 (t70) cc_final: 0.8400 (t70) REVERT: A 322 MET cc_start: 0.8920 (mmm) cc_final: 0.8695 (mmm) REVERT: A 333 LYS cc_start: 0.9347 (tppp) cc_final: 0.9094 (tppt) REVERT: A 335 GLU cc_start: 0.8872 (mm-30) cc_final: 0.8652 (mm-30) REVERT: A 355 TYR cc_start: 0.8889 (m-10) cc_final: 0.8683 (m-10) REVERT: A 366 LYS cc_start: 0.9457 (mtmt) cc_final: 0.9217 (mtmm) REVERT: A 390 GLN cc_start: 0.8714 (mt0) cc_final: 0.8395 (mt0) REVERT: A 396 ASP cc_start: 0.8846 (m-30) cc_final: 0.8426 (m-30) REVERT: A 405 LEU cc_start: 0.8677 (mt) cc_final: 0.8377 (mt) REVERT: A 406 ASP cc_start: 0.8151 (m-30) cc_final: 0.7883 (m-30) REVERT: A 407 ILE cc_start: 0.9299 (mt) cc_final: 0.9085 (mt) REVERT: A 421 GLU cc_start: 0.8849 (pp20) cc_final: 0.8576 (pp20) REVERT: A 483 GLU cc_start: 0.9505 (mp0) cc_final: 0.9229 (mp0) REVERT: A 491 PHE cc_start: 0.9713 (t80) cc_final: 0.9497 (t80) REVERT: A 493 MET cc_start: 0.8846 (tmm) cc_final: 0.8377 (tmm) REVERT: A 515 ASP cc_start: 0.9105 (m-30) cc_final: 0.8861 (m-30) REVERT: A 550 MET cc_start: 0.7327 (mtm) cc_final: 0.6966 (mtp) REVERT: A 583 SER cc_start: 0.9439 (m) cc_final: 0.9068 (p) REVERT: A 595 MET cc_start: 0.9298 (mmp) cc_final: 0.9018 (mmm) REVERT: A 615 MET cc_start: 0.9270 (mmp) cc_final: 0.8752 (mmp) REVERT: A 632 MET cc_start: 0.8282 (mtm) cc_final: 0.7951 (mtp) REVERT: A 639 ASP cc_start: 0.9189 (m-30) cc_final: 0.8919 (m-30) REVERT: A 645 GLN cc_start: 0.8893 (tp40) cc_final: 0.8693 (tp40) REVERT: A 669 ARG cc_start: 0.9089 (mtm-85) cc_final: 0.8737 (ttm110) REVERT: A 672 LEU cc_start: 0.9298 (mt) cc_final: 0.9023 (mt) REVERT: B 52 LYS cc_start: 0.9452 (tptp) cc_final: 0.9167 (tppt) REVERT: B 54 LYS cc_start: 0.9730 (ttmt) cc_final: 0.9495 (ttmm) REVERT: B 87 LYS cc_start: 0.9306 (tptp) cc_final: 0.8919 (tptp) REVERT: B 119 GLU cc_start: 0.9231 (mp0) cc_final: 0.8771 (mp0) REVERT: B 120 ASP cc_start: 0.9103 (m-30) cc_final: 0.8888 (m-30) REVERT: B 127 LEU cc_start: 0.9526 (mm) cc_final: 0.9186 (mm) REVERT: B 184 ARG cc_start: 0.9381 (tpp80) cc_final: 0.9138 (tpp80) REVERT: B 211 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8687 (mm-30) REVERT: B 250 TYR cc_start: 0.9157 (m-80) cc_final: 0.8740 (m-80) REVERT: B 260 ASP cc_start: 0.9260 (p0) cc_final: 0.9051 (p0) REVERT: B 288 PHE cc_start: 0.9281 (t80) cc_final: 0.8902 (t80) REVERT: B 322 MET cc_start: 0.9161 (mmm) cc_final: 0.8293 (mmm) REVERT: B 333 LYS cc_start: 0.9507 (tttp) cc_final: 0.9193 (ttmm) REVERT: B 348 MET cc_start: 0.9170 (ptt) cc_final: 0.8968 (ptp) REVERT: B 355 TYR cc_start: 0.9041 (m-80) cc_final: 0.8500 (m-80) REVERT: B 362 ASP cc_start: 0.8947 (m-30) cc_final: 0.8532 (m-30) REVERT: B 375 LYS cc_start: 0.9161 (mmmm) cc_final: 0.8777 (mmmm) REVERT: B 393 SER cc_start: 0.9507 (m) cc_final: 0.9111 (p) REVERT: B 402 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8138 (tm-30) REVERT: B 410 ASN cc_start: 0.8905 (m110) cc_final: 0.8570 (m110) REVERT: B 459 LYS cc_start: 0.9085 (mmtp) cc_final: 0.8571 (mtmt) REVERT: B 515 ASP cc_start: 0.9351 (m-30) cc_final: 0.8953 (m-30) REVERT: B 588 GLN cc_start: 0.9162 (mm-40) cc_final: 0.8908 (mm-40) REVERT: B 598 MET cc_start: 0.8966 (mtp) cc_final: 0.8674 (mtp) REVERT: B 615 MET cc_start: 0.9262 (mmp) cc_final: 0.8770 (mmp) REVERT: B 628 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8530 (mm-30) REVERT: B 632 MET cc_start: 0.8529 (mpp) cc_final: 0.8306 (mpp) REVERT: B 664 THR cc_start: 0.9243 (p) cc_final: 0.9002 (p) REVERT: B 667 LEU cc_start: 0.9331 (tp) cc_final: 0.9065 (tp) REVERT: B 668 ASN cc_start: 0.9288 (m110) cc_final: 0.9019 (m110) REVERT: B 677 ARG cc_start: 0.9273 (mmm-85) cc_final: 0.8810 (mmm-85) REVERT: C 21 PHE cc_start: 0.8902 (m-10) cc_final: 0.7996 (m-10) REVERT: C 87 LYS cc_start: 0.9022 (mtmm) cc_final: 0.8716 (mttt) REVERT: C 96 MET cc_start: 0.7063 (mmp) cc_final: 0.6781 (mmt) REVERT: C 204 TYR cc_start: 0.9335 (t80) cc_final: 0.8995 (t80) REVERT: C 207 LEU cc_start: 0.7941 (pp) cc_final: 0.7674 (pp) REVERT: C 286 VAL cc_start: 0.7225 (t) cc_final: 0.6965 (t) REVERT: D 45 LYS cc_start: 0.8647 (pttt) cc_final: 0.8277 (pttt) REVERT: D 46 TYR cc_start: 0.8598 (m-80) cc_final: 0.8069 (m-80) REVERT: D 96 MET cc_start: 0.8920 (tpt) cc_final: 0.8712 (tpp) REVERT: D 105 TYR cc_start: 0.9172 (m-10) cc_final: 0.8389 (m-10) REVERT: D 169 TYR cc_start: 0.9314 (m-80) cc_final: 0.8799 (m-80) REVERT: D 172 PHE cc_start: 0.8982 (m-80) cc_final: 0.8615 (m-80) REVERT: D 204 TYR cc_start: 0.9606 (t80) cc_final: 0.9237 (t80) REVERT: D 315 LEU cc_start: 0.9096 (mt) cc_final: 0.8884 (mp) outliers start: 2 outliers final: 0 residues processed: 656 average time/residue: 0.2811 time to fit residues: 271.6315 Evaluate side-chains 579 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 579 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 67 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 175 optimal weight: 6.9990 chunk 182 optimal weight: 6.9990 chunk 96 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 232 ASN A 313 HIS ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 HIS ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 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 = 0.3772 r_free = 0.3772 target = 0.138995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.098179 restraints weight = 40485.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.101967 restraints weight = 22390.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.104506 restraints weight = 14206.550| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.6192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16386 Z= 0.146 Angle : 0.582 10.159 22134 Z= 0.305 Chirality : 0.042 0.181 2360 Planarity : 0.003 0.045 2818 Dihedral : 10.663 176.660 2242 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 12.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.06 % Allowed : 1.81 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.19), residues: 1932 helix: 1.28 (0.15), residues: 1126 sheet: -0.34 (0.41), residues: 132 loop : 0.25 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 124 HIS 0.016 0.001 HIS C 201 PHE 0.024 0.002 PHE A 171 TYR 0.023 0.001 TYR D 130 ARG 0.010 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 871) hydrogen bonds : angle 4.79785 ( 2571) covalent geometry : bond 0.00320 (16386) covalent geometry : angle 0.58199 (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 664 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 663 time to evaluate : 1.991 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 28 LYS cc_start: 0.9572 (mmtt) cc_final: 0.9263 (mmtm) REVERT: A 31 GLU cc_start: 0.9045 (mp0) cc_final: 0.8706 (mp0) REVERT: A 106 LEU cc_start: 0.9409 (tp) cc_final: 0.9195 (tp) REVERT: A 118 TYR cc_start: 0.8843 (t80) cc_final: 0.8294 (t80) REVERT: A 119 GLU cc_start: 0.8883 (mp0) cc_final: 0.8471 (mp0) REVERT: A 143 LEU cc_start: 0.9257 (tp) cc_final: 0.8991 (tp) REVERT: A 148 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8533 (mt-10) REVERT: A 158 ASN cc_start: 0.9362 (m-40) cc_final: 0.9096 (m-40) REVERT: A 164 ARG cc_start: 0.8785 (ptt90) cc_final: 0.8552 (ptt90) REVERT: A 172 LEU cc_start: 0.9450 (mp) cc_final: 0.9004 (mp) REVERT: A 174 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8026 (mt-10) REVERT: A 181 ASP cc_start: 0.9131 (m-30) cc_final: 0.8620 (m-30) REVERT: A 214 LYS cc_start: 0.9106 (tppt) cc_final: 0.8795 (mmtm) REVERT: A 223 VAL cc_start: 0.9528 (m) cc_final: 0.9119 (p) REVERT: A 227 MET cc_start: 0.9360 (mtp) cc_final: 0.9078 (mtp) REVERT: A 228 LYS cc_start: 0.9371 (mmmt) cc_final: 0.8919 (mmmm) REVERT: A 290 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8558 (tm-30) REVERT: A 317 MET cc_start: 0.8654 (mtp) cc_final: 0.8272 (mtm) REVERT: A 333 LYS cc_start: 0.9395 (tppp) cc_final: 0.9065 (tptm) REVERT: A 355 TYR cc_start: 0.8971 (m-10) cc_final: 0.8625 (m-10) REVERT: A 366 LYS cc_start: 0.9451 (mtmt) cc_final: 0.9183 (mtmm) REVERT: A 396 ASP cc_start: 0.8692 (m-30) cc_final: 0.8287 (m-30) REVERT: A 406 ASP cc_start: 0.8168 (m-30) cc_final: 0.7958 (m-30) REVERT: A 413 SER cc_start: 0.8931 (t) cc_final: 0.8624 (t) REVERT: A 421 GLU cc_start: 0.8856 (pp20) cc_final: 0.8562 (pp20) REVERT: A 458 MET cc_start: 0.8857 (mmp) cc_final: 0.8551 (mmm) REVERT: A 483 GLU cc_start: 0.9492 (mp0) cc_final: 0.9262 (mp0) REVERT: A 493 MET cc_start: 0.8795 (tmm) cc_final: 0.8317 (tmm) REVERT: A 515 ASP cc_start: 0.9076 (m-30) cc_final: 0.8828 (m-30) REVERT: A 550 MET cc_start: 0.7436 (mtm) cc_final: 0.7086 (mtp) REVERT: A 583 SER cc_start: 0.9417 (m) cc_final: 0.8973 (t) REVERT: A 595 MET cc_start: 0.9088 (mmp) cc_final: 0.8826 (mmt) REVERT: A 615 MET cc_start: 0.9340 (mmp) cc_final: 0.8771 (mmp) REVERT: A 669 ARG cc_start: 0.9043 (mtm-85) cc_final: 0.8795 (ttm110) REVERT: A 672 LEU cc_start: 0.9275 (mt) cc_final: 0.9008 (mt) REVERT: B 52 LYS cc_start: 0.9455 (tptp) cc_final: 0.9162 (tppt) REVERT: B 67 GLU cc_start: 0.9079 (mp0) cc_final: 0.8768 (pm20) REVERT: B 75 GLU cc_start: 0.9301 (mp0) cc_final: 0.9014 (pm20) REVERT: B 87 LYS cc_start: 0.9348 (tptp) cc_final: 0.8970 (tptp) REVERT: B 119 GLU cc_start: 0.9198 (mp0) cc_final: 0.8748 (mp0) REVERT: B 127 LEU cc_start: 0.9556 (mm) cc_final: 0.9193 (mm) REVERT: B 184 ARG cc_start: 0.9388 (tpp80) cc_final: 0.9082 (tpp-160) REVERT: B 188 ILE cc_start: 0.9569 (mp) cc_final: 0.9337 (mp) REVERT: B 211 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8709 (mm-30) REVERT: B 232 ASN cc_start: 0.9159 (m-40) cc_final: 0.8857 (m-40) REVERT: B 250 TYR cc_start: 0.9117 (m-80) cc_final: 0.8689 (m-80) REVERT: B 260 ASP cc_start: 0.9355 (p0) cc_final: 0.9116 (p0) REVERT: B 286 ASP cc_start: 0.8588 (m-30) cc_final: 0.8174 (m-30) REVERT: B 288 PHE cc_start: 0.9252 (t80) cc_final: 0.9045 (t80) REVERT: B 290 GLU cc_start: 0.9402 (pt0) cc_final: 0.8948 (pp20) REVERT: B 291 LEU cc_start: 0.9654 (mt) cc_final: 0.9147 (mt) REVERT: B 321 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8320 (tm-30) REVERT: B 322 MET cc_start: 0.9159 (mmm) cc_final: 0.8315 (mmm) REVERT: B 333 LYS cc_start: 0.9523 (tttp) cc_final: 0.9260 (ttmm) REVERT: B 348 MET cc_start: 0.9133 (ptt) cc_final: 0.8906 (ptp) REVERT: B 355 TYR cc_start: 0.9057 (m-80) cc_final: 0.8526 (m-80) REVERT: B 362 ASP cc_start: 0.8786 (m-30) cc_final: 0.7949 (m-30) REVERT: B 393 SER cc_start: 0.9534 (m) cc_final: 0.9131 (p) REVERT: B 402 GLU cc_start: 0.8513 (tm-30) cc_final: 0.8144 (tm-30) REVERT: B 410 ASN cc_start: 0.8860 (m110) cc_final: 0.8545 (m110) REVERT: B 415 ASN cc_start: 0.9506 (t0) cc_final: 0.9306 (t0) REVERT: B 459 LYS cc_start: 0.9008 (mmtp) cc_final: 0.8518 (mtmt) REVERT: B 480 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8132 (pp20) REVERT: B 515 ASP cc_start: 0.9323 (m-30) cc_final: 0.8878 (m-30) REVERT: B 550 MET cc_start: 0.8507 (mmt) cc_final: 0.8246 (mmm) REVERT: B 583 SER cc_start: 0.9215 (p) cc_final: 0.8941 (t) REVERT: B 585 SER cc_start: 0.9023 (p) cc_final: 0.8285 (t) REVERT: B 598 MET cc_start: 0.8925 (mtp) cc_final: 0.8689 (mtp) REVERT: B 615 MET cc_start: 0.9213 (mmp) cc_final: 0.8814 (mmp) REVERT: B 626 TYR cc_start: 0.8906 (m-80) cc_final: 0.8051 (m-80) REVERT: B 628 GLU cc_start: 0.9091 (mt-10) cc_final: 0.8587 (mm-30) REVERT: B 632 MET cc_start: 0.8458 (mpp) cc_final: 0.7981 (mpp) REVERT: B 664 THR cc_start: 0.9302 (p) cc_final: 0.9058 (p) REVERT: B 667 LEU cc_start: 0.9343 (tp) cc_final: 0.9014 (tp) REVERT: B 668 ASN cc_start: 0.9248 (m110) cc_final: 0.8961 (m110) REVERT: B 677 ARG cc_start: 0.9264 (mmm-85) cc_final: 0.8793 (mmm-85) REVERT: C 17 PHE cc_start: 0.8090 (p90) cc_final: 0.7166 (p90) REVERT: C 204 TYR cc_start: 0.9358 (t80) cc_final: 0.9116 (t80) REVERT: D 46 TYR cc_start: 0.8647 (m-80) cc_final: 0.8007 (m-80) REVERT: D 105 TYR cc_start: 0.9185 (m-10) cc_final: 0.8409 (m-10) REVERT: D 169 TYR cc_start: 0.9314 (m-80) cc_final: 0.8817 (m-80) REVERT: D 172 PHE cc_start: 0.9039 (m-80) cc_final: 0.8630 (m-80) REVERT: D 204 TYR cc_start: 0.9600 (t80) cc_final: 0.9294 (t80) outliers start: 1 outliers final: 1 residues processed: 664 average time/residue: 0.2706 time to fit residues: 265.4268 Evaluate side-chains 591 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 590 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 31 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 156 optimal weight: 6.9990 chunk 21 optimal weight: 8.9990 chunk 115 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 169 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 177 optimal weight: 8.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 109 ASN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 180 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 232 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN C 25 ASN ** C 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.134387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.094476 restraints weight = 41277.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.098060 restraints weight = 22928.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.100484 restraints weight = 14707.455| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.6622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16386 Z= 0.220 Angle : 0.641 9.460 22134 Z= 0.335 Chirality : 0.043 0.174 2360 Planarity : 0.004 0.041 2818 Dihedral : 10.759 174.342 2242 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.87 (0.19), residues: 1932 helix: 1.08 (0.15), residues: 1149 sheet: -0.32 (0.42), residues: 136 loop : 0.06 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 623 HIS 0.017 0.002 HIS C 201 PHE 0.022 0.002 PHE A 171 TYR 0.022 0.002 TYR A 684 ARG 0.007 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03953 ( 871) hydrogen bonds : angle 4.98166 ( 2571) covalent geometry : bond 0.00471 (16386) covalent geometry : angle 0.64070 (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 645 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 645 time to evaluate : 1.915 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 28 LYS cc_start: 0.9576 (mmtt) cc_final: 0.9237 (mmmm) REVERT: A 31 GLU cc_start: 0.9046 (mp0) cc_final: 0.8666 (mp0) REVERT: A 119 GLU cc_start: 0.8961 (mp0) cc_final: 0.8577 (mp0) REVERT: A 142 ASN cc_start: 0.9258 (m-40) cc_final: 0.8908 (m110) REVERT: A 143 LEU cc_start: 0.9249 (tp) cc_final: 0.9041 (tp) REVERT: A 147 GLN cc_start: 0.8860 (mm110) cc_final: 0.8446 (mm110) REVERT: A 148 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8526 (mt-10) REVERT: A 158 ASN cc_start: 0.9389 (m-40) cc_final: 0.9111 (m-40) REVERT: A 172 LEU cc_start: 0.9509 (mp) cc_final: 0.9189 (mp) REVERT: A 173 LEU cc_start: 0.9666 (mt) cc_final: 0.9137 (mt) REVERT: A 174 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8185 (mt-10) REVERT: A 181 ASP cc_start: 0.8983 (m-30) cc_final: 0.8687 (m-30) REVERT: A 191 GLN cc_start: 0.9020 (mm-40) cc_final: 0.8641 (mp10) REVERT: A 223 VAL cc_start: 0.9540 (m) cc_final: 0.9156 (p) REVERT: A 227 MET cc_start: 0.9334 (mtp) cc_final: 0.9071 (mtp) REVERT: A 255 HIS cc_start: 0.8678 (t-90) cc_final: 0.8441 (t-90) REVERT: A 286 ASP cc_start: 0.8812 (m-30) cc_final: 0.8572 (m-30) REVERT: A 290 GLU cc_start: 0.8933 (tm-30) cc_final: 0.8471 (tm-30) REVERT: A 291 LEU cc_start: 0.9515 (mt) cc_final: 0.9313 (mt) REVERT: A 333 LYS cc_start: 0.9531 (tppp) cc_final: 0.9294 (tppp) REVERT: A 345 LYS cc_start: 0.9486 (mmmt) cc_final: 0.9053 (tttt) REVERT: A 355 TYR cc_start: 0.8832 (m-10) cc_final: 0.8508 (m-10) REVERT: A 362 ASP cc_start: 0.8409 (m-30) cc_final: 0.8028 (m-30) REVERT: A 366 LYS cc_start: 0.9443 (mtmt) cc_final: 0.9221 (mtmm) REVERT: A 385 VAL cc_start: 0.9516 (t) cc_final: 0.9303 (t) REVERT: A 396 ASP cc_start: 0.8808 (m-30) cc_final: 0.8425 (m-30) REVERT: A 406 ASP cc_start: 0.8176 (m-30) cc_final: 0.7713 (m-30) REVERT: A 421 GLU cc_start: 0.8869 (pp20) cc_final: 0.8547 (pp20) REVERT: A 446 ARG cc_start: 0.8098 (mmt90) cc_final: 0.7768 (mmt90) REVERT: A 458 MET cc_start: 0.8965 (mmp) cc_final: 0.8565 (mmp) REVERT: A 483 GLU cc_start: 0.9524 (mp0) cc_final: 0.9248 (mp0) REVERT: A 493 MET cc_start: 0.8832 (tmm) cc_final: 0.8261 (tmm) REVERT: A 515 ASP cc_start: 0.9110 (m-30) cc_final: 0.8832 (m-30) REVERT: A 583 SER cc_start: 0.9418 (m) cc_final: 0.9010 (t) REVERT: A 615 MET cc_start: 0.9330 (mmp) cc_final: 0.8696 (mmm) REVERT: A 632 MET cc_start: 0.8200 (mtm) cc_final: 0.7999 (mtp) REVERT: A 639 ASP cc_start: 0.9182 (m-30) cc_final: 0.8931 (m-30) REVERT: A 672 LEU cc_start: 0.9328 (mt) cc_final: 0.9057 (mt) REVERT: B 51 LEU cc_start: 0.9395 (tp) cc_final: 0.9177 (tp) REVERT: B 52 LYS cc_start: 0.9444 (tptp) cc_final: 0.9201 (tppt) REVERT: B 55 LEU cc_start: 0.9703 (mt) cc_final: 0.9493 (mt) REVERT: B 75 GLU cc_start: 0.9283 (mp0) cc_final: 0.8995 (pm20) REVERT: B 87 LYS cc_start: 0.9362 (tptp) cc_final: 0.8994 (tptp) REVERT: B 95 MET cc_start: 0.9239 (tpp) cc_final: 0.8907 (tpp) REVERT: B 119 GLU cc_start: 0.9283 (mp0) cc_final: 0.8860 (mp0) REVERT: B 127 LEU cc_start: 0.9585 (mm) cc_final: 0.9197 (mm) REVERT: B 184 ARG cc_start: 0.9438 (tpp80) cc_final: 0.9147 (tpp-160) REVERT: B 188 ILE cc_start: 0.9615 (mp) cc_final: 0.9411 (mp) REVERT: B 211 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8620 (mm-30) REVERT: B 228 LYS cc_start: 0.9320 (mmmm) cc_final: 0.8928 (tppt) REVERT: B 250 TYR cc_start: 0.9153 (m-80) cc_final: 0.8773 (m-80) REVERT: B 260 ASP cc_start: 0.9475 (p0) cc_final: 0.9186 (p0) REVERT: B 286 ASP cc_start: 0.8656 (m-30) cc_final: 0.8252 (m-30) REVERT: B 288 PHE cc_start: 0.9277 (t80) cc_final: 0.9021 (t80) REVERT: B 291 LEU cc_start: 0.9635 (mt) cc_final: 0.9174 (mt) REVERT: B 322 MET cc_start: 0.9153 (mmm) cc_final: 0.8225 (mmm) REVERT: B 333 LYS cc_start: 0.9495 (tttp) cc_final: 0.9196 (ttmm) REVERT: B 348 MET cc_start: 0.9142 (ptt) cc_final: 0.8549 (ptp) REVERT: B 355 TYR cc_start: 0.9015 (m-80) cc_final: 0.8559 (m-80) REVERT: B 362 ASP cc_start: 0.8766 (m-30) cc_final: 0.7891 (m-30) REVERT: B 391 VAL cc_start: 0.9318 (p) cc_final: 0.9095 (p) REVERT: B 393 SER cc_start: 0.9472 (m) cc_final: 0.9186 (p) REVERT: B 402 GLU cc_start: 0.8566 (tm-30) cc_final: 0.8142 (tm-30) REVERT: B 410 ASN cc_start: 0.8996 (m110) cc_final: 0.8624 (m110) REVERT: B 415 ASN cc_start: 0.9586 (t0) cc_final: 0.9347 (t0) REVERT: B 459 LYS cc_start: 0.9099 (mmtp) cc_final: 0.8775 (mppt) REVERT: B 480 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8192 (pp20) REVERT: B 487 PHE cc_start: 0.9678 (t80) cc_final: 0.9402 (t80) REVERT: B 515 ASP cc_start: 0.9341 (m-30) cc_final: 0.8893 (m-30) REVERT: B 550 MET cc_start: 0.8560 (mmt) cc_final: 0.8323 (mmm) REVERT: B 574 TYR cc_start: 0.8802 (m-80) cc_final: 0.8337 (m-10) REVERT: B 585 SER cc_start: 0.9061 (p) cc_final: 0.8427 (t) REVERT: B 615 MET cc_start: 0.9309 (mmp) cc_final: 0.8849 (mmp) REVERT: B 626 TYR cc_start: 0.9140 (m-80) cc_final: 0.8581 (m-80) REVERT: B 628 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8594 (mt-10) REVERT: B 632 MET cc_start: 0.8421 (mpp) cc_final: 0.8047 (mpp) REVERT: B 636 LYS cc_start: 0.9577 (mmtm) cc_final: 0.9264 (mmmm) REVERT: B 664 THR cc_start: 0.9376 (p) cc_final: 0.9137 (p) REVERT: B 667 LEU cc_start: 0.9395 (tp) cc_final: 0.9150 (tp) REVERT: B 668 ASN cc_start: 0.9302 (m110) cc_final: 0.8991 (m110) REVERT: B 677 ARG cc_start: 0.9259 (mmm-85) cc_final: 0.8756 (mmm-85) REVERT: C 17 PHE cc_start: 0.8064 (p90) cc_final: 0.7165 (p90) REVERT: C 154 PHE cc_start: 0.8299 (t80) cc_final: 0.7880 (t80) REVERT: C 204 TYR cc_start: 0.9354 (t80) cc_final: 0.9139 (t80) REVERT: C 281 ASP cc_start: 0.8708 (t0) cc_final: 0.7912 (p0) REVERT: D 46 TYR cc_start: 0.8654 (m-80) cc_final: 0.7981 (m-80) REVERT: D 169 TYR cc_start: 0.9423 (m-80) cc_final: 0.8893 (m-80) REVERT: D 172 PHE cc_start: 0.9135 (m-80) cc_final: 0.8671 (m-80) REVERT: D 204 TYR cc_start: 0.9590 (t80) cc_final: 0.9300 (t80) REVERT: D 259 PHE cc_start: 0.8064 (t80) cc_final: 0.7840 (t80) outliers start: 0 outliers final: 0 residues processed: 645 average time/residue: 0.2723 time to fit residues: 260.1170 Evaluate side-chains 573 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 573 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 39 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 chunk 23 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 175 optimal weight: 10.0000 chunk 24 optimal weight: 0.7980 chunk 5 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN A 646 GLN ** A 647 HIS ** 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 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 180 ASN B 320 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.138430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.098374 restraints weight = 40765.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.102096 restraints weight = 22509.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.104589 restraints weight = 14276.416| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3218 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3218 r_free = 0.3218 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3218 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.6869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16386 Z= 0.168 Angle : 0.619 8.769 22134 Z= 0.324 Chirality : 0.043 0.186 2360 Planarity : 0.003 0.054 2818 Dihedral : 10.680 172.758 2242 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.83 (0.19), residues: 1932 helix: 1.06 (0.15), residues: 1152 sheet: -0.25 (0.42), residues: 136 loop : -0.01 (0.24), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 124 HIS 0.013 0.001 HIS C 201 PHE 0.021 0.002 PHE B 491 TYR 0.023 0.002 TYR B 527 ARG 0.008 0.001 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 871) hydrogen bonds : angle 4.91882 ( 2571) covalent geometry : bond 0.00370 (16386) covalent geometry : angle 0.61888 (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 652 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 652 time to evaluate : 1.700 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 28 LYS cc_start: 0.9560 (mmtt) cc_final: 0.9198 (mmmm) REVERT: A 31 GLU cc_start: 0.9070 (mp0) cc_final: 0.8663 (mp0) REVERT: A 93 SER cc_start: 0.9452 (t) cc_final: 0.9240 (p) REVERT: A 106 LEU cc_start: 0.9399 (tp) cc_final: 0.9141 (tp) REVERT: A 119 GLU cc_start: 0.8917 (mp0) cc_final: 0.8566 (mp0) REVERT: A 142 ASN cc_start: 0.9273 (m-40) cc_final: 0.8882 (m110) REVERT: A 148 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8500 (mt-10) REVERT: A 158 ASN cc_start: 0.9401 (m-40) cc_final: 0.9128 (m-40) REVERT: A 172 LEU cc_start: 0.9485 (mp) cc_final: 0.9200 (mp) REVERT: A 174 GLU cc_start: 0.8475 (mt-10) cc_final: 0.7846 (mt-10) REVERT: A 181 ASP cc_start: 0.8935 (m-30) cc_final: 0.8670 (m-30) REVERT: A 223 VAL cc_start: 0.9510 (m) cc_final: 0.9116 (p) REVERT: A 227 MET cc_start: 0.9307 (mtp) cc_final: 0.9078 (mtp) REVERT: A 228 LYS cc_start: 0.9212 (mmmm) cc_final: 0.8912 (mmmm) REVERT: A 232 ASN cc_start: 0.8781 (m110) cc_final: 0.8191 (m110) REVERT: A 277 THR cc_start: 0.8592 (p) cc_final: 0.8123 (t) REVERT: A 286 ASP cc_start: 0.8769 (m-30) cc_final: 0.8539 (m-30) REVERT: A 290 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8440 (tm-30) REVERT: A 291 LEU cc_start: 0.9513 (mt) cc_final: 0.9268 (mt) REVERT: A 333 LYS cc_start: 0.9527 (tppp) cc_final: 0.9327 (tppp) REVERT: A 345 LYS cc_start: 0.9495 (mmmt) cc_final: 0.9097 (tttt) REVERT: A 362 ASP cc_start: 0.8433 (m-30) cc_final: 0.8127 (m-30) REVERT: A 366 LYS cc_start: 0.9444 (mtmt) cc_final: 0.9194 (mtmm) REVERT: A 396 ASP cc_start: 0.8793 (m-30) cc_final: 0.8339 (m-30) REVERT: A 405 LEU cc_start: 0.8530 (mt) cc_final: 0.8272 (mt) REVERT: A 421 GLU cc_start: 0.8887 (pp20) cc_final: 0.8571 (pp20) REVERT: A 446 ARG cc_start: 0.8151 (mmt90) cc_final: 0.7793 (mmt90) REVERT: A 458 MET cc_start: 0.8949 (mmp) cc_final: 0.8530 (mmp) REVERT: A 483 GLU cc_start: 0.9509 (mp0) cc_final: 0.9246 (mp0) REVERT: A 493 MET cc_start: 0.8769 (tmm) cc_final: 0.8213 (tmm) REVERT: A 515 ASP cc_start: 0.9077 (m-30) cc_final: 0.8793 (m-30) REVERT: A 583 SER cc_start: 0.9392 (m) cc_final: 0.8994 (t) REVERT: A 615 MET cc_start: 0.9342 (mmp) cc_final: 0.8706 (mmm) REVERT: A 639 ASP cc_start: 0.9126 (m-30) cc_final: 0.8886 (m-30) REVERT: A 672 LEU cc_start: 0.9304 (mt) cc_final: 0.9069 (mt) REVERT: B 51 LEU cc_start: 0.9345 (tp) cc_final: 0.9034 (tp) REVERT: B 52 LYS cc_start: 0.9446 (tptp) cc_final: 0.9194 (tppt) REVERT: B 55 LEU cc_start: 0.9702 (mt) cc_final: 0.9445 (mt) REVERT: B 75 GLU cc_start: 0.9288 (mp0) cc_final: 0.8973 (pm20) REVERT: B 87 LYS cc_start: 0.9327 (tptp) cc_final: 0.8994 (tptp) REVERT: B 95 MET cc_start: 0.9176 (tpp) cc_final: 0.8865 (tpp) REVERT: B 119 GLU cc_start: 0.9189 (mp0) cc_final: 0.8783 (mp0) REVERT: B 127 LEU cc_start: 0.9575 (mm) cc_final: 0.9192 (mm) REVERT: B 174 GLU cc_start: 0.7634 (tp30) cc_final: 0.7168 (tp30) REVERT: B 202 ASN cc_start: 0.9231 (t0) cc_final: 0.8047 (t0) REVERT: B 211 GLU cc_start: 0.9094 (mm-30) cc_final: 0.8629 (mm-30) REVERT: B 250 TYR cc_start: 0.9127 (m-80) cc_final: 0.8513 (m-80) REVERT: B 260 ASP cc_start: 0.9454 (p0) cc_final: 0.9190 (p0) REVERT: B 286 ASP cc_start: 0.8615 (m-30) cc_final: 0.8298 (m-30) REVERT: B 288 PHE cc_start: 0.9265 (t80) cc_final: 0.9057 (t80) REVERT: B 291 LEU cc_start: 0.9547 (mt) cc_final: 0.9283 (mt) REVERT: B 322 MET cc_start: 0.9151 (mmm) cc_final: 0.8221 (mmm) REVERT: B 333 LYS cc_start: 0.9513 (tttp) cc_final: 0.9201 (ttmm) REVERT: B 348 MET cc_start: 0.9016 (ptt) cc_final: 0.8580 (ptp) REVERT: B 355 TYR cc_start: 0.9020 (m-80) cc_final: 0.8441 (m-10) REVERT: B 361 GLN cc_start: 0.9083 (tt0) cc_final: 0.8848 (tp-100) REVERT: B 379 SER cc_start: 0.9185 (t) cc_final: 0.8901 (t) REVERT: B 410 ASN cc_start: 0.8918 (m110) cc_final: 0.8526 (m110) REVERT: B 459 LYS cc_start: 0.9094 (mmtp) cc_final: 0.8581 (mtmt) REVERT: B 472 LEU cc_start: 0.9557 (mm) cc_final: 0.9214 (mm) REVERT: B 480 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8162 (pp20) REVERT: B 487 PHE cc_start: 0.9685 (t80) cc_final: 0.9421 (t80) REVERT: B 515 ASP cc_start: 0.9292 (m-30) cc_final: 0.8880 (m-30) REVERT: B 550 MET cc_start: 0.8573 (mmt) cc_final: 0.8355 (mmm) REVERT: B 574 TYR cc_start: 0.8677 (m-80) cc_final: 0.8432 (m-10) REVERT: B 585 SER cc_start: 0.9057 (p) cc_final: 0.8370 (t) REVERT: B 602 GLU cc_start: 0.8042 (pt0) cc_final: 0.7834 (pt0) REVERT: B 615 MET cc_start: 0.9276 (mmp) cc_final: 0.8776 (mmp) REVERT: B 626 TYR cc_start: 0.8820 (m-80) cc_final: 0.8194 (m-80) REVERT: B 628 GLU cc_start: 0.9045 (mt-10) cc_final: 0.8520 (mm-30) REVERT: B 632 MET cc_start: 0.8449 (mpp) cc_final: 0.8188 (mpp) REVERT: B 636 LYS cc_start: 0.9585 (mmtm) cc_final: 0.9287 (mmmm) REVERT: B 650 GLN cc_start: 0.8676 (mt0) cc_final: 0.8330 (mt0) REVERT: B 664 THR cc_start: 0.9369 (p) cc_final: 0.9115 (p) REVERT: B 668 ASN cc_start: 0.9248 (m110) cc_final: 0.8927 (m110) REVERT: B 677 ARG cc_start: 0.9259 (mmm-85) cc_final: 0.8758 (mmm-85) REVERT: C 17 PHE cc_start: 0.8071 (p90) cc_final: 0.7333 (p90) REVERT: C 154 PHE cc_start: 0.8265 (t80) cc_final: 0.7843 (t80) REVERT: C 281 ASP cc_start: 0.8625 (t0) cc_final: 0.7892 (p0) REVERT: C 315 LEU cc_start: 0.9028 (tp) cc_final: 0.8778 (tp) REVERT: D 27 LYS cc_start: 0.9137 (pttp) cc_final: 0.8761 (pttm) REVERT: D 45 LYS cc_start: 0.8703 (pttt) cc_final: 0.8327 (pttt) REVERT: D 46 TYR cc_start: 0.8664 (m-80) cc_final: 0.8080 (m-80) REVERT: D 169 TYR cc_start: 0.9435 (m-80) cc_final: 0.8974 (m-80) REVERT: D 172 PHE cc_start: 0.9137 (m-80) cc_final: 0.8710 (m-80) REVERT: D 259 PHE cc_start: 0.8017 (t80) cc_final: 0.7695 (t80) REVERT: D 269 MET cc_start: 0.9279 (mtm) cc_final: 0.9077 (mtm) outliers start: 0 outliers final: 0 residues processed: 652 average time/residue: 0.2699 time to fit residues: 261.1617 Evaluate side-chains 568 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 568 time to evaluate : 1.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 96 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 159 optimal weight: 20.0000 chunk 72 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 52 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN C 25 ASN ** D 210 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 = 0.3762 r_free = 0.3762 target = 0.138350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.098827 restraints weight = 40485.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.102484 restraints weight = 22299.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.104947 restraints weight = 14269.806| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.7064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16386 Z= 0.175 Angle : 0.647 9.860 22134 Z= 0.338 Chirality : 0.044 0.207 2360 Planarity : 0.003 0.046 2818 Dihedral : 10.574 170.416 2242 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.76 (0.19), residues: 1932 helix: 1.01 (0.15), residues: 1148 sheet: -0.25 (0.42), residues: 136 loop : -0.06 (0.24), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 124 HIS 0.013 0.001 HIS C 201 PHE 0.027 0.002 PHE D 178 TYR 0.043 0.002 TYR C 142 ARG 0.008 0.001 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.03925 ( 871) hydrogen bonds : angle 5.00200 ( 2571) covalent geometry : bond 0.00389 (16386) covalent geometry : angle 0.64716 (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 653 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 653 time to evaluate : 1.885 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 28 LYS cc_start: 0.9539 (mmtt) cc_final: 0.9134 (mmmm) REVERT: A 31 GLU cc_start: 0.9084 (mp0) cc_final: 0.8654 (mp0) REVERT: A 93 SER cc_start: 0.9443 (t) cc_final: 0.9221 (p) REVERT: A 119 GLU cc_start: 0.8862 (mp0) cc_final: 0.8527 (mp0) REVERT: A 142 ASN cc_start: 0.9266 (m-40) cc_final: 0.8870 (m110) REVERT: A 147 GLN cc_start: 0.8764 (mm110) cc_final: 0.8502 (mm-40) REVERT: A 148 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8540 (mt-10) REVERT: A 158 ASN cc_start: 0.9389 (m-40) cc_final: 0.9117 (m-40) REVERT: A 172 LEU cc_start: 0.9527 (mp) cc_final: 0.9291 (mp) REVERT: A 174 GLU cc_start: 0.8388 (mt-10) cc_final: 0.7767 (mt-10) REVERT: A 181 ASP cc_start: 0.8865 (m-30) cc_final: 0.8610 (m-30) REVERT: A 223 VAL cc_start: 0.9523 (m) cc_final: 0.9123 (p) REVERT: A 227 MET cc_start: 0.9298 (mtp) cc_final: 0.9069 (mtp) REVERT: A 286 ASP cc_start: 0.8789 (m-30) cc_final: 0.8543 (m-30) REVERT: A 290 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8465 (tm-30) REVERT: A 291 LEU cc_start: 0.9489 (mt) cc_final: 0.9247 (mt) REVERT: A 333 LYS cc_start: 0.9514 (tppp) cc_final: 0.9296 (tppp) REVERT: A 355 TYR cc_start: 0.8903 (m-10) cc_final: 0.8632 (m-10) REVERT: A 362 ASP cc_start: 0.8444 (m-30) cc_final: 0.8122 (m-30) REVERT: A 366 LYS cc_start: 0.9467 (mtmt) cc_final: 0.9222 (mtmm) REVERT: A 383 SER cc_start: 0.9197 (p) cc_final: 0.8967 (p) REVERT: A 396 ASP cc_start: 0.8806 (m-30) cc_final: 0.8371 (m-30) REVERT: A 421 GLU cc_start: 0.8867 (pp20) cc_final: 0.8532 (pp20) REVERT: A 458 MET cc_start: 0.8872 (mmp) cc_final: 0.8579 (mmm) REVERT: A 483 GLU cc_start: 0.9517 (mp0) cc_final: 0.9230 (mp0) REVERT: A 493 MET cc_start: 0.8809 (tmm) cc_final: 0.8396 (tmm) REVERT: A 515 ASP cc_start: 0.9075 (m-30) cc_final: 0.8823 (m-30) REVERT: A 550 MET cc_start: 0.7977 (ptp) cc_final: 0.7775 (mtp) REVERT: A 583 SER cc_start: 0.9368 (m) cc_final: 0.8962 (t) REVERT: A 615 MET cc_start: 0.9307 (mmp) cc_final: 0.8607 (mmm) REVERT: A 639 ASP cc_start: 0.9094 (m-30) cc_final: 0.8893 (m-30) REVERT: A 672 LEU cc_start: 0.9319 (mt) cc_final: 0.9073 (mt) REVERT: A 680 LYS cc_start: 0.9264 (mttt) cc_final: 0.8903 (mttt) REVERT: B 51 LEU cc_start: 0.9372 (tp) cc_final: 0.9089 (tp) REVERT: B 52 LYS cc_start: 0.9453 (tptp) cc_final: 0.9228 (tppt) REVERT: B 55 LEU cc_start: 0.9709 (mt) cc_final: 0.9466 (mt) REVERT: B 75 GLU cc_start: 0.9287 (mp0) cc_final: 0.8986 (pm20) REVERT: B 87 LYS cc_start: 0.9345 (tptp) cc_final: 0.9022 (tptp) REVERT: B 95 MET cc_start: 0.9125 (tpp) cc_final: 0.8786 (tpp) REVERT: B 119 GLU cc_start: 0.9188 (mp0) cc_final: 0.8770 (mp0) REVERT: B 127 LEU cc_start: 0.9572 (mm) cc_final: 0.9190 (mm) REVERT: B 184 ARG cc_start: 0.9396 (tpp80) cc_final: 0.9192 (tpp80) REVERT: B 202 ASN cc_start: 0.9211 (t0) cc_final: 0.8728 (t0) REVERT: B 211 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8576 (mm-30) REVERT: B 217 GLU cc_start: 0.8834 (mp0) cc_final: 0.8588 (mp0) REVERT: B 218 ASN cc_start: 0.9475 (m110) cc_final: 0.9011 (t0) REVERT: B 250 TYR cc_start: 0.9240 (m-80) cc_final: 0.8747 (m-80) REVERT: B 260 ASP cc_start: 0.9474 (p0) cc_final: 0.9227 (p0) REVERT: B 286 ASP cc_start: 0.8659 (m-30) cc_final: 0.8429 (m-30) REVERT: B 288 PHE cc_start: 0.9232 (t80) cc_final: 0.9012 (t80) REVERT: B 291 LEU cc_start: 0.9547 (mt) cc_final: 0.9297 (mt) REVERT: B 322 MET cc_start: 0.9172 (mmm) cc_final: 0.8170 (mmm) REVERT: B 333 LYS cc_start: 0.9512 (tttp) cc_final: 0.9194 (ttmm) REVERT: B 348 MET cc_start: 0.8815 (ptt) cc_final: 0.8029 (ptp) REVERT: B 351 SER cc_start: 0.8879 (p) cc_final: 0.8637 (p) REVERT: B 355 TYR cc_start: 0.9029 (m-80) cc_final: 0.8472 (m-10) REVERT: B 361 GLN cc_start: 0.9097 (tt0) cc_final: 0.8773 (tp-100) REVERT: B 375 LYS cc_start: 0.9162 (mmmm) cc_final: 0.8717 (mmmm) REVERT: B 379 SER cc_start: 0.9288 (t) cc_final: 0.8924 (t) REVERT: B 392 SER cc_start: 0.9070 (m) cc_final: 0.8315 (p) REVERT: B 402 GLU cc_start: 0.8597 (tm-30) cc_final: 0.8199 (tm-30) REVERT: B 410 ASN cc_start: 0.8978 (m110) cc_final: 0.8661 (m110) REVERT: B 459 LYS cc_start: 0.9151 (mmtp) cc_final: 0.8812 (mptt) REVERT: B 472 LEU cc_start: 0.9515 (mm) cc_final: 0.9267 (mm) REVERT: B 480 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8114 (pp20) REVERT: B 505 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8536 (mt-10) REVERT: B 515 ASP cc_start: 0.9297 (m-30) cc_final: 0.8772 (m-30) REVERT: B 550 MET cc_start: 0.8534 (mmt) cc_final: 0.8317 (mmm) REVERT: B 574 TYR cc_start: 0.8633 (m-80) cc_final: 0.8316 (m-10) REVERT: B 585 SER cc_start: 0.8976 (p) cc_final: 0.8199 (t) REVERT: B 591 THR cc_start: 0.8853 (p) cc_final: 0.8576 (p) REVERT: B 602 GLU cc_start: 0.8019 (pt0) cc_final: 0.7695 (pt0) REVERT: B 626 TYR cc_start: 0.8850 (m-80) cc_final: 0.8240 (m-80) REVERT: B 628 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8469 (mm-30) REVERT: B 632 MET cc_start: 0.8392 (mpp) cc_final: 0.8160 (mpp) REVERT: B 636 LYS cc_start: 0.9586 (mmtm) cc_final: 0.9336 (mmmm) REVERT: B 656 LEU cc_start: 0.9428 (mt) cc_final: 0.9175 (mt) REVERT: B 664 THR cc_start: 0.9423 (p) cc_final: 0.9109 (p) REVERT: B 668 ASN cc_start: 0.9247 (m110) cc_final: 0.8908 (m110) REVERT: B 677 ARG cc_start: 0.9254 (mmm-85) cc_final: 0.8760 (mmm-85) REVERT: C 17 PHE cc_start: 0.8183 (p90) cc_final: 0.7414 (p90) REVERT: C 87 LYS cc_start: 0.8573 (mtmm) cc_final: 0.8169 (mttt) REVERT: C 149 ASP cc_start: 0.8221 (m-30) cc_final: 0.8004 (m-30) REVERT: C 154 PHE cc_start: 0.8301 (t80) cc_final: 0.7881 (t80) REVERT: C 281 ASP cc_start: 0.8566 (t0) cc_final: 0.7789 (p0) REVERT: C 315 LEU cc_start: 0.8983 (tp) cc_final: 0.8773 (tp) REVERT: D 46 TYR cc_start: 0.8705 (m-80) cc_final: 0.8235 (m-80) REVERT: D 123 GLU cc_start: 0.8909 (mp0) cc_final: 0.8660 (pm20) REVERT: D 169 TYR cc_start: 0.9515 (m-80) cc_final: 0.9078 (m-80) REVERT: D 172 PHE cc_start: 0.9242 (m-80) cc_final: 0.8812 (m-80) REVERT: D 259 PHE cc_start: 0.8051 (t80) cc_final: 0.7814 (t80) outliers start: 0 outliers final: 0 residues processed: 653 average time/residue: 0.2647 time to fit residues: 257.9092 Evaluate side-chains 581 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 581 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 111 optimal weight: 3.9990 chunk 102 optimal weight: 6.9990 chunk 182 optimal weight: 9.9990 chunk 107 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 115 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 188 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** 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 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.137539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.098287 restraints weight = 41052.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.101842 restraints weight = 22266.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.104302 restraints weight = 14236.099| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.7349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16386 Z= 0.188 Angle : 0.687 14.225 22134 Z= 0.358 Chirality : 0.046 0.551 2360 Planarity : 0.004 0.056 2818 Dihedral : 10.498 168.576 2242 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.63 (0.19), residues: 1932 helix: 0.91 (0.15), residues: 1153 sheet: -0.23 (0.43), residues: 136 loop : -0.14 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 30 HIS 0.012 0.001 HIS C 201 PHE 0.021 0.002 PHE D 178 TYR 0.038 0.002 TYR C 142 ARG 0.009 0.001 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 871) hydrogen bonds : angle 5.14485 ( 2571) covalent geometry : bond 0.00413 (16386) covalent geometry : angle 0.68725 (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 640 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 640 time to evaluate : 1.856 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 28 LYS cc_start: 0.9534 (mmtt) cc_final: 0.9116 (mmmm) REVERT: A 31 GLU cc_start: 0.9100 (mp0) cc_final: 0.8640 (mp0) REVERT: A 89 PHE cc_start: 0.9302 (t80) cc_final: 0.9091 (t80) REVERT: A 93 SER cc_start: 0.9447 (t) cc_final: 0.9226 (p) REVERT: A 119 GLU cc_start: 0.8918 (mp0) cc_final: 0.8550 (mp0) REVERT: A 142 ASN cc_start: 0.9266 (m-40) cc_final: 0.8865 (m110) REVERT: A 147 GLN cc_start: 0.8788 (mm110) cc_final: 0.8489 (mm-40) REVERT: A 148 GLU cc_start: 0.8890 (mt-10) cc_final: 0.8533 (mt-10) REVERT: A 158 ASN cc_start: 0.9387 (m-40) cc_final: 0.9124 (m-40) REVERT: A 172 LEU cc_start: 0.9500 (mp) cc_final: 0.9300 (mp) REVERT: A 174 GLU cc_start: 0.8396 (mt-10) cc_final: 0.7814 (mt-10) REVERT: A 181 ASP cc_start: 0.8866 (m-30) cc_final: 0.8432 (m-30) REVERT: A 223 VAL cc_start: 0.9516 (m) cc_final: 0.9086 (p) REVERT: A 227 MET cc_start: 0.9274 (mtp) cc_final: 0.9055 (mtp) REVERT: A 232 ASN cc_start: 0.8908 (m110) cc_final: 0.8234 (m-40) REVERT: A 257 ASP cc_start: 0.9038 (m-30) cc_final: 0.8649 (m-30) REVERT: A 277 THR cc_start: 0.8788 (p) cc_final: 0.8345 (t) REVERT: A 290 GLU cc_start: 0.8946 (tm-30) cc_final: 0.8490 (tm-30) REVERT: A 291 LEU cc_start: 0.9463 (mt) cc_final: 0.9242 (mt) REVERT: A 333 LYS cc_start: 0.9504 (tppp) cc_final: 0.9284 (tppp) REVERT: A 348 MET cc_start: 0.8389 (ptp) cc_final: 0.7990 (ptt) REVERT: A 355 TYR cc_start: 0.8789 (m-10) cc_final: 0.8515 (m-10) REVERT: A 362 ASP cc_start: 0.8461 (m-30) cc_final: 0.8135 (m-30) REVERT: A 366 LYS cc_start: 0.9462 (mtmt) cc_final: 0.9212 (mtmm) REVERT: A 379 SER cc_start: 0.8306 (t) cc_final: 0.7930 (t) REVERT: A 396 ASP cc_start: 0.8813 (m-30) cc_final: 0.8385 (m-30) REVERT: A 421 GLU cc_start: 0.8849 (pp20) cc_final: 0.8516 (pp20) REVERT: A 446 ARG cc_start: 0.8212 (mtp85) cc_final: 0.7664 (mmt180) REVERT: A 458 MET cc_start: 0.8883 (mmp) cc_final: 0.8531 (mmm) REVERT: A 483 GLU cc_start: 0.9519 (mp0) cc_final: 0.9234 (mp0) REVERT: A 493 MET cc_start: 0.8804 (tmm) cc_final: 0.8378 (tmm) REVERT: A 515 ASP cc_start: 0.9083 (m-30) cc_final: 0.8819 (m-30) REVERT: A 583 SER cc_start: 0.9378 (m) cc_final: 0.8974 (t) REVERT: A 615 MET cc_start: 0.9324 (mmp) cc_final: 0.8618 (mmm) REVERT: A 672 LEU cc_start: 0.9315 (mt) cc_final: 0.9075 (mt) REVERT: A 680 LYS cc_start: 0.9251 (mttt) cc_final: 0.8862 (mttt) REVERT: B 51 LEU cc_start: 0.9428 (tp) cc_final: 0.9095 (tp) REVERT: B 52 LYS cc_start: 0.9441 (tptp) cc_final: 0.9225 (tppt) REVERT: B 55 LEU cc_start: 0.9718 (mt) cc_final: 0.9465 (mt) REVERT: B 75 GLU cc_start: 0.9292 (mp0) cc_final: 0.8992 (pm20) REVERT: B 87 LYS cc_start: 0.9348 (tptp) cc_final: 0.9043 (tptp) REVERT: B 95 MET cc_start: 0.9088 (tpp) cc_final: 0.8802 (tpp) REVERT: B 119 GLU cc_start: 0.9235 (mp0) cc_final: 0.8830 (mp0) REVERT: B 127 LEU cc_start: 0.9569 (mm) cc_final: 0.9191 (mm) REVERT: B 184 ARG cc_start: 0.9457 (tpp80) cc_final: 0.9144 (tpp80) REVERT: B 188 ILE cc_start: 0.9615 (mp) cc_final: 0.9379 (mp) REVERT: B 202 ASN cc_start: 0.9203 (t0) cc_final: 0.8805 (t0) REVERT: B 211 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8567 (mm-30) REVERT: B 217 GLU cc_start: 0.8851 (mp0) cc_final: 0.8595 (mp0) REVERT: B 218 ASN cc_start: 0.9470 (m110) cc_final: 0.9012 (t0) REVERT: B 250 TYR cc_start: 0.9239 (m-80) cc_final: 0.8702 (m-80) REVERT: B 260 ASP cc_start: 0.9477 (p0) cc_final: 0.9233 (p0) REVERT: B 286 ASP cc_start: 0.8747 (m-30) cc_final: 0.8451 (m-30) REVERT: B 291 LEU cc_start: 0.9558 (mt) cc_final: 0.9335 (mt) REVERT: B 321 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8173 (tm-30) REVERT: B 322 MET cc_start: 0.9182 (mmm) cc_final: 0.8386 (mmm) REVERT: B 333 LYS cc_start: 0.9505 (tttp) cc_final: 0.9185 (ttmm) REVERT: B 344 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8886 (mm-30) REVERT: B 355 TYR cc_start: 0.9049 (m-80) cc_final: 0.8441 (m-10) REVERT: B 361 GLN cc_start: 0.9068 (tt0) cc_final: 0.8809 (tp-100) REVERT: B 362 ASP cc_start: 0.8846 (m-30) cc_final: 0.8246 (m-30) REVERT: B 375 LYS cc_start: 0.9100 (mmmm) cc_final: 0.8638 (mmmm) REVERT: B 379 SER cc_start: 0.9280 (t) cc_final: 0.8959 (t) REVERT: B 392 SER cc_start: 0.8940 (m) cc_final: 0.8285 (p) REVERT: B 403 ILE cc_start: 0.9408 (mm) cc_final: 0.9188 (mm) REVERT: B 410 ASN cc_start: 0.8918 (m110) cc_final: 0.8648 (m110) REVERT: B 459 LYS cc_start: 0.9112 (mmtp) cc_final: 0.8826 (mptt) REVERT: B 472 LEU cc_start: 0.9496 (mm) cc_final: 0.9216 (mm) REVERT: B 480 GLU cc_start: 0.8546 (mt-10) cc_final: 0.8201 (pp20) REVERT: B 505 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8420 (mt-10) REVERT: B 515 ASP cc_start: 0.9295 (m-30) cc_final: 0.8757 (m-30) REVERT: B 550 MET cc_start: 0.8553 (mmt) cc_final: 0.8326 (mmm) REVERT: B 585 SER cc_start: 0.9065 (p) cc_final: 0.8311 (t) REVERT: B 586 TYR cc_start: 0.9016 (m-80) cc_final: 0.8687 (m-10) REVERT: B 602 GLU cc_start: 0.7771 (pt0) cc_final: 0.7212 (pt0) REVERT: B 626 TYR cc_start: 0.8937 (m-80) cc_final: 0.8243 (m-80) REVERT: B 628 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8787 (mm-30) REVERT: B 636 LYS cc_start: 0.9593 (mmtm) cc_final: 0.9328 (mmmm) REVERT: B 656 LEU cc_start: 0.9448 (mt) cc_final: 0.9174 (mt) REVERT: B 664 THR cc_start: 0.9423 (p) cc_final: 0.9093 (p) REVERT: B 668 ASN cc_start: 0.9177 (m110) cc_final: 0.8883 (m-40) REVERT: B 677 ARG cc_start: 0.9249 (mmm-85) cc_final: 0.8769 (mmm-85) REVERT: C 17 PHE cc_start: 0.8253 (p90) cc_final: 0.7686 (p90) REVERT: C 87 LYS cc_start: 0.8483 (mtmm) cc_final: 0.8234 (mttt) REVERT: C 98 ASN cc_start: 0.7961 (m110) cc_final: 0.7468 (m110) REVERT: C 149 ASP cc_start: 0.8033 (m-30) cc_final: 0.7793 (m-30) REVERT: C 154 PHE cc_start: 0.8392 (t80) cc_final: 0.7893 (t80) REVERT: C 204 TYR cc_start: 0.9230 (t80) cc_final: 0.9026 (t80) REVERT: C 281 ASP cc_start: 0.8611 (t0) cc_final: 0.7841 (p0) REVERT: C 315 LEU cc_start: 0.8998 (tp) cc_final: 0.8729 (tp) REVERT: D 27 LYS cc_start: 0.9269 (pttp) cc_final: 0.9043 (pttm) REVERT: D 46 TYR cc_start: 0.8809 (m-80) cc_final: 0.8131 (m-80) REVERT: D 169 TYR cc_start: 0.9482 (m-80) cc_final: 0.9129 (m-80) REVERT: D 172 PHE cc_start: 0.9173 (m-80) cc_final: 0.8803 (m-80) REVERT: D 173 TYR cc_start: 0.8183 (t80) cc_final: 0.7588 (t80) REVERT: D 259 PHE cc_start: 0.8041 (t80) cc_final: 0.7682 (t80) REVERT: D 313 GLU cc_start: 0.8747 (mp0) cc_final: 0.8379 (mp0) outliers start: 0 outliers final: 0 residues processed: 640 average time/residue: 0.2749 time to fit residues: 262.7758 Evaluate side-chains 571 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 571 time to evaluate : 1.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 137 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 chunk 160 optimal weight: 20.0000 chunk 106 optimal weight: 2.9990 chunk 120 optimal weight: 0.8980 chunk 135 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 127 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** 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 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN C 91 ASN ** C 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 GLN ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.138959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.100175 restraints weight = 40930.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.103806 restraints weight = 22518.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.106278 restraints weight = 14420.806| |-----------------------------------------------------------------------------| r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.7547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 16386 Z= 0.159 Angle : 0.678 14.059 22134 Z= 0.354 Chirality : 0.045 0.409 2360 Planarity : 0.004 0.054 2818 Dihedral : 10.323 166.849 2242 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.19), residues: 1932 helix: 0.81 (0.15), residues: 1151 sheet: -0.25 (0.43), residues: 132 loop : -0.21 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 124 HIS 0.012 0.001 HIS C 201 PHE 0.022 0.002 PHE D 178 TYR 0.035 0.002 TYR C 142 ARG 0.009 0.001 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.04125 ( 871) hydrogen bonds : angle 5.16773 ( 2571) covalent geometry : bond 0.00353 (16386) covalent geometry : angle 0.67806 (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 629 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 629 time to evaluate : 1.914 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 28 LYS cc_start: 0.9540 (mmtt) cc_final: 0.9110 (mmmm) REVERT: A 31 GLU cc_start: 0.9090 (mp0) cc_final: 0.8636 (mp0) REVERT: A 93 SER cc_start: 0.9404 (t) cc_final: 0.9175 (p) REVERT: A 119 GLU cc_start: 0.8816 (mp0) cc_final: 0.8472 (mp0) REVERT: A 136 LYS cc_start: 0.9382 (tptt) cc_final: 0.9000 (tptm) REVERT: A 143 LEU cc_start: 0.9175 (tp) cc_final: 0.8955 (tp) REVERT: A 147 GLN cc_start: 0.8725 (mm110) cc_final: 0.8518 (mm-40) REVERT: A 148 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8536 (mt-10) REVERT: A 158 ASN cc_start: 0.9390 (m-40) cc_final: 0.9189 (m-40) REVERT: A 174 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7769 (mt-10) REVERT: A 181 ASP cc_start: 0.8723 (m-30) cc_final: 0.8521 (m-30) REVERT: A 195 LEU cc_start: 0.9461 (mt) cc_final: 0.9216 (mt) REVERT: A 223 VAL cc_start: 0.9506 (m) cc_final: 0.9080 (p) REVERT: A 227 MET cc_start: 0.9263 (mtp) cc_final: 0.9052 (mtp) REVERT: A 232 ASN cc_start: 0.8635 (m110) cc_final: 0.8180 (m110) REVERT: A 257 ASP cc_start: 0.9189 (m-30) cc_final: 0.8728 (m-30) REVERT: A 277 THR cc_start: 0.8722 (p) cc_final: 0.8309 (t) REVERT: A 290 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8456 (tm-30) REVERT: A 291 LEU cc_start: 0.9468 (mt) cc_final: 0.9174 (mt) REVERT: A 333 LYS cc_start: 0.9471 (tppp) cc_final: 0.9255 (tppp) REVERT: A 348 MET cc_start: 0.8474 (ptp) cc_final: 0.8010 (ptt) REVERT: A 355 TYR cc_start: 0.8758 (m-10) cc_final: 0.8526 (m-10) REVERT: A 366 LYS cc_start: 0.9483 (mtmt) cc_final: 0.9223 (mtmm) REVERT: A 396 ASP cc_start: 0.8549 (m-30) cc_final: 0.8023 (m-30) REVERT: A 402 GLU cc_start: 0.8973 (tp30) cc_final: 0.8625 (tp30) REVERT: A 418 ASN cc_start: 0.9242 (m-40) cc_final: 0.8815 (m-40) REVERT: A 421 GLU cc_start: 0.8711 (pp20) cc_final: 0.8349 (pp20) REVERT: A 427 LYS cc_start: 0.9256 (ttpt) cc_final: 0.9000 (ttpt) REVERT: A 446 ARG cc_start: 0.8187 (mtp85) cc_final: 0.7605 (mmt180) REVERT: A 458 MET cc_start: 0.8859 (mmp) cc_final: 0.8521 (mmm) REVERT: A 483 GLU cc_start: 0.9523 (mp0) cc_final: 0.9231 (mp0) REVERT: A 493 MET cc_start: 0.8829 (tmm) cc_final: 0.8254 (tmm) REVERT: A 515 ASP cc_start: 0.9069 (m-30) cc_final: 0.8849 (m-30) REVERT: A 583 SER cc_start: 0.9344 (m) cc_final: 0.8930 (t) REVERT: A 615 MET cc_start: 0.9247 (mmp) cc_final: 0.8518 (mmm) REVERT: A 646 GLN cc_start: 0.9397 (pt0) cc_final: 0.9019 (pt0) REVERT: A 672 LEU cc_start: 0.9254 (mt) cc_final: 0.8994 (mt) REVERT: A 680 LYS cc_start: 0.9223 (mttt) cc_final: 0.8851 (mttt) REVERT: B 51 LEU cc_start: 0.9434 (tp) cc_final: 0.9116 (tp) REVERT: B 52 LYS cc_start: 0.9442 (tptp) cc_final: 0.9199 (tppt) REVERT: B 55 LEU cc_start: 0.9725 (mt) cc_final: 0.9480 (mt) REVERT: B 75 GLU cc_start: 0.9296 (mp0) cc_final: 0.9007 (pm20) REVERT: B 87 LYS cc_start: 0.9326 (tptp) cc_final: 0.9030 (tptp) REVERT: B 95 MET cc_start: 0.9158 (tpp) cc_final: 0.8746 (tpp) REVERT: B 106 LEU cc_start: 0.9209 (tp) cc_final: 0.8967 (tt) REVERT: B 119 GLU cc_start: 0.9167 (mp0) cc_final: 0.8777 (mp0) REVERT: B 127 LEU cc_start: 0.9562 (mm) cc_final: 0.9181 (mm) REVERT: B 184 ARG cc_start: 0.9437 (tpp80) cc_final: 0.9142 (tpp80) REVERT: B 188 ILE cc_start: 0.9593 (mp) cc_final: 0.9389 (mp) REVERT: B 202 ASN cc_start: 0.9258 (t0) cc_final: 0.8391 (t0) REVERT: B 211 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8540 (mm-30) REVERT: B 217 GLU cc_start: 0.8871 (mp0) cc_final: 0.8600 (mp0) REVERT: B 218 ASN cc_start: 0.9450 (m110) cc_final: 0.9000 (t0) REVERT: B 250 TYR cc_start: 0.9206 (m-80) cc_final: 0.8819 (m-80) REVERT: B 260 ASP cc_start: 0.9465 (p0) cc_final: 0.9238 (p0) REVERT: B 283 VAL cc_start: 0.9561 (t) cc_final: 0.9358 (t) REVERT: B 286 ASP cc_start: 0.8719 (m-30) cc_final: 0.8406 (m-30) REVERT: B 291 LEU cc_start: 0.9524 (mt) cc_final: 0.9321 (mt) REVERT: B 321 GLU cc_start: 0.8381 (tm-30) cc_final: 0.8179 (tm-30) REVERT: B 322 MET cc_start: 0.9178 (mmm) cc_final: 0.8416 (mmm) REVERT: B 333 LYS cc_start: 0.9521 (tttp) cc_final: 0.8983 (tttp) REVERT: B 355 TYR cc_start: 0.9039 (m-80) cc_final: 0.8331 (m-10) REVERT: B 361 GLN cc_start: 0.9024 (tt0) cc_final: 0.8703 (tp-100) REVERT: B 362 ASP cc_start: 0.8814 (m-30) cc_final: 0.8214 (m-30) REVERT: B 375 LYS cc_start: 0.9038 (mmmm) cc_final: 0.8544 (mmmm) REVERT: B 378 PHE cc_start: 0.9210 (p90) cc_final: 0.8856 (p90) REVERT: B 379 SER cc_start: 0.9349 (t) cc_final: 0.8970 (t) REVERT: B 392 SER cc_start: 0.9141 (m) cc_final: 0.8172 (p) REVERT: B 410 ASN cc_start: 0.8696 (m110) cc_final: 0.8407 (m110) REVERT: B 459 LYS cc_start: 0.9088 (mmtp) cc_final: 0.8595 (mtmt) REVERT: B 472 LEU cc_start: 0.9437 (mm) cc_final: 0.9138 (mm) REVERT: B 505 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8551 (mt-10) REVERT: B 515 ASP cc_start: 0.9270 (m-30) cc_final: 0.8828 (m-30) REVERT: B 585 SER cc_start: 0.9006 (p) cc_final: 0.8182 (t) REVERT: B 586 TYR cc_start: 0.9047 (m-80) cc_final: 0.8580 (m-10) REVERT: B 591 THR cc_start: 0.8878 (p) cc_final: 0.8594 (p) REVERT: B 597 ILE cc_start: 0.9532 (pt) cc_final: 0.9327 (pt) REVERT: B 602 GLU cc_start: 0.7743 (pt0) cc_final: 0.6907 (pt0) REVERT: B 626 TYR cc_start: 0.8802 (m-80) cc_final: 0.8015 (m-80) REVERT: B 636 LYS cc_start: 0.9591 (mmtm) cc_final: 0.9160 (mmmm) REVERT: B 640 MET cc_start: 0.9386 (ttm) cc_final: 0.9177 (ttm) REVERT: B 656 LEU cc_start: 0.9491 (mt) cc_final: 0.9182 (mt) REVERT: B 664 THR cc_start: 0.9390 (p) cc_final: 0.9080 (p) REVERT: B 668 ASN cc_start: 0.9125 (m110) cc_final: 0.8838 (m-40) REVERT: B 677 ARG cc_start: 0.9211 (mmm-85) cc_final: 0.8758 (mmm-85) REVERT: C 17 PHE cc_start: 0.8301 (p90) cc_final: 0.7453 (p90) REVERT: C 87 LYS cc_start: 0.8555 (mtmm) cc_final: 0.8322 (mttt) REVERT: C 98 ASN cc_start: 0.7620 (m110) cc_final: 0.7261 (m110) REVERT: C 149 ASP cc_start: 0.8048 (m-30) cc_final: 0.7826 (m-30) REVERT: C 154 PHE cc_start: 0.8457 (t80) cc_final: 0.7812 (t80) REVERT: C 204 TYR cc_start: 0.9251 (t80) cc_final: 0.8999 (t80) REVERT: C 281 ASP cc_start: 0.8693 (t0) cc_final: 0.7983 (p0) REVERT: D 27 LYS cc_start: 0.9257 (pttp) cc_final: 0.9008 (pttm) REVERT: D 46 TYR cc_start: 0.8784 (m-80) cc_final: 0.8174 (m-80) REVERT: D 53 ASP cc_start: 0.8516 (t0) cc_final: 0.8259 (t70) REVERT: D 109 PHE cc_start: 0.8504 (m-10) cc_final: 0.8077 (m-10) REVERT: D 123 GLU cc_start: 0.8681 (mp0) cc_final: 0.8332 (pm20) REVERT: D 169 TYR cc_start: 0.9523 (m-80) cc_final: 0.9203 (m-80) REVERT: D 172 PHE cc_start: 0.9163 (m-80) cc_final: 0.8830 (m-80) REVERT: D 173 TYR cc_start: 0.8241 (t80) cc_final: 0.7675 (t80) REVERT: D 259 PHE cc_start: 0.7958 (t80) cc_final: 0.7586 (t80) REVERT: D 313 GLU cc_start: 0.8723 (mp0) cc_final: 0.8473 (mp0) outliers start: 0 outliers final: 0 residues processed: 629 average time/residue: 0.2914 time to fit residues: 277.7651 Evaluate side-chains 571 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 571 time to evaluate : 1.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 81 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 105 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 190 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 180 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.139270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.100715 restraints weight = 41108.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.104384 restraints weight = 22428.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.106852 restraints weight = 14201.732| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.7670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16386 Z= 0.158 Angle : 0.673 12.338 22134 Z= 0.355 Chirality : 0.045 0.285 2360 Planarity : 0.004 0.051 2818 Dihedral : 10.179 164.008 2242 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.19), residues: 1932 helix: 0.79 (0.15), residues: 1150 sheet: -0.21 (0.43), residues: 132 loop : -0.13 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 124 HIS 0.011 0.001 HIS C 201 PHE 0.021 0.002 PHE B 171 TYR 0.031 0.002 TYR C 142 ARG 0.010 0.001 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.04081 ( 871) hydrogen bonds : angle 5.15127 ( 2571) covalent geometry : bond 0.00348 (16386) covalent geometry : angle 0.67315 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6687.01 seconds wall clock time: 117 minutes 47.96 seconds (7067.96 seconds total)