Starting phenix.real_space_refine on Sat Jun 14 07:08:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzk_45070/06_2025/9bzk_45070_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzk_45070/06_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_45070/06_2025/9bzk_45070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzk_45070/06_2025/9bzk_45070.map" model { file = "/net/cci-nas-00/data/ceres_data/9bzk_45070/06_2025/9bzk_45070_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzk_45070/06_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-5710/modules/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 9.80, 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 1.8 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: 1.62 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: 4.95 Time building geometry restraints manager: 5.10 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 37.210 Find NCS groups from input model: 0.780 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.350 ------------------------------------------------------------------------------- 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 : 1.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8069 (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: 0.6682 (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: 0.9136 (mp) REVERT: A 179 LEU cc_start: 0.8735 (tp) cc_final: 0.8512 (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: 0.8864 (mt) REVERT: A 202 ASN cc_start: 0.9213 (t0) cc_final: 0.8922 (t0) REVERT: A 232 ASN cc_start: 0.8042 (OUTLIER) cc_final: 0.7813 (m-40) REVERT: A 236 TYR cc_start: 0.8422 (t80) cc_final: 0.8004 (t80) REVERT: A 264 THR cc_start: 0.8918 (p) cc_final: 0.8552 (m) REVERT: A 275 VAL cc_start: 0.8957 (m) cc_final: 0.8594 (m) REVERT: A 278 LEU cc_start: 0.8110 (tp) cc_final: 0.7816 (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: 0.7966 (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: 0.8120 (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: 0.8326 (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: 0.7821 (mtm) REVERT: B 191 GLN cc_start: 0.8710 (mm-40) cc_final: 0.8094 (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: 0.6931 (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: 0.8352 (tp) REVERT: B 322 MET cc_start: 0.7656 (mmm) cc_final: 0.6066 (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: 0.7157 (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: 0.7478 (m-80) REVERT: B 561 LEU cc_start: 0.8223 (tp) cc_final: 0.8013 (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: 0.8008 (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: 0.4858 (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: 0.5603 (p) outliers start: 24 outliers final: 7 residues processed: 928 average time/residue: 0.2926 time to fit residues: 387.5647 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 : 1.723 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.147175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.104621 restraints weight = 37602.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.108611 restraints weight = 21487.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.111264 restraints weight = 13865.539| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3273 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3273 r_free = 0.3273 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.4225 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= 0.179 Angle : 0.634 12.229 22134 Z= 0.338 Chirality : 0.044 0.263 2360 Planarity : 0.004 0.075 2818 Dihedral : 11.224 175.467 2242 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.17 % Allowed : 2.51 % Favored : 97.32 % 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: 1.33 (0.19), residues: 1932 helix: 1.31 (0.15), residues: 1128 sheet: -0.07 (0.41), residues: 134 loop : 0.57 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 558 HIS 0.009 0.001 HIS A 438 PHE 0.027 0.002 PHE D 259 TYR 0.026 0.002 TYR A 498 ARG 0.008 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.04515 ( 871) hydrogen bonds : angle 5.02017 ( 2571) covalent geometry : bond 0.00382 (16386) covalent geometry : angle 0.63389 (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: 3 poor density : 744 time to evaluate : 1.686 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 29 ASP cc_start: 0.9290 (t0) cc_final: 0.8762 (t70) REVERT: A 82 LYS cc_start: 0.9688 (mtpp) cc_final: 0.9420 (mmtp) REVERT: A 118 TYR cc_start: 0.8939 (t80) cc_final: 0.8523 (t80) REVERT: A 119 GLU cc_start: 0.8869 (mp0) cc_final: 0.8328 (mp0) REVERT: A 143 LEU cc_start: 0.9249 (tp) cc_final: 0.8942 (tp) REVERT: A 147 GLN cc_start: 0.9103 (mt0) cc_final: 0.7543 (mt0) REVERT: A 148 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8509 (mt-10) REVERT: A 150 GLN cc_start: 0.9310 (tp40) cc_final: 0.9039 (tp40) REVERT: A 172 LEU cc_start: 0.9513 (mp) cc_final: 0.8905 (mp) REVERT: A 173 LEU cc_start: 0.9531 (mt) cc_final: 0.9094 (mt) REVERT: A 176 ASN cc_start: 0.8718 (t0) cc_final: 0.8404 (t0) REVERT: A 181 ASP cc_start: 0.9027 (m-30) cc_final: 0.8819 (m-30) REVERT: A 187 ASP cc_start: 0.9402 (t70) cc_final: 0.8797 (t0) REVERT: A 188 ILE cc_start: 0.9709 (mt) cc_final: 0.9413 (mt) REVERT: A 191 GLN cc_start: 0.8884 (mm-40) cc_final: 0.8295 (mp10) REVERT: A 195 LEU cc_start: 0.9546 (mt) cc_final: 0.9269 (mt) REVERT: A 202 ASN cc_start: 0.9304 (t0) cc_final: 0.8935 (t0) REVERT: A 214 LYS cc_start: 0.9058 (tppt) cc_final: 0.8784 (mmtt) REVERT: A 221 LYS cc_start: 0.8916 (mmtp) cc_final: 0.8505 (mmtp) REVERT: A 223 VAL cc_start: 0.9610 (m) cc_final: 0.9162 (p) REVERT: A 243 ARG cc_start: 0.6838 (tmt-80) cc_final: 0.6604 (tpt-90) REVERT: A 257 ASP cc_start: 0.9266 (m-30) cc_final: 0.9001 (m-30) REVERT: A 270 ASP cc_start: 0.7987 (t70) cc_final: 0.7459 (t70) REVERT: A 314 MET cc_start: 0.9326 (ttt) cc_final: 0.9091 (ttt) REVERT: A 317 MET cc_start: 0.8147 (mtp) cc_final: 0.7820 (mtp) REVERT: A 319 MET cc_start: 0.9134 (tpp) cc_final: 0.8894 (tpp) REVERT: A 322 MET cc_start: 0.8493 (mmp) cc_final: 0.7858 (mmm) REVERT: A 326 PHE cc_start: 0.9593 (m-10) cc_final: 0.8850 (m-80) REVERT: A 335 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8526 (mm-30) REVERT: A 348 MET cc_start: 0.8796 (tpt) cc_final: 0.8433 (tpp) REVERT: A 355 TYR cc_start: 0.9005 (m-10) cc_final: 0.8767 (m-10) REVERT: A 357 TYR cc_start: 0.8973 (m-10) cc_final: 0.8554 (m-10) REVERT: A 366 LYS cc_start: 0.9391 (mtmt) cc_final: 0.9153 (mtmm) REVERT: A 377 LYS cc_start: 0.9025 (mttt) cc_final: 0.8776 (mtmm) REVERT: A 385 VAL cc_start: 0.9428 (t) cc_final: 0.8986 (t) REVERT: A 406 ASP cc_start: 0.8129 (m-30) cc_final: 0.7460 (m-30) REVERT: A 407 ILE cc_start: 0.9070 (mt) cc_final: 0.8839 (mt) REVERT: A 418 ASN cc_start: 0.9432 (m-40) cc_final: 0.9070 (m-40) REVERT: A 421 GLU cc_start: 0.8730 (pp20) cc_final: 0.8319 (pp20) REVERT: A 444 ASP cc_start: 0.8286 (t0) cc_final: 0.7836 (t0) REVERT: A 493 MET cc_start: 0.8987 (tmm) cc_final: 0.8589 (tmm) REVERT: A 515 ASP cc_start: 0.9036 (m-30) cc_final: 0.8824 (m-30) REVERT: A 521 THR cc_start: 0.8467 (p) cc_final: 0.7874 (t) REVERT: A 550 MET cc_start: 0.7288 (mtm) cc_final: 0.6944 (mtp) REVERT: A 583 SER cc_start: 0.9453 (m) cc_final: 0.8874 (p) REVERT: A 588 GLN cc_start: 0.9003 (mm-40) cc_final: 0.8070 (mm-40) REVERT: A 595 MET cc_start: 0.9295 (mmp) cc_final: 0.9087 (mmp) REVERT: A 598 MET cc_start: 0.8397 (mtm) cc_final: 0.7855 (mtm) REVERT: A 615 MET cc_start: 0.8858 (mmp) cc_final: 0.8332 (mmp) REVERT: A 645 GLN cc_start: 0.8513 (tp40) cc_final: 0.7922 (tp40) REVERT: A 668 ASN cc_start: 0.9152 (m110) cc_final: 0.8825 (m110) REVERT: A 680 LYS cc_start: 0.9267 (mttt) cc_final: 0.8872 (mttt) REVERT: A 684 TYR cc_start: 0.7791 (m-10) cc_final: 0.7000 (m-80) REVERT: B 12 LEU cc_start: 0.9356 (mp) cc_final: 0.8980 (mt) REVERT: B 51 LEU cc_start: 0.9021 (tp) cc_final: 0.8687 (tp) REVERT: B 87 LYS cc_start: 0.9331 (tptp) cc_final: 0.9039 (tptp) REVERT: B 99 LYS cc_start: 0.9550 (mmmt) cc_final: 0.9209 (mmmt) REVERT: B 107 LYS cc_start: 0.9396 (mttt) cc_final: 0.9175 (mptt) REVERT: B 133 ASP cc_start: 0.8734 (t0) cc_final: 0.8490 (t0) REVERT: B 211 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8126 (mm-30) REVERT: B 236 TYR cc_start: 0.9072 (t80) cc_final: 0.8588 (t80) REVERT: B 250 TYR cc_start: 0.9223 (m-80) cc_final: 0.8807 (m-80) REVERT: B 286 ASP cc_start: 0.8212 (m-30) cc_final: 0.7697 (m-30) REVERT: B 308 LYS cc_start: 0.9478 (mtmt) cc_final: 0.9256 (ptpp) REVERT: B 312 GLN cc_start: 0.8695 (pm20) cc_final: 0.8300 (pm20) REVERT: B 322 MET cc_start: 0.9016 (mmm) cc_final: 0.8139 (mmm) REVERT: B 326 PHE cc_start: 0.9123 (m-80) cc_final: 0.8514 (m-80) REVERT: B 348 MET cc_start: 0.9012 (ptp) cc_final: 0.8492 (ptt) REVERT: B 352 GLU cc_start: 0.9107 (mt-10) cc_final: 0.8693 (mt-10) REVERT: B 355 TYR cc_start: 0.8995 (m-80) cc_final: 0.8484 (m-80) REVERT: B 362 ASP cc_start: 0.8569 (m-30) cc_final: 0.7789 (m-30) REVERT: B 403 ILE cc_start: 0.9472 (mp) cc_final: 0.9216 (tp) REVERT: B 415 ASN cc_start: 0.9576 (t0) cc_final: 0.9316 (t0) REVERT: B 459 LYS cc_start: 0.9156 (mmmm) cc_final: 0.8842 (mmtm) REVERT: B 460 SER cc_start: 0.8792 (t) cc_final: 0.8592 (t) REVERT: B 493 MET cc_start: 0.9627 (tmm) cc_final: 0.9364 (tmm) REVERT: B 494 MET cc_start: 0.9556 (mtp) cc_final: 0.9324 (mtp) REVERT: B 515 ASP cc_start: 0.9292 (m-30) cc_final: 0.8884 (m-30) REVERT: B 522 TYR cc_start: 0.8912 (m-10) cc_final: 0.8400 (m-10) REVERT: B 558 TRP cc_start: 0.9172 (m100) cc_final: 0.8405 (m100) REVERT: B 599 GLU cc_start: 0.8581 (pt0) cc_final: 0.8254 (pt0) REVERT: B 601 ILE cc_start: 0.9511 (mm) cc_final: 0.9133 (tp) REVERT: B 603 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8669 (tp30) REVERT: B 615 MET cc_start: 0.9265 (mmp) cc_final: 0.8767 (mmp) REVERT: B 618 LEU cc_start: 0.9120 (tp) cc_final: 0.8916 (tp) REVERT: B 640 MET cc_start: 0.9169 (tpp) cc_final: 0.8901 (tpp) REVERT: B 664 THR cc_start: 0.9147 (p) cc_final: 0.8945 (p) REVERT: B 667 LEU cc_start: 0.9257 (tp) cc_final: 0.9006 (tp) REVERT: B 684 TYR cc_start: 0.7667 (m-10) cc_final: 0.6573 (m-10) REVERT: C 17 PHE cc_start: 0.7239 (p90) cc_final: 0.6122 (p90) REVERT: C 21 PHE cc_start: 0.8968 (m-10) cc_final: 0.8137 (m-10) REVERT: C 87 LYS cc_start: 0.8887 (mtmm) cc_final: 0.8614 (mtmt) REVERT: C 283 ASN cc_start: 0.2201 (p0) cc_final: 0.1915 (p0) REVERT: D 46 TYR cc_start: 0.8591 (m-80) cc_final: 0.8109 (m-80) REVERT: D 105 TYR cc_start: 0.8917 (m-10) cc_final: 0.8404 (m-10) REVERT: D 169 TYR cc_start: 0.8827 (m-80) cc_final: 0.8356 (m-80) REVERT: D 194 ILE cc_start: 0.9834 (mt) cc_final: 0.9598 (mm) REVERT: D 197 ASP cc_start: 0.9107 (m-30) cc_final: 0.8823 (m-30) REVERT: D 204 TYR cc_start: 0.9557 (t80) cc_final: 0.9252 (t80) REVERT: D 313 GLU cc_start: 0.8442 (mp0) cc_final: 0.8204 (mp0) outliers start: 3 outliers final: 0 residues processed: 744 average time/residue: 0.2821 time to fit residues: 307.6286 Evaluate side-chains 612 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 612 time to evaluate : 1.818 ------------------------------------------------------------------------------- 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: 0.0270 chunk 168 optimal weight: 7.9990 chunk 175 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 47 optimal weight: 8.9990 chunk 191 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 chunk 171 optimal weight: 5.9990 chunk 189 optimal weight: 8.9990 chunk 141 optimal weight: 8.9990 overall best weight: 3.2046 ------------------------------------------------------------------------------- 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 232 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.134484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.094440 restraints weight = 40287.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.098035 restraints weight = 22242.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.100427 restraints weight = 14306.768| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 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 = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.5334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 16386 Z= 0.256 Angle : 0.662 10.962 22134 Z= 0.346 Chirality : 0.043 0.195 2360 Planarity : 0.004 0.052 2818 Dihedral : 11.084 178.413 2242 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.06 % Allowed : 2.39 % Favored : 97.55 % 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: 1.10 (0.19), residues: 1932 helix: 1.19 (0.15), residues: 1143 sheet: -0.04 (0.42), residues: 136 loop : 0.28 (0.23), residues: 653 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 0.028 0.002 PHE A 171 TYR 0.033 0.002 TYR B 574 ARG 0.011 0.001 ARG A 121 Details of bonding type rmsd hydrogen bonds : bond 0.04243 ( 871) hydrogen bonds : angle 4.91085 ( 2571) covalent geometry : bond 0.00536 (16386) covalent geometry : angle 0.66250 (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 663 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 662 time to evaluate : 1.682 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 29 ASP cc_start: 0.9243 (t0) cc_final: 0.8753 (t70) REVERT: A 118 TYR cc_start: 0.8985 (t80) cc_final: 0.8750 (t80) REVERT: A 119 GLU cc_start: 0.8997 (mp0) cc_final: 0.8534 (mp0) REVERT: A 125 VAL cc_start: 0.9498 (t) cc_final: 0.9271 (t) REVERT: A 150 GLN cc_start: 0.9346 (tp40) cc_final: 0.9036 (tp40) REVERT: A 172 LEU cc_start: 0.9526 (mp) cc_final: 0.9024 (mp) REVERT: A 173 LEU cc_start: 0.9598 (mt) cc_final: 0.9387 (mt) REVERT: A 181 ASP cc_start: 0.9152 (m-30) cc_final: 0.8933 (m-30) REVERT: A 191 GLN cc_start: 0.8942 (mm-40) cc_final: 0.8353 (mp10) REVERT: A 214 LYS cc_start: 0.9153 (tppt) cc_final: 0.8843 (mmtm) REVERT: A 223 VAL cc_start: 0.9514 (m) cc_final: 0.9257 (p) REVERT: A 243 ARG cc_start: 0.6804 (tmt-80) cc_final: 0.6386 (tpt90) REVERT: A 252 ASN cc_start: 0.9279 (t0) cc_final: 0.9028 (t0) REVERT: A 257 ASP cc_start: 0.9357 (m-30) cc_final: 0.8931 (m-30) REVERT: A 277 THR cc_start: 0.8895 (p) cc_final: 0.8536 (p) REVERT: A 295 ASP cc_start: 0.8738 (t70) cc_final: 0.8446 (t70) REVERT: A 317 MET cc_start: 0.8172 (mtp) cc_final: 0.7810 (mtp) REVERT: A 355 TYR cc_start: 0.8977 (m-10) cc_final: 0.8768 (m-10) REVERT: A 366 LYS cc_start: 0.9360 (mtmt) cc_final: 0.9086 (mtmm) REVERT: A 377 LYS cc_start: 0.9128 (mttt) cc_final: 0.8848 (mtmm) REVERT: A 386 LEU cc_start: 0.9591 (mt) cc_final: 0.9139 (mt) REVERT: A 407 ILE cc_start: 0.9226 (mt) cc_final: 0.8966 (mt) REVERT: A 421 GLU cc_start: 0.8848 (pp20) cc_final: 0.8572 (pp20) REVERT: A 444 ASP cc_start: 0.8364 (t0) cc_final: 0.7733 (t0) REVERT: A 446 ARG cc_start: 0.7959 (mmt90) cc_final: 0.7459 (mmm-85) REVERT: A 483 GLU cc_start: 0.9500 (mp0) cc_final: 0.9167 (pm20) REVERT: A 493 MET cc_start: 0.8857 (tmm) cc_final: 0.8416 (tmm) REVERT: A 515 ASP cc_start: 0.9126 (m-30) cc_final: 0.8911 (m-30) REVERT: A 528 PHE cc_start: 0.9208 (m-80) cc_final: 0.8654 (m-10) REVERT: A 550 MET cc_start: 0.7388 (mtm) cc_final: 0.7020 (mtp) REVERT: A 561 LEU cc_start: 0.9472 (tp) cc_final: 0.9254 (tp) REVERT: A 583 SER cc_start: 0.9488 (m) cc_final: 0.9138 (p) REVERT: A 595 MET cc_start: 0.9366 (mmp) cc_final: 0.8993 (mmt) REVERT: A 615 MET cc_start: 0.9188 (mmp) cc_final: 0.8753 (mmp) REVERT: A 639 ASP cc_start: 0.9249 (m-30) cc_final: 0.9033 (m-30) REVERT: A 672 LEU cc_start: 0.9279 (mt) cc_final: 0.9030 (mt) REVERT: B 51 LEU cc_start: 0.9302 (tp) cc_final: 0.9091 (tp) REVERT: B 52 LYS cc_start: 0.9401 (tptp) cc_final: 0.9138 (tppt) REVERT: B 87 LYS cc_start: 0.9326 (tptp) cc_final: 0.9069 (tptp) REVERT: B 89 PHE cc_start: 0.9223 (t80) cc_final: 0.9016 (t80) REVERT: B 99 LYS cc_start: 0.9564 (mmmt) cc_final: 0.9246 (mmmt) REVERT: B 119 GLU cc_start: 0.9314 (mp0) cc_final: 0.8887 (mp0) REVERT: B 147 GLN cc_start: 0.9127 (mt0) cc_final: 0.8689 (mm-40) REVERT: B 158 ASN cc_start: 0.9328 (m110) cc_final: 0.8800 (t0) REVERT: B 211 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8462 (mm-30) REVERT: B 250 TYR cc_start: 0.9209 (m-80) cc_final: 0.8842 (m-80) REVERT: B 290 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8322 (tm-30) REVERT: B 322 MET cc_start: 0.9171 (mmm) cc_final: 0.8323 (mmm) REVERT: B 355 TYR cc_start: 0.8992 (m-80) cc_final: 0.8526 (m-80) REVERT: B 362 ASP cc_start: 0.8743 (m-30) cc_final: 0.8025 (m-30) REVERT: B 393 SER cc_start: 0.9622 (m) cc_final: 0.8903 (p) REVERT: B 410 ASN cc_start: 0.9018 (m110) cc_final: 0.8656 (m110) REVERT: B 415 ASN cc_start: 0.9576 (t0) cc_final: 0.9313 (t0) REVERT: B 459 LYS cc_start: 0.9117 (mmtp) cc_final: 0.8807 (mptt) REVERT: B 480 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8107 (pp20) REVERT: B 515 ASP cc_start: 0.9353 (m-30) cc_final: 0.8894 (m-30) REVERT: B 522 TYR cc_start: 0.9033 (m-10) cc_final: 0.8731 (m-10) REVERT: B 588 GLN cc_start: 0.9256 (mm-40) cc_final: 0.8959 (mm-40) REVERT: B 599 GLU cc_start: 0.8653 (pt0) cc_final: 0.8213 (pt0) REVERT: B 615 MET cc_start: 0.9270 (mmp) cc_final: 0.8958 (mmp) REVERT: B 632 MET cc_start: 0.8684 (mpp) cc_final: 0.7987 (mpp) REVERT: B 645 GLN cc_start: 0.9337 (tp40) cc_final: 0.8836 (tp-100) REVERT: B 668 ASN cc_start: 0.9363 (m110) cc_final: 0.9012 (m-40) REVERT: C 17 PHE cc_start: 0.7303 (p90) cc_final: 0.6287 (p90) REVERT: C 21 PHE cc_start: 0.8911 (m-10) cc_final: 0.8032 (m-10) REVERT: C 97 GLU cc_start: 0.7627 (tp30) cc_final: 0.7271 (tp30) REVERT: C 98 ASN cc_start: 0.8070 (m-40) cc_final: 0.7848 (m-40) REVERT: C 204 TYR cc_start: 0.9231 (t80) cc_final: 0.8969 (t80) REVERT: D 20 MET cc_start: 0.8202 (ttp) cc_final: 0.7959 (ptm) REVERT: D 46 TYR cc_start: 0.8566 (m-80) cc_final: 0.8034 (m-80) REVERT: D 96 MET cc_start: 0.8731 (tpt) cc_final: 0.8461 (tpp) REVERT: D 105 TYR cc_start: 0.9074 (m-10) cc_final: 0.8590 (m-10) REVERT: D 109 PHE cc_start: 0.8684 (m-10) cc_final: 0.8481 (m-80) REVERT: D 119 ASN cc_start: 0.8882 (t0) cc_final: 0.8650 (t0) REVERT: D 130 TYR cc_start: 0.7070 (m-80) cc_final: 0.6763 (m-80) REVERT: D 169 TYR cc_start: 0.9077 (m-80) cc_final: 0.8604 (m-80) REVERT: D 172 PHE cc_start: 0.8951 (m-80) cc_final: 0.8660 (m-80) REVERT: D 177 TYR cc_start: 0.8978 (t80) cc_final: 0.8744 (t80) REVERT: D 204 TYR cc_start: 0.9621 (t80) cc_final: 0.9196 (t80) REVERT: D 313 GLU cc_start: 0.8414 (mp0) cc_final: 0.8195 (mp0) outliers start: 1 outliers final: 0 residues processed: 662 average time/residue: 0.2813 time to fit residues: 273.8863 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 : 1.740 ------------------------------------------------------------------------------- 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: 8.9990 chunk 99 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 69 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 148 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 242 GLN ** 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** B 158 ASN ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 568 HIS 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.138246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.097657 restraints weight = 39928.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.101413 restraints weight = 22132.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.103896 restraints weight = 14234.692| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 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 = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.5794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16386 Z= 0.145 Angle : 0.582 9.978 22134 Z= 0.304 Chirality : 0.042 0.218 2360 Planarity : 0.003 0.043 2818 Dihedral : 10.806 179.537 2242 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.12 % Allowed : 1.92 % Favored : 97.96 % 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: 1.19 (0.19), residues: 1932 helix: 1.28 (0.15), residues: 1118 sheet: 0.21 (0.44), residues: 118 loop : 0.25 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 30 HIS 0.022 0.001 HIS C 201 PHE 0.021 0.002 PHE A 171 TYR 0.024 0.001 TYR B 574 ARG 0.008 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 871) hydrogen bonds : angle 4.80432 ( 2571) covalent geometry : bond 0.00314 (16386) covalent geometry : angle 0.58212 (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 664 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 662 time to evaluate : 1.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 31 GLU cc_start: 0.9083 (mp0) cc_final: 0.8751 (mp0) REVERT: A 54 LYS cc_start: 0.9620 (ttmm) cc_final: 0.9318 (ttmt) REVERT: A 106 LEU cc_start: 0.9477 (tp) cc_final: 0.9178 (tp) REVERT: A 118 TYR cc_start: 0.8838 (t80) cc_final: 0.8270 (t80) REVERT: A 119 GLU cc_start: 0.8866 (mp0) cc_final: 0.8415 (mp0) REVERT: A 136 LYS cc_start: 0.9339 (tttp) cc_final: 0.9052 (tptt) REVERT: A 143 LEU cc_start: 0.9266 (tp) cc_final: 0.9029 (tp) REVERT: A 148 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8637 (mt-10) REVERT: A 150 GLN cc_start: 0.9480 (tp40) cc_final: 0.9228 (tp40) REVERT: A 164 ARG cc_start: 0.8761 (ptt90) cc_final: 0.8438 (ptt90) REVERT: A 172 LEU cc_start: 0.9493 (mp) cc_final: 0.9009 (mp) REVERT: A 214 LYS cc_start: 0.9099 (tppt) cc_final: 0.8820 (mmtm) REVERT: A 223 VAL cc_start: 0.9573 (m) cc_final: 0.9256 (p) REVERT: A 252 ASN cc_start: 0.9230 (t0) cc_final: 0.8852 (t0) REVERT: A 277 THR cc_start: 0.8718 (p) cc_final: 0.8505 (p) REVERT: A 295 ASP cc_start: 0.8692 (t70) cc_final: 0.8399 (t70) REVERT: A 335 GLU cc_start: 0.7939 (mp0) cc_final: 0.7389 (mp0) REVERT: A 355 TYR cc_start: 0.8879 (m-10) cc_final: 0.8666 (m-10) REVERT: A 366 LYS cc_start: 0.9434 (mtmt) cc_final: 0.9160 (mtmm) REVERT: A 390 GLN cc_start: 0.8654 (mt0) cc_final: 0.8345 (mt0) REVERT: A 396 ASP cc_start: 0.8816 (m-30) cc_final: 0.8355 (m-30) REVERT: A 405 LEU cc_start: 0.8661 (mt) cc_final: 0.8312 (mt) REVERT: A 406 ASP cc_start: 0.8221 (m-30) cc_final: 0.7908 (m-30) REVERT: A 407 ILE cc_start: 0.9261 (mt) cc_final: 0.9038 (mt) REVERT: A 421 GLU cc_start: 0.8839 (pp20) cc_final: 0.8560 (pp20) REVERT: A 493 MET cc_start: 0.8841 (tmm) cc_final: 0.8363 (tmm) REVERT: A 515 ASP cc_start: 0.9105 (m-30) cc_final: 0.8777 (m-30) REVERT: A 516 GLN cc_start: 0.9003 (mp10) cc_final: 0.8705 (mp10) REVERT: A 528 PHE cc_start: 0.9141 (m-80) cc_final: 0.8451 (m-10) REVERT: A 550 MET cc_start: 0.7312 (mtm) cc_final: 0.6867 (mtp) REVERT: A 583 SER cc_start: 0.9425 (m) cc_final: 0.9052 (p) REVERT: A 595 MET cc_start: 0.9162 (mmp) cc_final: 0.8802 (mmt) REVERT: A 615 MET cc_start: 0.9252 (mmp) cc_final: 0.8751 (mmp) REVERT: A 632 MET cc_start: 0.8192 (mtm) cc_final: 0.7929 (mtp) REVERT: A 639 ASP cc_start: 0.9122 (m-30) cc_final: 0.8830 (m-30) REVERT: A 657 PHE cc_start: 0.8904 (m-80) cc_final: 0.8569 (m-80) REVERT: A 672 LEU cc_start: 0.9283 (mt) cc_final: 0.9010 (mt) REVERT: A 680 LYS cc_start: 0.9225 (mttt) cc_final: 0.8808 (mttt) REVERT: B 52 LYS cc_start: 0.9453 (tptp) cc_final: 0.9161 (tppt) REVERT: B 75 GLU cc_start: 0.9301 (mp0) cc_final: 0.9003 (pm20) REVERT: B 87 LYS cc_start: 0.9322 (tptp) cc_final: 0.8922 (tptp) REVERT: B 95 MET cc_start: 0.9174 (tpp) cc_final: 0.8949 (tpp) REVERT: B 119 GLU cc_start: 0.9233 (mp0) cc_final: 0.8805 (mp0) REVERT: B 127 LEU cc_start: 0.9511 (mm) cc_final: 0.9173 (mm) REVERT: B 147 GLN cc_start: 0.8993 (mt0) cc_final: 0.8628 (mm-40) REVERT: B 184 ARG cc_start: 0.9372 (tpp80) cc_final: 0.9136 (tpp80) REVERT: B 223 VAL cc_start: 0.9236 (m) cc_final: 0.8739 (m) REVERT: B 250 TYR cc_start: 0.9143 (m-80) cc_final: 0.8697 (m-80) REVERT: B 288 PHE cc_start: 0.9243 (t80) cc_final: 0.8864 (t80) REVERT: B 322 MET cc_start: 0.9182 (mmm) cc_final: 0.8283 (mmm) REVERT: B 333 LYS cc_start: 0.9504 (tttp) cc_final: 0.9259 (ttmm) REVERT: B 348 MET cc_start: 0.9167 (ptt) cc_final: 0.8580 (ptp) REVERT: B 355 TYR cc_start: 0.9072 (m-80) cc_final: 0.8530 (m-80) REVERT: B 362 ASP cc_start: 0.8953 (m-30) cc_final: 0.8548 (m-30) REVERT: B 375 LYS cc_start: 0.9129 (mmmm) cc_final: 0.8474 (mmmm) REVERT: B 393 SER cc_start: 0.9502 (m) cc_final: 0.9060 (p) REVERT: B 402 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8135 (tm-30) REVERT: B 410 ASN cc_start: 0.8866 (m110) cc_final: 0.8546 (m110) REVERT: B 459 LYS cc_start: 0.9065 (mmtp) cc_final: 0.8521 (mtmt) REVERT: B 480 GLU cc_start: 0.8758 (mt-10) cc_final: 0.7998 (pp20) REVERT: B 515 ASP cc_start: 0.9336 (m-30) cc_final: 0.8924 (m-30) REVERT: B 588 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8942 (mm-40) REVERT: B 598 MET cc_start: 0.8845 (mtp) cc_final: 0.8597 (mtp) REVERT: B 599 GLU cc_start: 0.8731 (pt0) cc_final: 0.8189 (pt0) REVERT: B 601 ILE cc_start: 0.9529 (mm) cc_final: 0.9078 (tp) REVERT: B 615 MET cc_start: 0.9282 (mmp) cc_final: 0.8904 (mmp) REVERT: B 626 TYR cc_start: 0.8685 (m-80) cc_final: 0.7958 (m-80) REVERT: B 628 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8590 (mm-30) REVERT: B 632 MET cc_start: 0.8521 (mpp) cc_final: 0.7916 (mpp) REVERT: B 640 MET cc_start: 0.9431 (tpp) cc_final: 0.9064 (tpp) REVERT: B 645 GLN cc_start: 0.9270 (tp40) cc_final: 0.8959 (tp-100) REVERT: B 664 THR cc_start: 0.9284 (p) cc_final: 0.9017 (p) REVERT: B 667 LEU cc_start: 0.9329 (tp) cc_final: 0.9033 (tp) REVERT: B 668 ASN cc_start: 0.9250 (m110) cc_final: 0.8964 (m110) REVERT: B 677 ARG cc_start: 0.9272 (mmm-85) cc_final: 0.8828 (mmm-85) REVERT: C 87 LYS cc_start: 0.8849 (mtmm) cc_final: 0.8538 (mttt) REVERT: C 97 GLU cc_start: 0.7456 (tp30) cc_final: 0.7239 (mm-30) REVERT: C 286 VAL cc_start: 0.7209 (t) cc_final: 0.6936 (t) REVERT: D 45 LYS cc_start: 0.8642 (pttt) cc_final: 0.8278 (pttt) REVERT: D 46 TYR cc_start: 0.8615 (m-80) cc_final: 0.8096 (m-80) REVERT: D 105 TYR cc_start: 0.9255 (m-10) cc_final: 0.8573 (m-10) REVERT: D 169 TYR cc_start: 0.9272 (m-80) cc_final: 0.8775 (m-80) REVERT: D 172 PHE cc_start: 0.8914 (m-80) cc_final: 0.8572 (m-80) REVERT: D 204 TYR cc_start: 0.9613 (t80) cc_final: 0.9277 (t80) outliers start: 2 outliers final: 1 residues processed: 662 average time/residue: 0.2783 time to fit residues: 271.9862 Evaluate side-chains 598 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 597 time to evaluate : 1.921 ------------------------------------------------------------------------------- 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: 0.3980 chunk 41 optimal weight: 0.4980 chunk 57 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 51 optimal weight: 0.0470 chunk 175 optimal weight: 9.9990 chunk 182 optimal weight: 10.0000 chunk 96 optimal weight: 0.6980 chunk 86 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 21 optimal weight: 0.2980 overall best weight: 0.3878 ------------------------------------------------------------------------------- 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 A 232 ASN A 313 HIS A 370 ASN ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN A 647 HIS ** A 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN D 210 GLN D 238 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.143340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.102325 restraints weight = 39953.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.106273 restraints weight = 22063.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.108858 restraints weight = 13970.018| |-----------------------------------------------------------------------------| r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3295 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3295 r_free = 0.3295 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 = 0.3295 r_free = 0.3295 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3295 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.6184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 16386 Z= 0.122 Angle : 0.572 10.564 22134 Z= 0.298 Chirality : 0.044 0.604 2360 Planarity : 0.003 0.045 2818 Dihedral : 10.494 176.861 2242 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.12 % Allowed : 1.57 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.19), residues: 1932 helix: 1.32 (0.16), residues: 1118 sheet: -0.01 (0.41), residues: 130 loop : 0.23 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 124 HIS 0.016 0.001 HIS C 201 PHE 0.024 0.002 PHE D 154 TYR 0.019 0.001 TYR B 574 ARG 0.006 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.03697 ( 871) hydrogen bonds : angle 4.75295 ( 2571) covalent geometry : bond 0.00261 (16386) covalent geometry : angle 0.57153 (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 674 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 672 time to evaluate : 1.723 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 31 GLU cc_start: 0.9045 (mp0) cc_final: 0.8772 (mp0) REVERT: A 101 TYR cc_start: 0.9325 (m-80) cc_final: 0.9117 (m-10) REVERT: A 118 TYR cc_start: 0.8662 (t80) cc_final: 0.8203 (t80) REVERT: A 119 GLU cc_start: 0.8792 (mp0) cc_final: 0.8344 (mp0) REVERT: A 143 LEU cc_start: 0.9239 (tp) cc_final: 0.9006 (tp) REVERT: A 148 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8494 (mt-10) REVERT: A 164 ARG cc_start: 0.8762 (ptt90) cc_final: 0.8510 (ptt90) REVERT: A 172 LEU cc_start: 0.9454 (mp) cc_final: 0.9077 (mp) REVERT: A 173 LEU cc_start: 0.9613 (mt) cc_final: 0.9405 (mt) REVERT: A 174 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8181 (mt-10) REVERT: A 181 ASP cc_start: 0.9138 (m-30) cc_final: 0.8690 (m-30) REVERT: A 214 LYS cc_start: 0.8991 (tppt) cc_final: 0.8595 (mmtt) REVERT: A 232 ASN cc_start: 0.8863 (t160) cc_final: 0.8656 (t0) REVERT: A 252 ASN cc_start: 0.9084 (t0) cc_final: 0.8549 (t0) REVERT: A 257 ASP cc_start: 0.9192 (m-30) cc_final: 0.8836 (m-30) REVERT: A 277 THR cc_start: 0.8564 (p) cc_final: 0.8061 (t) REVERT: A 317 MET cc_start: 0.8798 (mtp) cc_final: 0.8306 (mtm) REVERT: A 335 GLU cc_start: 0.7853 (mp0) cc_final: 0.7461 (mp0) REVERT: A 348 MET cc_start: 0.8882 (tpp) cc_final: 0.8342 (tpp) REVERT: A 355 TYR cc_start: 0.8949 (m-10) cc_final: 0.8709 (m-10) REVERT: A 366 LYS cc_start: 0.9448 (mtmt) cc_final: 0.9170 (mtmm) REVERT: A 396 ASP cc_start: 0.8604 (m-30) cc_final: 0.8207 (m-30) REVERT: A 413 SER cc_start: 0.8922 (t) cc_final: 0.8530 (t) REVERT: A 418 ASN cc_start: 0.9296 (m110) cc_final: 0.8940 (m-40) REVERT: A 421 GLU cc_start: 0.8852 (pp20) cc_final: 0.8496 (pp20) REVERT: A 458 MET cc_start: 0.8705 (mmp) cc_final: 0.8352 (mmm) REVERT: A 493 MET cc_start: 0.8796 (tmm) cc_final: 0.8311 (tmm) REVERT: A 515 ASP cc_start: 0.9078 (m-30) cc_final: 0.8822 (m-30) REVERT: A 561 LEU cc_start: 0.9445 (tp) cc_final: 0.9241 (tp) REVERT: A 583 SER cc_start: 0.9377 (m) cc_final: 0.8934 (t) REVERT: A 595 MET cc_start: 0.9009 (mmp) cc_final: 0.8731 (mmt) REVERT: A 615 MET cc_start: 0.9293 (mmp) cc_final: 0.8664 (mmm) REVERT: A 639 ASP cc_start: 0.9045 (m-30) cc_final: 0.8805 (m-30) REVERT: A 657 PHE cc_start: 0.8937 (m-80) cc_final: 0.8624 (m-80) REVERT: A 669 ARG cc_start: 0.9095 (mtm-85) cc_final: 0.8803 (ttm110) REVERT: A 672 LEU cc_start: 0.9222 (mt) cc_final: 0.8968 (mt) REVERT: A 680 LYS cc_start: 0.9360 (mttt) cc_final: 0.8902 (mttt) REVERT: B 51 LEU cc_start: 0.9257 (tp) cc_final: 0.9022 (tp) REVERT: B 52 LYS cc_start: 0.9462 (tptp) cc_final: 0.9156 (tppt) REVERT: B 54 LYS cc_start: 0.9649 (ttmt) cc_final: 0.9446 (ttmm) REVERT: B 67 GLU cc_start: 0.9028 (mp0) cc_final: 0.8768 (pm20) REVERT: B 75 GLU cc_start: 0.9319 (mp0) cc_final: 0.9004 (pm20) REVERT: B 87 LYS cc_start: 0.9309 (tptp) cc_final: 0.8916 (tptp) REVERT: B 95 MET cc_start: 0.9149 (tpp) cc_final: 0.8808 (tpp) REVERT: B 119 GLU cc_start: 0.9119 (mp0) cc_final: 0.8775 (mp0) REVERT: B 127 LEU cc_start: 0.9558 (mm) cc_final: 0.9196 (mm) REVERT: B 147 GLN cc_start: 0.8958 (mt0) cc_final: 0.8656 (mm-40) REVERT: B 179 LEU cc_start: 0.9786 (tp) cc_final: 0.9484 (tp) REVERT: B 184 ARG cc_start: 0.9370 (tpp80) cc_final: 0.9021 (tpp-160) REVERT: B 202 ASN cc_start: 0.9349 (t0) cc_final: 0.8435 (t0) REVERT: B 223 VAL cc_start: 0.9170 (m) cc_final: 0.8679 (m) REVERT: B 228 LYS cc_start: 0.9380 (mmmm) cc_final: 0.8684 (mmtt) REVERT: B 232 ASN cc_start: 0.9358 (m-40) cc_final: 0.9098 (m110) REVERT: B 250 TYR cc_start: 0.9114 (m-80) cc_final: 0.8698 (m-80) REVERT: B 283 VAL cc_start: 0.9629 (t) cc_final: 0.9333 (t) REVERT: B 286 ASP cc_start: 0.8593 (m-30) cc_final: 0.8133 (m-30) REVERT: B 290 GLU cc_start: 0.9421 (pt0) cc_final: 0.9001 (pp20) REVERT: B 291 LEU cc_start: 0.9645 (mt) cc_final: 0.9172 (mt) REVERT: B 321 GLU cc_start: 0.8505 (tm-30) cc_final: 0.8293 (tm-30) REVERT: B 322 MET cc_start: 0.9154 (mmm) cc_final: 0.8236 (mmm) REVERT: B 333 LYS cc_start: 0.9499 (tttp) cc_final: 0.9242 (ttmm) REVERT: B 348 MET cc_start: 0.8868 (ptt) cc_final: 0.8304 (ptp) REVERT: B 355 TYR cc_start: 0.9093 (m-80) cc_final: 0.8504 (m-80) REVERT: B 362 ASP cc_start: 0.8858 (m-30) cc_final: 0.8106 (m-30) REVERT: B 373 ILE cc_start: 0.9572 (mt) cc_final: 0.9357 (mt) REVERT: B 378 PHE cc_start: 0.8979 (p90) cc_final: 0.8769 (p90) REVERT: B 390 GLN cc_start: 0.9071 (mt0) cc_final: 0.8840 (mm110) REVERT: B 393 SER cc_start: 0.9524 (m) cc_final: 0.9119 (p) REVERT: B 402 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8105 (tm-30) REVERT: B 410 ASN cc_start: 0.8801 (m110) cc_final: 0.8492 (m110) REVERT: B 446 ARG cc_start: 0.8192 (mmt-90) cc_final: 0.7989 (mmp80) REVERT: B 459 LYS cc_start: 0.8892 (mmtp) cc_final: 0.8421 (mtmt) REVERT: B 480 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8126 (pp20) REVERT: B 515 ASP cc_start: 0.9277 (m-30) cc_final: 0.8805 (m-30) REVERT: B 550 MET cc_start: 0.8259 (mmp) cc_final: 0.8017 (mmm) REVERT: B 583 SER cc_start: 0.9186 (p) cc_final: 0.8942 (t) REVERT: B 585 SER cc_start: 0.8966 (p) cc_final: 0.8309 (t) REVERT: B 597 ILE cc_start: 0.9581 (pt) cc_final: 0.9368 (pt) REVERT: B 599 GLU cc_start: 0.8675 (pt0) cc_final: 0.8151 (pt0) REVERT: B 601 ILE cc_start: 0.9478 (mm) cc_final: 0.9216 (mm) REVERT: B 615 MET cc_start: 0.9074 (mmp) cc_final: 0.8570 (mmp) REVERT: B 626 TYR cc_start: 0.8675 (m-80) cc_final: 0.7601 (m-80) REVERT: B 628 GLU cc_start: 0.9046 (mt-10) cc_final: 0.8628 (mm-30) REVERT: B 632 MET cc_start: 0.8384 (mpp) cc_final: 0.8000 (mpp) REVERT: B 634 MET cc_start: 0.9393 (mmm) cc_final: 0.9032 (mmp) REVERT: B 645 GLN cc_start: 0.9269 (tp40) cc_final: 0.8979 (tp-100) REVERT: B 648 ILE cc_start: 0.9431 (mm) cc_final: 0.9171 (mm) REVERT: B 656 LEU cc_start: 0.9463 (mt) cc_final: 0.9215 (mt) REVERT: B 664 THR cc_start: 0.9293 (p) cc_final: 0.9071 (p) REVERT: B 667 LEU cc_start: 0.9338 (tp) cc_final: 0.9043 (tp) REVERT: B 668 ASN cc_start: 0.9251 (m110) cc_final: 0.9004 (m-40) REVERT: B 677 ARG cc_start: 0.9233 (mmm-85) cc_final: 0.8782 (mmm-85) REVERT: C 17 PHE cc_start: 0.7987 (p90) cc_final: 0.7071 (p90) REVERT: C 87 LYS cc_start: 0.8532 (mtmm) cc_final: 0.8295 (mttt) REVERT: D 45 LYS cc_start: 0.8624 (pttt) cc_final: 0.8260 (pttt) REVERT: D 46 TYR cc_start: 0.8593 (m-80) cc_final: 0.8051 (m-80) REVERT: D 105 TYR cc_start: 0.9247 (m-10) cc_final: 0.8512 (m-10) REVERT: D 123 GLU cc_start: 0.8959 (mp0) cc_final: 0.8411 (pp20) REVERT: D 124 TRP cc_start: 0.5347 (t60) cc_final: 0.5124 (t60) REVERT: D 169 TYR cc_start: 0.9305 (m-80) cc_final: 0.8904 (m-80) REVERT: D 172 PHE cc_start: 0.8771 (m-80) cc_final: 0.8448 (m-80) REVERT: D 204 TYR cc_start: 0.9604 (t80) cc_final: 0.9295 (t80) REVERT: D 241 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7519 (mp0) outliers start: 2 outliers final: 0 residues processed: 674 average time/residue: 0.2920 time to fit residues: 293.9979 Evaluate side-chains 597 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 596 time to evaluate : 1.979 ------------------------------------------------------------------------------- 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: 9.9990 chunk 126 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 69 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 115 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 113 optimal weight: 5.9990 chunk 177 optimal weight: 10.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 232 ASN A 242 GLN ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 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 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 501 GLN C 23 ASN C 25 ASN ** D 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.132096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.092555 restraints weight = 42306.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.095994 restraints weight = 23473.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.098362 restraints weight = 15108.027| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 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 = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 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 : 0.007 0.064 16386 Z= 0.328 Angle : 0.757 14.020 22134 Z= 0.395 Chirality : 0.046 0.217 2360 Planarity : 0.004 0.048 2818 Dihedral : 11.049 172.379 2242 Min Nonbonded Distance : 1.662 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.06 % Allowed : 2.04 % 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: 0.41 (0.18), residues: 1932 helix: 0.65 (0.15), residues: 1165 sheet: -0.63 (0.39), residues: 140 loop : 0.04 (0.25), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 623 HIS 0.016 0.002 HIS C 201 PHE 0.025 0.003 PHE D 166 TYR 0.026 0.002 TYR D 130 ARG 0.009 0.001 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.04446 ( 871) hydrogen bonds : angle 5.20047 ( 2571) covalent geometry : bond 0.00682 (16386) covalent geometry : angle 0.75744 (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 643 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 642 time to evaluate : 2.186 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: 0.9464 (mmtt) cc_final: 0.9245 (mmmm) REVERT: A 31 GLU cc_start: 0.9068 (mp0) cc_final: 0.8813 (mp0) REVERT: A 119 GLU cc_start: 0.9056 (mp0) cc_final: 0.8753 (mp0) REVERT: A 142 ASN cc_start: 0.9298 (m-40) cc_final: 0.8966 (m110) REVERT: A 149 TYR cc_start: 0.9297 (t80) cc_final: 0.8318 (t80) REVERT: A 150 GLN cc_start: 0.9302 (tp40) cc_final: 0.9097 (tp40) REVERT: A 158 ASN cc_start: 0.9376 (m-40) cc_final: 0.9076 (m-40) REVERT: A 172 LEU cc_start: 0.9553 (mp) cc_final: 0.9320 (mp) REVERT: A 174 GLU cc_start: 0.8379 (mt-10) cc_final: 0.8085 (mt-10) REVERT: A 181 ASP cc_start: 0.9025 (m-30) cc_final: 0.8734 (m-30) REVERT: A 191 GLN cc_start: 0.9058 (mm110) cc_final: 0.8656 (mp10) REVERT: A 214 LYS cc_start: 0.9104 (tppt) cc_final: 0.8880 (mmtm) REVERT: A 254 PHE cc_start: 0.8788 (m-80) cc_final: 0.8186 (m-10) REVERT: A 259 ASN cc_start: 0.9106 (p0) cc_final: 0.8798 (p0) REVERT: A 286 ASP cc_start: 0.8803 (m-30) cc_final: 0.8563 (m-30) REVERT: A 290 GLU cc_start: 0.8975 (tm-30) cc_final: 0.8540 (tm-30) REVERT: A 317 MET cc_start: 0.8845 (mtp) cc_final: 0.8554 (mtp) REVERT: A 335 GLU cc_start: 0.7980 (mp0) cc_final: 0.7578 (mp0) REVERT: A 348 MET cc_start: 0.8787 (tpp) cc_final: 0.7811 (tpp) REVERT: A 355 TYR cc_start: 0.8816 (m-10) cc_final: 0.8610 (m-10) REVERT: A 357 TYR cc_start: 0.8813 (m-80) cc_final: 0.7688 (m-80) REVERT: A 362 ASP cc_start: 0.8487 (m-30) cc_final: 0.8057 (m-30) REVERT: A 366 LYS cc_start: 0.9417 (mtmt) cc_final: 0.9134 (mtmm) REVERT: A 383 SER cc_start: 0.9117 (p) cc_final: 0.8508 (p) REVERT: A 396 ASP cc_start: 0.8695 (m-30) cc_final: 0.8238 (m-30) REVERT: A 406 ASP cc_start: 0.8112 (m-30) cc_final: 0.7840 (m-30) REVERT: A 407 ILE cc_start: 0.9194 (mt) cc_final: 0.8938 (mt) REVERT: A 413 SER cc_start: 0.8651 (t) cc_final: 0.8431 (t) REVERT: A 417 LEU cc_start: 0.9696 (tt) cc_final: 0.9457 (tt) REVERT: A 421 GLU cc_start: 0.8850 (pp20) cc_final: 0.8550 (pp20) REVERT: A 458 MET cc_start: 0.8995 (mmp) cc_final: 0.8538 (mmp) REVERT: A 459 LYS cc_start: 0.8972 (mttp) cc_final: 0.8599 (mtpt) REVERT: A 493 MET cc_start: 0.8839 (tmm) cc_final: 0.8397 (tmm) REVERT: A 515 ASP cc_start: 0.9118 (m-30) cc_final: 0.8841 (m-30) REVERT: A 583 SER cc_start: 0.9435 (m) cc_final: 0.9122 (p) REVERT: A 615 MET cc_start: 0.9278 (mmp) cc_final: 0.8685 (mmp) REVERT: A 626 TYR cc_start: 0.9321 (m-80) cc_final: 0.8941 (m-80) REVERT: A 639 ASP cc_start: 0.9136 (m-30) cc_final: 0.8921 (m-30) REVERT: A 641 ILE cc_start: 0.9696 (mm) cc_final: 0.9404 (mm) REVERT: A 654 PHE cc_start: 0.9321 (t80) cc_final: 0.8836 (t80) REVERT: A 672 LEU cc_start: 0.9365 (mt) cc_final: 0.9103 (mt) REVERT: A 684 TYR cc_start: 0.8640 (m-80) cc_final: 0.8362 (m-80) REVERT: B 51 LEU cc_start: 0.9522 (tp) cc_final: 0.9235 (tp) REVERT: B 52 LYS cc_start: 0.9426 (tptp) cc_final: 0.9206 (tppt) REVERT: B 55 LEU cc_start: 0.9704 (mt) cc_final: 0.9463 (mt) REVERT: B 75 GLU cc_start: 0.9289 (mp0) cc_final: 0.9016 (pm20) REVERT: B 87 LYS cc_start: 0.9407 (tptp) cc_final: 0.9027 (tptp) REVERT: B 119 GLU cc_start: 0.9410 (mp0) cc_final: 0.8979 (mp0) REVERT: B 120 ASP cc_start: 0.9183 (m-30) cc_final: 0.8966 (m-30) REVERT: B 184 ARG cc_start: 0.9439 (tpp80) cc_final: 0.9135 (tpp-160) REVERT: B 188 ILE cc_start: 0.9645 (mp) cc_final: 0.9323 (mp) REVERT: B 192 LEU cc_start: 0.9424 (mp) cc_final: 0.9207 (mp) REVERT: B 203 LEU cc_start: 0.9619 (mt) cc_final: 0.9402 (mt) REVERT: B 223 VAL cc_start: 0.9412 (m) cc_final: 0.8927 (m) REVERT: B 232 ASN cc_start: 0.9476 (m-40) cc_final: 0.9253 (m110) REVERT: B 235 ARG cc_start: 0.8951 (ttm110) cc_final: 0.8668 (ttm110) REVERT: B 250 TYR cc_start: 0.9236 (m-80) cc_final: 0.8729 (m-80) REVERT: B 257 ASP cc_start: 0.9033 (m-30) cc_final: 0.8244 (m-30) REVERT: B 260 ASP cc_start: 0.9504 (p0) cc_final: 0.9206 (p0) REVERT: B 286 ASP cc_start: 0.8583 (m-30) cc_final: 0.8218 (m-30) REVERT: B 291 LEU cc_start: 0.9629 (mt) cc_final: 0.9158 (mt) REVERT: B 322 MET cc_start: 0.9137 (mmm) cc_final: 0.8190 (mmm) REVERT: B 333 LYS cc_start: 0.9397 (tttp) cc_final: 0.9085 (ttmm) REVERT: B 348 MET cc_start: 0.9188 (ptt) cc_final: 0.8256 (ptt) REVERT: B 355 TYR cc_start: 0.9005 (m-80) cc_final: 0.8571 (m-80) REVERT: B 362 ASP cc_start: 0.8731 (m-30) cc_final: 0.8029 (m-30) REVERT: B 392 SER cc_start: 0.9061 (m) cc_final: 0.8397 (p) REVERT: B 393 SER cc_start: 0.9470 (m) cc_final: 0.9242 (p) REVERT: B 402 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8218 (tm-30) REVERT: B 407 ILE cc_start: 0.9182 (mt) cc_final: 0.8882 (mt) REVERT: B 410 ASN cc_start: 0.8946 (m110) cc_final: 0.8713 (m110) REVERT: B 415 ASN cc_start: 0.9520 (t0) cc_final: 0.9234 (t0) REVERT: B 446 ARG cc_start: 0.8354 (mmt-90) cc_final: 0.8074 (mmm160) REVERT: B 459 LYS cc_start: 0.9210 (mmtp) cc_final: 0.9002 (mptt) REVERT: B 480 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8105 (pp20) REVERT: B 515 ASP cc_start: 0.9363 (m-30) cc_final: 0.8936 (m-30) REVERT: B 550 MET cc_start: 0.8436 (mmp) cc_final: 0.8005 (mmm) REVERT: B 585 SER cc_start: 0.9132 (p) cc_final: 0.8586 (t) REVERT: B 615 MET cc_start: 0.9368 (mmp) cc_final: 0.9018 (mmp) REVERT: B 628 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8529 (mt-10) REVERT: B 632 MET cc_start: 0.8364 (mpp) cc_final: 0.8085 (mpp) REVERT: B 636 LYS cc_start: 0.9587 (mmtm) cc_final: 0.9264 (mmmm) REVERT: B 645 GLN cc_start: 0.9366 (tp40) cc_final: 0.9142 (tp-100) REVERT: B 650 GLN cc_start: 0.9072 (mt0) cc_final: 0.8811 (mt0) REVERT: B 656 LEU cc_start: 0.9544 (mt) cc_final: 0.9336 (mt) REVERT: B 664 THR cc_start: 0.9320 (p) cc_final: 0.9043 (p) REVERT: B 667 LEU cc_start: 0.9437 (tp) cc_final: 0.9230 (tp) REVERT: B 668 ASN cc_start: 0.9373 (m110) cc_final: 0.9034 (m110) REVERT: B 677 ARG cc_start: 0.9271 (mmm-85) cc_final: 0.8871 (mmm-85) REVERT: C 17 PHE cc_start: 0.8071 (p90) cc_final: 0.7259 (p90) REVERT: C 154 PHE cc_start: 0.8400 (t80) cc_final: 0.7933 (t80) REVERT: C 204 TYR cc_start: 0.9278 (t80) cc_final: 0.9067 (t80) REVERT: D 23 ASN cc_start: 0.9522 (m110) cc_final: 0.9285 (m110) REVERT: D 46 TYR cc_start: 0.8674 (m-80) cc_final: 0.7979 (m-80) REVERT: D 169 TYR cc_start: 0.9474 (m-80) cc_final: 0.8864 (m-80) REVERT: D 172 PHE cc_start: 0.9342 (m-80) cc_final: 0.8911 (m-80) REVERT: D 177 TYR cc_start: 0.9272 (t80) cc_final: 0.8909 (t80) REVERT: D 197 ASP cc_start: 0.9101 (m-30) cc_final: 0.8826 (m-30) REVERT: D 204 TYR cc_start: 0.9587 (t80) cc_final: 0.9350 (t80) REVERT: D 212 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8448 (tt) REVERT: D 259 PHE cc_start: 0.8073 (t80) cc_final: 0.7805 (t80) outliers start: 1 outliers final: 0 residues processed: 643 average time/residue: 0.2832 time to fit residues: 270.3096 Evaluate side-chains 566 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 565 time to evaluate : 1.692 ------------------------------------------------------------------------------- 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: 2.9990 chunk 85 optimal weight: 0.6980 chunk 161 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 184 optimal weight: 8.9990 chunk 119 optimal weight: 0.6980 chunk 175 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 646 GLN ** A 647 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.139888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.099793 restraints weight = 40385.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.103546 restraints weight = 21994.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.106151 restraints weight = 13943.527| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.7078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16386 Z= 0.139 Angle : 0.612 9.749 22134 Z= 0.320 Chirality : 0.043 0.195 2360 Planarity : 0.003 0.045 2818 Dihedral : 10.684 176.489 2242 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.75 (0.19), residues: 1932 helix: 0.97 (0.15), residues: 1151 sheet: -0.59 (0.40), residues: 142 loop : 0.09 (0.24), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 30 HIS 0.012 0.001 HIS C 201 PHE 0.034 0.002 PHE D 154 TYR 0.032 0.002 TYR B 612 ARG 0.007 0.001 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 871) hydrogen bonds : angle 5.02798 ( 2571) covalent geometry : bond 0.00305 (16386) covalent geometry : angle 0.61188 (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 657 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 657 time to evaluate : 1.840 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.9419 (mmtt) cc_final: 0.9089 (mmtm) REVERT: A 31 GLU cc_start: 0.9108 (mp0) cc_final: 0.8718 (mp0) REVERT: A 101 TYR cc_start: 0.9446 (m-80) cc_final: 0.9234 (m-10) REVERT: A 106 LEU cc_start: 0.9311 (tp) cc_final: 0.9028 (tp) REVERT: A 119 GLU cc_start: 0.8842 (mp0) cc_final: 0.8482 (mp0) REVERT: A 142 ASN cc_start: 0.9277 (m-40) cc_final: 0.8929 (m110) REVERT: A 147 GLN cc_start: 0.8623 (mm110) cc_final: 0.7796 (mm-40) REVERT: A 148 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8461 (mt-10) REVERT: A 158 ASN cc_start: 0.9375 (m-40) cc_final: 0.9104 (m-40) REVERT: A 172 LEU cc_start: 0.9509 (mp) cc_final: 0.9249 (mp) REVERT: A 174 GLU cc_start: 0.8526 (mt-10) cc_final: 0.7869 (mt-10) REVERT: A 181 ASP cc_start: 0.8933 (m-30) cc_final: 0.8451 (m-30) REVERT: A 243 ARG cc_start: 0.5987 (ttt-90) cc_final: 0.5515 (tmt-80) REVERT: A 257 ASP cc_start: 0.9209 (m-30) cc_final: 0.8844 (m-30) REVERT: A 259 ASN cc_start: 0.9096 (p0) cc_final: 0.8798 (p0) REVERT: A 277 THR cc_start: 0.8753 (p) cc_final: 0.8266 (t) REVERT: A 286 ASP cc_start: 0.8790 (m-30) cc_final: 0.8586 (m-30) REVERT: A 290 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8393 (tm-30) REVERT: A 291 LEU cc_start: 0.9552 (mt) cc_final: 0.9338 (mt) REVERT: A 335 GLU cc_start: 0.7982 (mp0) cc_final: 0.7759 (mp0) REVERT: A 348 MET cc_start: 0.8845 (tpp) cc_final: 0.7789 (tpp) REVERT: A 355 TYR cc_start: 0.8869 (m-10) cc_final: 0.8647 (m-10) REVERT: A 362 ASP cc_start: 0.8449 (m-30) cc_final: 0.8106 (m-30) REVERT: A 366 LYS cc_start: 0.9452 (mtmt) cc_final: 0.9182 (mtmm) REVERT: A 385 VAL cc_start: 0.9463 (t) cc_final: 0.9171 (t) REVERT: A 396 ASP cc_start: 0.8769 (m-30) cc_final: 0.8356 (m-30) REVERT: A 418 ASN cc_start: 0.9148 (m110) cc_final: 0.8594 (m110) REVERT: A 421 GLU cc_start: 0.8777 (pp20) cc_final: 0.8543 (pp20) REVERT: A 441 GLU cc_start: 0.9193 (mm-30) cc_final: 0.8989 (mm-30) REVERT: A 458 MET cc_start: 0.8952 (mmp) cc_final: 0.8454 (mmp) REVERT: A 483 GLU cc_start: 0.9502 (mp0) cc_final: 0.9244 (mp0) REVERT: A 493 MET cc_start: 0.8823 (tmm) cc_final: 0.8244 (tmm) REVERT: A 515 ASP cc_start: 0.9104 (m-30) cc_final: 0.8760 (m-30) REVERT: A 583 SER cc_start: 0.9394 (m) cc_final: 0.8979 (t) REVERT: A 599 GLU cc_start: 0.8796 (pt0) cc_final: 0.8372 (pt0) REVERT: A 601 ILE cc_start: 0.9235 (tp) cc_final: 0.8788 (mm) REVERT: A 602 GLU cc_start: 0.7444 (tm-30) cc_final: 0.7212 (tm-30) REVERT: A 615 MET cc_start: 0.9343 (mmp) cc_final: 0.8699 (mmm) REVERT: A 639 ASP cc_start: 0.9083 (m-30) cc_final: 0.8789 (m-30) REVERT: A 650 GLN cc_start: 0.8636 (mt0) cc_final: 0.7641 (mt0) REVERT: A 669 ARG cc_start: 0.9052 (mtm-85) cc_final: 0.8665 (ttm110) REVERT: A 672 LEU cc_start: 0.9300 (mt) cc_final: 0.9048 (mt) REVERT: A 680 LYS cc_start: 0.9221 (mttt) cc_final: 0.8719 (mttt) REVERT: B 51 LEU cc_start: 0.9360 (tp) cc_final: 0.9097 (tp) REVERT: B 52 LYS cc_start: 0.9450 (tptp) cc_final: 0.9199 (tppt) REVERT: B 55 LEU cc_start: 0.9693 (mt) cc_final: 0.9445 (mt) REVERT: B 75 GLU cc_start: 0.9299 (mp0) cc_final: 0.8973 (pm20) REVERT: B 87 LYS cc_start: 0.9287 (tptp) cc_final: 0.8937 (tptp) REVERT: B 89 PHE cc_start: 0.9201 (t80) cc_final: 0.8907 (t80) REVERT: B 106 LEU cc_start: 0.9211 (tp) cc_final: 0.8901 (tt) REVERT: B 119 GLU cc_start: 0.9234 (mp0) cc_final: 0.8850 (mp0) REVERT: B 127 LEU cc_start: 0.9567 (mm) cc_final: 0.9183 (mm) REVERT: B 188 ILE cc_start: 0.9598 (mp) cc_final: 0.9326 (mp) REVERT: B 203 LEU cc_start: 0.9520 (mt) cc_final: 0.9299 (mt) REVERT: B 223 VAL cc_start: 0.9305 (m) cc_final: 0.8819 (m) REVERT: B 228 LYS cc_start: 0.9395 (mmmm) cc_final: 0.8724 (tppt) REVERT: B 232 ASN cc_start: 0.9428 (m-40) cc_final: 0.9136 (m-40) REVERT: B 250 TYR cc_start: 0.9079 (m-80) cc_final: 0.8621 (m-80) REVERT: B 257 ASP cc_start: 0.9036 (m-30) cc_final: 0.8198 (m-30) REVERT: B 260 ASP cc_start: 0.9473 (p0) cc_final: 0.9245 (p0) REVERT: B 286 ASP cc_start: 0.8613 (m-30) cc_final: 0.8132 (m-30) REVERT: B 291 LEU cc_start: 0.9567 (mt) cc_final: 0.9362 (mt) REVERT: B 322 MET cc_start: 0.9192 (mmm) cc_final: 0.8224 (mmm) REVERT: B 333 LYS cc_start: 0.9469 (tttp) cc_final: 0.9214 (ttmm) REVERT: B 344 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8932 (mm-30) REVERT: B 348 MET cc_start: 0.9146 (ptt) cc_final: 0.8248 (ptt) REVERT: B 355 TYR cc_start: 0.9058 (m-80) cc_final: 0.8614 (m-80) REVERT: B 392 SER cc_start: 0.9012 (m) cc_final: 0.8429 (p) REVERT: B 402 GLU cc_start: 0.8577 (tm-30) cc_final: 0.7995 (tm-30) REVERT: B 410 ASN cc_start: 0.8857 (m110) cc_final: 0.8524 (m110) REVERT: B 445 ILE cc_start: 0.9277 (mm) cc_final: 0.8539 (mm) REVERT: B 446 ARG cc_start: 0.8314 (mmt-90) cc_final: 0.7970 (mmp80) REVERT: B 459 LYS cc_start: 0.9138 (mmtp) cc_final: 0.8611 (mtmt) REVERT: B 480 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8106 (pp20) REVERT: B 515 ASP cc_start: 0.9300 (m-30) cc_final: 0.8819 (m-30) REVERT: B 516 GLN cc_start: 0.9359 (mm-40) cc_final: 0.9133 (mp10) REVERT: B 585 SER cc_start: 0.9009 (p) cc_final: 0.8431 (t) REVERT: B 615 MET cc_start: 0.9286 (mmp) cc_final: 0.9056 (mmp) REVERT: B 628 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8723 (mp0) REVERT: B 632 MET cc_start: 0.8368 (mpp) cc_final: 0.8103 (mpp) REVERT: B 636 LYS cc_start: 0.9547 (mmtm) cc_final: 0.9276 (mmmm) REVERT: B 645 GLN cc_start: 0.9297 (tp40) cc_final: 0.8949 (tp-100) REVERT: B 650 GLN cc_start: 0.8982 (mt0) cc_final: 0.8774 (mt0) REVERT: B 664 THR cc_start: 0.9418 (p) cc_final: 0.9142 (p) REVERT: B 668 ASN cc_start: 0.9272 (m110) cc_final: 0.8964 (m-40) REVERT: B 677 ARG cc_start: 0.9249 (mmm-85) cc_final: 0.8772 (mmm-85) REVERT: C 17 PHE cc_start: 0.8097 (p90) cc_final: 0.7313 (p90) REVERT: C 87 LYS cc_start: 0.8497 (mtmm) cc_final: 0.8269 (mttt) REVERT: C 154 PHE cc_start: 0.8346 (t80) cc_final: 0.7910 (t80) REVERT: C 204 TYR cc_start: 0.9312 (t80) cc_final: 0.9035 (t80) REVERT: C 281 ASP cc_start: 0.8783 (t0) cc_final: 0.8093 (p0) REVERT: D 23 ASN cc_start: 0.9511 (m110) cc_final: 0.9295 (m110) REVERT: D 46 TYR cc_start: 0.8696 (m-80) cc_final: 0.8199 (m-80) REVERT: D 169 TYR cc_start: 0.9451 (m-80) cc_final: 0.9024 (m-80) REVERT: D 172 PHE cc_start: 0.9131 (m-80) cc_final: 0.8712 (m-80) REVERT: D 177 TYR cc_start: 0.9162 (t80) cc_final: 0.8913 (t80) REVERT: D 259 PHE cc_start: 0.7978 (t80) cc_final: 0.7689 (t80) outliers start: 0 outliers final: 0 residues processed: 657 average time/residue: 0.2809 time to fit residues: 275.7327 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 : 1.877 ------------------------------------------------------------------------------- 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: 0.8980 chunk 30 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 159 optimal weight: 20.0000 chunk 72 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 183 optimal weight: 0.5980 chunk 52 optimal weight: 0.8980 chunk 180 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 150 GLN A 191 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** 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** C 23 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.138833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.099403 restraints weight = 40225.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.103082 restraints weight = 21867.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.105532 restraints weight = 13867.992| |-----------------------------------------------------------------------------| r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 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 = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.105 | | 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: 0.7627 moved from start: 0.7280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16386 Z= 0.138 Angle : 0.628 9.309 22134 Z= 0.330 Chirality : 0.044 0.187 2360 Planarity : 0.003 0.043 2818 Dihedral : 10.447 175.667 2242 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % 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: 0.81 (0.19), residues: 1932 helix: 1.03 (0.15), residues: 1148 sheet: -0.43 (0.41), residues: 144 loop : 0.09 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 124 HIS 0.013 0.001 HIS C 201 PHE 0.027 0.002 PHE D 178 TYR 0.031 0.002 TYR C 142 ARG 0.012 0.001 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 871) hydrogen bonds : angle 5.05020 ( 2571) covalent geometry : bond 0.00303 (16386) covalent geometry : angle 0.62850 (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 648 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 648 time to evaluate : 1.828 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: 0.9377 (mmtt) cc_final: 0.9029 (mmtm) REVERT: A 31 GLU cc_start: 0.9144 (mp0) cc_final: 0.8719 (mp0) REVERT: A 51 LEU cc_start: 0.9139 (tp) cc_final: 0.8820 (tp) REVERT: A 101 TYR cc_start: 0.9420 (m-80) cc_final: 0.9181 (m-10) REVERT: A 119 GLU cc_start: 0.8872 (mp0) cc_final: 0.8479 (mp0) REVERT: A 142 ASN cc_start: 0.9252 (m-40) cc_final: 0.8937 (m110) REVERT: A 147 GLN cc_start: 0.8628 (mm110) cc_final: 0.7839 (mm-40) REVERT: A 148 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8524 (mt-10) REVERT: A 158 ASN cc_start: 0.9370 (m-40) cc_final: 0.9165 (m-40) REVERT: A 172 LEU cc_start: 0.9475 (mp) cc_final: 0.9244 (mp) REVERT: A 174 GLU cc_start: 0.8412 (mt-10) cc_final: 0.7735 (mt-10) REVERT: A 181 ASP cc_start: 0.8871 (m-30) cc_final: 0.8401 (m-30) REVERT: A 257 ASP cc_start: 0.9326 (m-30) cc_final: 0.9027 (m-30) REVERT: A 277 THR cc_start: 0.8733 (p) cc_final: 0.8274 (t) REVERT: A 290 GLU cc_start: 0.8861 (tm-30) cc_final: 0.8395 (tm-30) REVERT: A 291 LEU cc_start: 0.9554 (mt) cc_final: 0.9325 (mt) REVERT: A 333 LYS cc_start: 0.9499 (tppp) cc_final: 0.9269 (tppp) REVERT: A 335 GLU cc_start: 0.8020 (mp0) cc_final: 0.7657 (mp0) REVERT: A 362 ASP cc_start: 0.8331 (m-30) cc_final: 0.8018 (m-30) REVERT: A 366 LYS cc_start: 0.9462 (mtmt) cc_final: 0.9200 (mtmm) REVERT: A 396 ASP cc_start: 0.8592 (m-30) cc_final: 0.7722 (m-30) REVERT: A 406 ASP cc_start: 0.8184 (m-30) cc_final: 0.7972 (m-30) REVERT: A 418 ASN cc_start: 0.9133 (m110) cc_final: 0.8564 (m110) REVERT: A 421 GLU cc_start: 0.8757 (pp20) cc_final: 0.8498 (pp20) REVERT: A 441 GLU cc_start: 0.9200 (mm-30) cc_final: 0.8987 (mm-30) REVERT: A 458 MET cc_start: 0.8823 (mmp) cc_final: 0.8362 (mmp) REVERT: A 483 GLU cc_start: 0.9525 (mp0) cc_final: 0.9278 (mp0) REVERT: A 493 MET cc_start: 0.8853 (tmm) cc_final: 0.8254 (tmm) REVERT: A 515 ASP cc_start: 0.9127 (m-30) cc_final: 0.8794 (m-30) REVERT: A 583 SER cc_start: 0.9359 (m) cc_final: 0.8904 (t) REVERT: A 599 GLU cc_start: 0.8869 (pt0) cc_final: 0.8604 (pt0) REVERT: A 601 ILE cc_start: 0.9282 (tp) cc_final: 0.8856 (mm) REVERT: A 615 MET cc_start: 0.9269 (mmp) cc_final: 0.9002 (mmp) REVERT: A 639 ASP cc_start: 0.9041 (m-30) cc_final: 0.8726 (m-30) REVERT: A 658 LEU cc_start: 0.9679 (mt) cc_final: 0.9342 (mt) REVERT: A 672 LEU cc_start: 0.9239 (mt) cc_final: 0.8974 (mt) REVERT: B 51 LEU cc_start: 0.9336 (tp) cc_final: 0.9129 (tp) REVERT: B 52 LYS cc_start: 0.9437 (tptp) cc_final: 0.9187 (tppt) REVERT: B 55 LEU cc_start: 0.9707 (mt) cc_final: 0.9486 (mt) REVERT: B 75 GLU cc_start: 0.9295 (mp0) cc_final: 0.8983 (pm20) REVERT: B 87 LYS cc_start: 0.9269 (tptp) cc_final: 0.8969 (tptp) REVERT: B 89 PHE cc_start: 0.9151 (t80) cc_final: 0.8898 (t80) REVERT: B 106 LEU cc_start: 0.9202 (tp) cc_final: 0.8956 (tt) REVERT: B 119 GLU cc_start: 0.9190 (mp0) cc_final: 0.8788 (mp0) REVERT: B 127 LEU cc_start: 0.9579 (mm) cc_final: 0.9199 (mm) REVERT: B 139 GLU cc_start: 0.9260 (mp0) cc_final: 0.8947 (mp0) REVERT: B 184 ARG cc_start: 0.9418 (tpp80) cc_final: 0.8894 (tpp80) REVERT: B 211 GLU cc_start: 0.8640 (mm-30) cc_final: 0.7963 (mm-30) REVERT: B 217 GLU cc_start: 0.8862 (mp0) cc_final: 0.8620 (mp0) REVERT: B 218 ASN cc_start: 0.9425 (m110) cc_final: 0.8952 (t0) REVERT: B 223 VAL cc_start: 0.9311 (m) cc_final: 0.8821 (m) REVERT: B 228 LYS cc_start: 0.9390 (mmmm) cc_final: 0.8690 (tppt) REVERT: B 232 ASN cc_start: 0.9418 (m-40) cc_final: 0.9126 (m-40) REVERT: B 250 TYR cc_start: 0.9124 (m-80) cc_final: 0.8774 (m-80) REVERT: B 257 ASP cc_start: 0.9069 (m-30) cc_final: 0.8707 (m-30) REVERT: B 260 ASP cc_start: 0.9439 (p0) cc_final: 0.9200 (p0) REVERT: B 263 ASP cc_start: 0.9092 (m-30) cc_final: 0.8691 (m-30) REVERT: B 283 VAL cc_start: 0.9582 (t) cc_final: 0.9380 (t) REVERT: B 286 ASP cc_start: 0.8687 (m-30) cc_final: 0.7936 (m-30) REVERT: B 322 MET cc_start: 0.9167 (mmm) cc_final: 0.8215 (mmm) REVERT: B 333 LYS cc_start: 0.9417 (tttp) cc_final: 0.9102 (ttmm) REVERT: B 344 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8981 (mm-30) REVERT: B 355 TYR cc_start: 0.9086 (m-80) cc_final: 0.8508 (m-10) REVERT: B 361 GLN cc_start: 0.9068 (tt0) cc_final: 0.8806 (tt0) REVERT: B 362 ASP cc_start: 0.8749 (m-30) cc_final: 0.7822 (m-30) REVERT: B 392 SER cc_start: 0.9070 (m) cc_final: 0.7905 (p) REVERT: B 398 ASP cc_start: 0.9064 (m-30) cc_final: 0.8846 (m-30) REVERT: B 410 ASN cc_start: 0.8783 (m110) cc_final: 0.8422 (m110) REVERT: B 415 ASN cc_start: 0.9523 (t0) cc_final: 0.9322 (t0) REVERT: B 425 ILE cc_start: 0.9654 (mt) cc_final: 0.9446 (mt) REVERT: B 440 SER cc_start: 0.9666 (p) cc_final: 0.9455 (p) REVERT: B 445 ILE cc_start: 0.9227 (mm) cc_final: 0.8522 (mm) REVERT: B 459 LYS cc_start: 0.9090 (mmtp) cc_final: 0.8583 (mtmt) REVERT: B 480 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8087 (pp20) REVERT: B 515 ASP cc_start: 0.9271 (m-30) cc_final: 0.8816 (m-30) REVERT: B 522 TYR cc_start: 0.8693 (m-10) cc_final: 0.8478 (m-10) REVERT: B 531 TYR cc_start: 0.8495 (m-80) cc_final: 0.8262 (m-80) REVERT: B 585 SER cc_start: 0.9016 (p) cc_final: 0.8484 (t) REVERT: B 606 TYR cc_start: 0.8247 (m-80) cc_final: 0.7946 (m-10) REVERT: B 615 MET cc_start: 0.9328 (mmp) cc_final: 0.9085 (mmp) REVERT: B 628 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8727 (mp0) REVERT: B 636 LYS cc_start: 0.9550 (mmtm) cc_final: 0.9251 (mmmm) REVERT: B 640 MET cc_start: 0.9410 (ttm) cc_final: 0.9148 (ttm) REVERT: B 645 GLN cc_start: 0.9315 (tp40) cc_final: 0.9010 (tp-100) REVERT: B 664 THR cc_start: 0.9425 (p) cc_final: 0.9133 (p) REVERT: B 668 ASN cc_start: 0.9170 (m110) cc_final: 0.8880 (m-40) REVERT: B 677 ARG cc_start: 0.9224 (mmm-85) cc_final: 0.8791 (mmm-85) REVERT: C 17 PHE cc_start: 0.8285 (p90) cc_final: 0.7749 (p90) REVERT: C 281 ASP cc_start: 0.8777 (t0) cc_final: 0.8117 (p0) REVERT: D 46 TYR cc_start: 0.8810 (m-80) cc_final: 0.8115 (m-80) REVERT: D 96 MET cc_start: 0.8850 (mmm) cc_final: 0.8580 (tpt) REVERT: D 169 TYR cc_start: 0.9460 (m-80) cc_final: 0.9119 (m-80) REVERT: D 172 PHE cc_start: 0.9158 (m-80) cc_final: 0.8828 (m-80) REVERT: D 259 PHE cc_start: 0.7954 (t80) cc_final: 0.7583 (t80) outliers start: 0 outliers final: 0 residues processed: 648 average time/residue: 0.2825 time to fit residues: 273.7004 Evaluate side-chains 574 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 574 time to evaluate : 1.758 ------------------------------------------------------------------------------- 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: 0.8980 chunk 102 optimal weight: 1.9990 chunk 182 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 115 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 188 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 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** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 28 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.139948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.099748 restraints weight = 40644.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.103463 restraints weight = 22326.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.106003 restraints weight = 14167.331| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 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 = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.7500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16386 Z= 0.149 Angle : 0.659 11.429 22134 Z= 0.347 Chirality : 0.044 0.190 2360 Planarity : 0.003 0.050 2818 Dihedral : 10.267 170.302 2242 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.19), residues: 1932 helix: 0.95 (0.15), residues: 1148 sheet: -0.47 (0.41), residues: 144 loop : 0.01 (0.24), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 124 HIS 0.012 0.001 HIS C 201 PHE 0.034 0.002 PHE D 154 TYR 0.042 0.002 TYR A 683 ARG 0.008 0.001 ARG A 604 Details of bonding type rmsd hydrogen bonds : bond 0.03900 ( 871) hydrogen bonds : angle 5.16875 ( 2571) covalent geometry : bond 0.00329 (16386) covalent geometry : angle 0.65945 (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 631 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 631 time to evaluate : 1.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.9356 (mmtt) cc_final: 0.8996 (mmtm) REVERT: A 31 GLU cc_start: 0.9136 (mp0) cc_final: 0.8719 (mp0) REVERT: A 101 TYR cc_start: 0.9396 (m-80) cc_final: 0.9173 (m-10) REVERT: A 119 GLU cc_start: 0.8772 (mp0) cc_final: 0.8420 (mp0) REVERT: A 125 VAL cc_start: 0.9591 (t) cc_final: 0.9358 (t) REVERT: A 136 LYS cc_start: 0.9306 (tptt) cc_final: 0.8975 (tptm) REVERT: A 147 GLN cc_start: 0.8605 (mm110) cc_final: 0.7795 (mm-40) REVERT: A 148 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8525 (mt-10) REVERT: A 158 ASN cc_start: 0.9406 (m-40) cc_final: 0.9197 (m-40) REVERT: A 172 LEU cc_start: 0.9463 (mp) cc_final: 0.9237 (mp) REVERT: A 174 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7647 (mt-10) REVERT: A 181 ASP cc_start: 0.8901 (m-30) cc_final: 0.8455 (m-30) REVERT: A 195 LEU cc_start: 0.9509 (mt) cc_final: 0.9227 (mt) REVERT: A 221 LYS cc_start: 0.8707 (mmtm) cc_final: 0.8500 (mttp) REVERT: A 257 ASP cc_start: 0.9303 (m-30) cc_final: 0.9021 (m-30) REVERT: A 277 THR cc_start: 0.8746 (p) cc_final: 0.8313 (t) REVERT: A 290 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8397 (tm-30) REVERT: A 291 LEU cc_start: 0.9544 (mt) cc_final: 0.9319 (mt) REVERT: A 295 ASP cc_start: 0.9061 (t0) cc_final: 0.8723 (t0) REVERT: A 333 LYS cc_start: 0.9490 (tppp) cc_final: 0.9277 (tppp) REVERT: A 335 GLU cc_start: 0.8104 (mp0) cc_final: 0.7751 (mp0) REVERT: A 366 LYS cc_start: 0.9476 (mtmt) cc_final: 0.9131 (mtmm) REVERT: A 385 VAL cc_start: 0.9426 (t) cc_final: 0.9067 (t) REVERT: A 396 ASP cc_start: 0.8640 (m-30) cc_final: 0.7803 (m-30) REVERT: A 417 LEU cc_start: 0.9617 (tt) cc_final: 0.9401 (tt) REVERT: A 418 ASN cc_start: 0.9013 (m110) cc_final: 0.8473 (m110) REVERT: A 421 GLU cc_start: 0.8735 (pp20) cc_final: 0.8467 (pp20) REVERT: A 441 GLU cc_start: 0.9210 (mm-30) cc_final: 0.8984 (mm-30) REVERT: A 458 MET cc_start: 0.8804 (mmp) cc_final: 0.8464 (mmm) REVERT: A 483 GLU cc_start: 0.9488 (mp0) cc_final: 0.9267 (mp0) REVERT: A 493 MET cc_start: 0.8826 (tmm) cc_final: 0.8229 (tmm) REVERT: A 515 ASP cc_start: 0.9116 (m-30) cc_final: 0.8853 (m-30) REVERT: A 583 SER cc_start: 0.9340 (m) cc_final: 0.8907 (t) REVERT: A 599 GLU cc_start: 0.8975 (pt0) cc_final: 0.8754 (pt0) REVERT: A 601 ILE cc_start: 0.9235 (tp) cc_final: 0.8766 (mm) REVERT: A 602 GLU cc_start: 0.7426 (tm-30) cc_final: 0.7015 (tm-30) REVERT: A 639 ASP cc_start: 0.9047 (m-30) cc_final: 0.8758 (m-30) REVERT: A 650 GLN cc_start: 0.8596 (mt0) cc_final: 0.7792 (mt0) REVERT: A 658 LEU cc_start: 0.9596 (mt) cc_final: 0.9354 (mt) REVERT: A 672 LEU cc_start: 0.9237 (mt) cc_final: 0.8977 (mt) REVERT: B 51 LEU cc_start: 0.9379 (tp) cc_final: 0.9126 (tp) REVERT: B 52 LYS cc_start: 0.9418 (tptp) cc_final: 0.9201 (tppt) REVERT: B 55 LEU cc_start: 0.9711 (mt) cc_final: 0.9470 (mt) REVERT: B 75 GLU cc_start: 0.9274 (mp0) cc_final: 0.8958 (pm20) REVERT: B 87 LYS cc_start: 0.9254 (tptp) cc_final: 0.8992 (tptp) REVERT: B 95 MET cc_start: 0.9184 (tpp) cc_final: 0.8805 (tpp) REVERT: B 119 GLU cc_start: 0.9244 (mp0) cc_final: 0.8835 (mp0) REVERT: B 127 LEU cc_start: 0.9584 (mm) cc_final: 0.9209 (mm) REVERT: B 184 ARG cc_start: 0.9416 (tpp80) cc_final: 0.8888 (tpp80) REVERT: B 211 GLU cc_start: 0.8645 (mm-30) cc_final: 0.8069 (mm-30) REVERT: B 217 GLU cc_start: 0.8862 (mp0) cc_final: 0.8615 (mp0) REVERT: B 218 ASN cc_start: 0.9430 (m110) cc_final: 0.8980 (t0) REVERT: B 223 VAL cc_start: 0.9346 (m) cc_final: 0.8928 (m) REVERT: B 228 LYS cc_start: 0.9365 (mmmm) cc_final: 0.8702 (tppt) REVERT: B 232 ASN cc_start: 0.9458 (m-40) cc_final: 0.9125 (m-40) REVERT: B 250 TYR cc_start: 0.9225 (m-80) cc_final: 0.8763 (m-80) REVERT: B 260 ASP cc_start: 0.9450 (p0) cc_final: 0.9237 (p0) REVERT: B 286 ASP cc_start: 0.8684 (m-30) cc_final: 0.7965 (m-30) REVERT: B 322 MET cc_start: 0.9171 (mmm) cc_final: 0.8245 (mmm) REVERT: B 333 LYS cc_start: 0.9436 (tttp) cc_final: 0.9106 (ttmm) REVERT: B 344 GLU cc_start: 0.9227 (mt-10) cc_final: 0.8951 (mm-30) REVERT: B 355 TYR cc_start: 0.9090 (m-80) cc_final: 0.8494 (m-10) REVERT: B 362 ASP cc_start: 0.8758 (m-30) cc_final: 0.7940 (m-30) REVERT: B 392 SER cc_start: 0.8780 (m) cc_final: 0.8187 (p) REVERT: B 407 ILE cc_start: 0.9093 (mt) cc_final: 0.8804 (mt) REVERT: B 456 LYS cc_start: 0.9412 (ttpt) cc_final: 0.9212 (ttpp) REVERT: B 459 LYS cc_start: 0.9076 (mmtp) cc_final: 0.8825 (mptt) REVERT: B 480 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8180 (pp20) REVERT: B 505 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8564 (mt-10) REVERT: B 515 ASP cc_start: 0.9277 (m-30) cc_final: 0.8749 (m-30) REVERT: B 585 SER cc_start: 0.8977 (p) cc_final: 0.8423 (t) REVERT: B 606 TYR cc_start: 0.8342 (m-80) cc_final: 0.8022 (m-10) REVERT: B 615 MET cc_start: 0.9242 (mmp) cc_final: 0.9000 (mmp) REVERT: B 636 LYS cc_start: 0.9549 (mmtm) cc_final: 0.9249 (mmmm) REVERT: B 664 THR cc_start: 0.9415 (p) cc_final: 0.9115 (p) REVERT: B 668 ASN cc_start: 0.9178 (m110) cc_final: 0.8887 (m-40) REVERT: B 677 ARG cc_start: 0.9193 (mmm-85) cc_final: 0.8789 (mmm-85) REVERT: C 17 PHE cc_start: 0.8373 (p90) cc_final: 0.7630 (p90) REVERT: C 87 LYS cc_start: 0.8508 (mtmm) cc_final: 0.8282 (mttt) REVERT: C 149 ASP cc_start: 0.8624 (m-30) cc_final: 0.8423 (m-30) REVERT: C 211 GLU cc_start: 0.7014 (mp0) cc_final: 0.6488 (pp20) REVERT: C 281 ASP cc_start: 0.8807 (t0) cc_final: 0.8209 (p0) REVERT: D 46 TYR cc_start: 0.8821 (m-80) cc_final: 0.8214 (m-80) REVERT: D 169 TYR cc_start: 0.9519 (m-80) cc_final: 0.8751 (m-80) REVERT: D 172 PHE cc_start: 0.9143 (m-80) cc_final: 0.8693 (m-80) REVERT: D 173 TYR cc_start: 0.8068 (t80) cc_final: 0.7460 (t80) outliers start: 0 outliers final: 0 residues processed: 631 average time/residue: 0.2926 time to fit residues: 281.6035 Evaluate side-chains 563 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 563 time to evaluate : 1.768 ------------------------------------------------------------------------------- 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: 0.0060 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 chunk 160 optimal weight: 30.0000 chunk 106 optimal weight: 7.9990 chunk 120 optimal weight: 0.5980 chunk 135 optimal weight: 0.9990 chunk 148 optimal weight: 6.9990 chunk 127 optimal weight: 0.4980 chunk 68 optimal weight: 8.9990 chunk 70 optimal weight: 0.6980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 447 ASN ** A 647 HIS ** 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 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.142601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.103152 restraints weight = 40476.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.106845 restraints weight = 22055.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.109351 restraints weight = 13998.748| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.7765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16386 Z= 0.135 Angle : 0.666 12.697 22134 Z= 0.351 Chirality : 0.044 0.179 2360 Planarity : 0.003 0.058 2818 Dihedral : 9.999 162.531 2242 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 13.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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: 0.71 (0.19), residues: 1932 helix: 0.90 (0.15), residues: 1147 sheet: 0.19 (0.45), residues: 120 loop : -0.04 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 124 HIS 0.011 0.001 HIS C 201 PHE 0.037 0.002 PHE D 154 TYR 0.048 0.002 TYR B 471 ARG 0.007 0.001 ARG A 164 Details of bonding type rmsd hydrogen bonds : bond 0.04012 ( 871) hydrogen bonds : angle 5.18926 ( 2571) covalent geometry : bond 0.00293 (16386) covalent geometry : angle 0.66562 (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 638 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 638 time to evaluate : 2.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 LYS cc_start: 0.9368 (mmtt) cc_final: 0.8975 (mmtm) REVERT: A 31 GLU cc_start: 0.9116 (mp0) cc_final: 0.8667 (mp0) REVERT: A 109 ASN cc_start: 0.9324 (m-40) cc_final: 0.9120 (m110) REVERT: A 119 GLU cc_start: 0.8786 (mp0) cc_final: 0.8368 (mp0) REVERT: A 148 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8511 (mt-10) REVERT: A 174 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7889 (mt-10) REVERT: A 181 ASP cc_start: 0.8859 (m-30) cc_final: 0.8450 (m-30) REVERT: A 195 LEU cc_start: 0.9499 (mt) cc_final: 0.9218 (mt) REVERT: A 257 ASP cc_start: 0.9321 (m-30) cc_final: 0.9004 (m-30) REVERT: A 277 THR cc_start: 0.8791 (p) cc_final: 0.8364 (t) REVERT: A 290 GLU cc_start: 0.8837 (tm-30) cc_final: 0.8410 (tm-30) REVERT: A 291 LEU cc_start: 0.9540 (mt) cc_final: 0.9333 (mt) REVERT: A 295 ASP cc_start: 0.9099 (t0) cc_final: 0.8819 (t0) REVERT: A 322 MET cc_start: 0.8983 (mmp) cc_final: 0.8706 (mmm) REVERT: A 333 LYS cc_start: 0.9481 (tppp) cc_final: 0.9233 (tppp) REVERT: A 335 GLU cc_start: 0.8157 (mp0) cc_final: 0.7790 (mp0) REVERT: A 345 LYS cc_start: 0.9392 (mmmt) cc_final: 0.8974 (tttt) REVERT: A 348 MET cc_start: 0.8831 (mmp) cc_final: 0.8367 (mtt) REVERT: A 366 LYS cc_start: 0.9496 (mtmt) cc_final: 0.9238 (mtmm) REVERT: A 385 VAL cc_start: 0.9396 (t) cc_final: 0.9067 (t) REVERT: A 396 ASP cc_start: 0.8501 (m-30) cc_final: 0.8028 (m-30) REVERT: A 418 ASN cc_start: 0.9010 (m110) cc_final: 0.8522 (m110) REVERT: A 421 GLU cc_start: 0.8766 (pp20) cc_final: 0.8449 (pp20) REVERT: A 441 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8993 (mm-30) REVERT: A 458 MET cc_start: 0.8652 (mmp) cc_final: 0.8253 (mmm) REVERT: A 483 GLU cc_start: 0.9489 (mp0) cc_final: 0.9253 (mp0) REVERT: A 493 MET cc_start: 0.8887 (tmm) cc_final: 0.8298 (tmm) REVERT: A 494 MET cc_start: 0.9012 (mmt) cc_final: 0.8498 (mmt) REVERT: A 515 ASP cc_start: 0.9114 (m-30) cc_final: 0.8853 (m-30) REVERT: A 583 SER cc_start: 0.9347 (m) cc_final: 0.8881 (t) REVERT: A 599 GLU cc_start: 0.9060 (pt0) cc_final: 0.8587 (pt0) REVERT: A 601 ILE cc_start: 0.9213 (tp) cc_final: 0.8800 (mm) REVERT: A 602 GLU cc_start: 0.7365 (tm-30) cc_final: 0.7018 (tm-30) REVERT: A 615 MET cc_start: 0.9327 (mmm) cc_final: 0.8943 (mmm) REVERT: A 639 ASP cc_start: 0.8984 (m-30) cc_final: 0.8703 (m-30) REVERT: A 645 GLN cc_start: 0.8619 (tp-100) cc_final: 0.8285 (tp40) REVERT: A 650 GLN cc_start: 0.8454 (mt0) cc_final: 0.7738 (mt0) REVERT: A 658 LEU cc_start: 0.9599 (mt) cc_final: 0.9392 (mt) REVERT: A 672 LEU cc_start: 0.9229 (mt) cc_final: 0.8953 (mt) REVERT: B 12 LEU cc_start: 0.9357 (mp) cc_final: 0.9109 (tp) REVERT: B 51 LEU cc_start: 0.9417 (tp) cc_final: 0.9194 (tp) REVERT: B 52 LYS cc_start: 0.9443 (tptp) cc_final: 0.9187 (tppt) REVERT: B 55 LEU cc_start: 0.9716 (mt) cc_final: 0.9485 (mt) REVERT: B 75 GLU cc_start: 0.9293 (mp0) cc_final: 0.8975 (pm20) REVERT: B 87 LYS cc_start: 0.9296 (tptp) cc_final: 0.9085 (tptp) REVERT: B 95 MET cc_start: 0.9206 (tpp) cc_final: 0.8794 (tpp) REVERT: B 106 LEU cc_start: 0.9210 (tp) cc_final: 0.8802 (tt) REVERT: B 119 GLU cc_start: 0.9132 (mp0) cc_final: 0.8739 (mp0) REVERT: B 127 LEU cc_start: 0.9576 (mm) cc_final: 0.9188 (mm) REVERT: B 184 ARG cc_start: 0.9420 (tpp80) cc_final: 0.8887 (tpp80) REVERT: B 211 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8238 (mm-30) REVERT: B 217 GLU cc_start: 0.8894 (mp0) cc_final: 0.8647 (mp0) REVERT: B 218 ASN cc_start: 0.9404 (m110) cc_final: 0.9061 (t0) REVERT: B 221 LYS cc_start: 0.8795 (mmtp) cc_final: 0.8504 (mmmm) REVERT: B 223 VAL cc_start: 0.9311 (m) cc_final: 0.8926 (m) REVERT: B 228 LYS cc_start: 0.9344 (mmmm) cc_final: 0.8641 (tppt) REVERT: B 232 ASN cc_start: 0.9423 (m-40) cc_final: 0.9120 (m-40) REVERT: B 250 TYR cc_start: 0.9191 (m-80) cc_final: 0.8826 (m-80) REVERT: B 263 ASP cc_start: 0.9016 (m-30) cc_final: 0.8674 (m-30) REVERT: B 286 ASP cc_start: 0.8684 (m-30) cc_final: 0.7958 (m-30) REVERT: B 322 MET cc_start: 0.9194 (mmm) cc_final: 0.8257 (mmm) REVERT: B 333 LYS cc_start: 0.9453 (tttp) cc_final: 0.9218 (ttmm) REVERT: B 344 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8967 (mm-30) REVERT: B 355 TYR cc_start: 0.9081 (m-80) cc_final: 0.8449 (m-10) REVERT: B 362 ASP cc_start: 0.8771 (m-30) cc_final: 0.7852 (m-30) REVERT: B 375 LYS cc_start: 0.9022 (mmmm) cc_final: 0.8568 (mmmm) REVERT: B 392 SER cc_start: 0.8879 (m) cc_final: 0.7892 (p) REVERT: B 434 ASP cc_start: 0.9284 (m-30) cc_final: 0.8995 (m-30) REVERT: B 459 LYS cc_start: 0.9061 (mmtp) cc_final: 0.8558 (mtmt) REVERT: B 460 SER cc_start: 0.9274 (p) cc_final: 0.9047 (p) REVERT: B 468 LEU cc_start: 0.9252 (tp) cc_final: 0.9002 (tp) REVERT: B 493 MET cc_start: 0.9445 (tmm) cc_final: 0.8896 (tmm) REVERT: B 505 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8535 (mt-10) REVERT: B 515 ASP cc_start: 0.9260 (m-30) cc_final: 0.8817 (m-30) REVERT: B 531 TYR cc_start: 0.8398 (m-80) cc_final: 0.8124 (m-80) REVERT: B 585 SER cc_start: 0.8929 (p) cc_final: 0.8421 (t) REVERT: B 591 THR cc_start: 0.8445 (p) cc_final: 0.8204 (p) REVERT: B 598 MET cc_start: 0.8954 (mtp) cc_final: 0.8569 (mtp) REVERT: B 606 TYR cc_start: 0.8268 (m-80) cc_final: 0.7950 (m-10) REVERT: B 615 MET cc_start: 0.9183 (mmp) cc_final: 0.8874 (mmp) REVERT: B 636 LYS cc_start: 0.9547 (mmtm) cc_final: 0.9215 (mmmm) REVERT: B 664 THR cc_start: 0.9418 (p) cc_final: 0.9115 (p) REVERT: B 668 ASN cc_start: 0.9123 (m110) cc_final: 0.8853 (m-40) REVERT: B 677 ARG cc_start: 0.9196 (mmm-85) cc_final: 0.8804 (mmm-85) REVERT: C 17 PHE cc_start: 0.8499 (p90) cc_final: 0.7888 (p90) REVERT: C 149 ASP cc_start: 0.8581 (m-30) cc_final: 0.8379 (m-30) REVERT: C 211 GLU cc_start: 0.7048 (mp0) cc_final: 0.6611 (pp20) REVERT: C 281 ASP cc_start: 0.8849 (t0) cc_final: 0.8258 (p0) REVERT: C 282 ILE cc_start: 0.6464 (mm) cc_final: 0.5516 (mm) REVERT: D 46 TYR cc_start: 0.8812 (m-80) cc_final: 0.8210 (m-80) REVERT: D 96 MET cc_start: 0.8437 (tpt) cc_final: 0.8193 (mmm) REVERT: D 169 TYR cc_start: 0.9133 (m-80) cc_final: 0.8851 (m-80) REVERT: D 172 PHE cc_start: 0.8989 (m-80) cc_final: 0.8681 (m-80) REVERT: D 173 TYR cc_start: 0.8608 (t80) cc_final: 0.8287 (t80) REVERT: D 236 TYR cc_start: 0.8871 (t80) cc_final: 0.8602 (t80) REVERT: D 313 GLU cc_start: 0.8717 (mp0) cc_final: 0.8387 (mp0) outliers start: 0 outliers final: 0 residues processed: 638 average time/residue: 0.3017 time to fit residues: 286.9742 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 : 1.767 ------------------------------------------------------------------------------- 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: 5.9990 chunk 16 optimal weight: 8.9990 chunk 2 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 190 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 180 optimal weight: 0.9980 chunk 108 optimal weight: 6.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 410 ASN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 647 HIS B 320 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 GLN ** D 28 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 = 0.3771 r_free = 0.3771 target = 0.134488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.096322 restraints weight = 40919.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.099805 restraints weight = 22349.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.102148 restraints weight = 14326.804| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 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 = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.7904 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= 0.187 Angle : 0.696 10.571 22134 Z= 0.370 Chirality : 0.045 0.186 2360 Planarity : 0.004 0.045 2818 Dihedral : 10.005 162.219 2242 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.06 % Allowed : 0.23 % Favored : 99.71 % 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: 0.55 (0.19), residues: 1932 helix: 0.76 (0.15), residues: 1165 sheet: 0.12 (0.44), residues: 124 loop : -0.11 (0.24), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 623 HIS 0.009 0.001 HIS C 201 PHE 0.025 0.002 PHE A 254 TYR 0.027 0.002 TYR A 683 ARG 0.010 0.001 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.04080 ( 871) hydrogen bonds : angle 5.27383 ( 2571) covalent geometry : bond 0.00406 (16386) covalent geometry : angle 0.69628 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7155.94 seconds wall clock time: 124 minutes 40.93 seconds (7480.93 seconds total)