Starting phenix.real_space_refine on Sat Jun 14 06:55:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzf_45066/06_2025/9bzf_45066_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzf_45066/06_2025/9bzf_45066.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bzf_45066/06_2025/9bzf_45066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzf_45066/06_2025/9bzf_45066.map" model { file = "/net/cci-nas-00/data/ceres_data/9bzf_45066/06_2025/9bzf_45066_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzf_45066/06_2025/9bzf_45066_neut.cif" } resolution = 4.4 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): 0.04s 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: 8.98, per 1000 atoms: 0.56 Number of scatterers: 16038 At special positions: 0 Unit cell: (100.386, 126.75, 130.806, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 82 16.00 P 16 15.00 Mg 2 11.99 O 3092 8.00 N 2614 7.00 C 10228 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.28 Conformation dependent library (CDL) restraints added in 1.9 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: 1.74 Creating SS restraints... Processing helix chain 'A' and resid 7 through 15 Processing helix chain 'A' and resid 25 through 39 removed outlier: 4.103A pdb=" N ASP A 29 " --> pdb=" O GLN A 25 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS A 30 " --> pdb=" O PHE A 26 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 3.985A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.953A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.664A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 195 Processing helix chain 'A' and resid 221 through 237 removed outlier: 4.127A pdb=" N GLY A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 264 Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.574A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 removed outlier: 3.695A pdb=" N MET A 317 " --> pdb=" O MET A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 329 removed outlier: 5.393A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 366 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 442 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 583 through 588 removed outlier: 3.628A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 678 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 25 through 40 removed outlier: 4.119A pdb=" N ASP B 29 " --> pdb=" O GLN B 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS B 30 " --> pdb=" O PHE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.074A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 removed outlier: 3.959A pdb=" N LYS B 87 " --> pdb=" O THR B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.676A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.646A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 removed outlier: 3.729A pdb=" N MET B 317 " --> pdb=" O MET B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 329 removed outlier: 6.027A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 442 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 516 through 519 removed outlier: 3.633A pdb=" N GLY B 519 " --> pdb=" O GLN B 516 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 516 through 519' Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.067A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.515A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.934A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 321 removed outlier: 3.669A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 321 " --> pdb=" O ASP C 318 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.876A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing sheet with id=AA1, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AA2, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.360A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 170 through 174 removed outlier: 6.478A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA5, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA6, first strand: chain 'A' and resid 656 through 658 removed outlier: 6.478A pdb=" N LEU A 656 " --> pdb=" O ARG A 686 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.185A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 149 through 151 removed outlier: 4.049A pdb=" N CYS B 409 " --> pdb=" O CYS B 170 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLY B 247 " --> pdb=" O SER B 279 " (cutoff:3.500A) removed outlier: 7.807A pdb=" N GLY B 281 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA B 249 " --> pdb=" O GLY B 281 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL B 283 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LEU B 251 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AB1, first strand: chain 'B' and resid 601 through 606 Processing sheet with id=AB2, first strand: chain 'B' and resid 656 through 659 873 hydrogen bonds defined for protein. 2571 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.29 Time building geometry restraints manager: 4.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4889 1.34 - 1.46: 3089 1.46 - 1.58: 8227 1.58 - 1.70: 25 1.70 - 1.82: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.060 1.25e-02 6.40e+03 2.34e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.038 1.20e-02 6.94e+03 1.01e+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 9.15e+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 7.42e+00 bond pdb=" CA ILE C 35 " pdb=" CB ILE C 35 " ideal model delta sigma weight residual 1.537 1.568 -0.031 1.21e-02 6.83e+03 6.76e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 21571 2.10 - 4.19: 521 4.19 - 6.29: 37 6.29 - 8.39: 1 8.39 - 10.49: 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 110.54 116.61 -6.07 1.36e+00 5.41e-01 1.99e+01 angle pdb=" N LEU C 167 " pdb=" CA LEU C 167 " pdb=" C LEU C 167 " ideal model delta sigma weight residual 111.71 116.09 -4.38 1.15e+00 7.56e-01 1.45e+01 angle pdb=" N TYR C 247 " pdb=" CA TYR C 247 " pdb=" C TYR C 247 " ideal model delta sigma weight residual 113.50 117.83 -4.33 1.23e+00 6.61e-01 1.24e+01 angle pdb=" N ASN D 38 " pdb=" CA ASN D 38 " pdb=" C ASN D 38 " ideal model delta sigma weight residual 111.71 115.67 -3.96 1.15e+00 7.56e-01 1.18e+01 angle pdb=" C MET D 74 " pdb=" N PRO D 75 " pdb=" CA PRO D 75 " ideal model delta sigma weight residual 119.19 115.55 3.64 1.06e+00 8.90e-01 1.18e+01 ... (remaining 22129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 9469 35.80 - 71.59: 338 71.59 - 107.39: 37 107.39 - 143.19: 3 143.19 - 178.99: 3 Dihedral angle restraints: 9850 sinusoidal: 4092 harmonic: 5758 Sorted by residual: dihedral pdb=" C2 TTP A 803 " pdb=" C1' TTP A 803 " pdb=" N1 TTP A 803 " pdb=" O4' TTP A 803 " ideal model delta sinusoidal sigma weight residual -58.32 120.67 -178.99 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C2 TTP B 801 " pdb=" C1' TTP B 801 " pdb=" N1 TTP B 801 " pdb=" O4' TTP B 801 " ideal model delta sinusoidal sigma weight residual 301.68 151.17 150.51 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 31.89 148.08 1 2.00e+01 2.50e-03 4.44e+01 ... (remaining 9847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2141 0.093 - 0.187: 187 0.187 - 0.280: 27 0.280 - 0.373: 3 0.373 - 0.466: 2 Chirality restraints: 2360 Sorted by residual: chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.44e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.57e+00 chirality pdb=" CA TYR D 169 " pdb=" N TYR D 169 " pdb=" C TYR D 169 " pdb=" CB TYR D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.95e+00 ... (remaining 2357 not shown) Planarity restraints: 2818 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET D 74 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO D 75 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 75 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 75 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 92 " -0.018 2.00e-02 2.50e+03 1.13e-02 2.22e+00 pdb=" CG PHE D 92 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE D 92 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE D 92 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE D 92 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 92 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 92 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 177 " -0.017 2.00e-02 2.50e+03 9.84e-03 1.94e+00 pdb=" CG TYR C 177 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TYR C 177 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 177 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR C 177 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 177 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 177 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR C 177 " -0.010 2.00e-02 2.50e+03 ... (remaining 2815 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 132 2.51 - 3.11: 11553 3.11 - 3.70: 27046 3.70 - 4.30: 41515 4.30 - 4.90: 65404 Nonbonded interactions: 145650 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 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 1.966 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OG1 THR A 108 " pdb=" OD1 ASP A 110 " model vdw 2.012 3.040 ... (remaining 145645 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 688) selection = (chain 'B' and resid 6 through 688) } ncs_group { reference = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.350 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: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 36.680 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6035 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 16386 Z= 0.316 Angle : 0.740 10.486 22134 Z= 0.463 Chirality : 0.058 0.466 2360 Planarity : 0.003 0.041 2818 Dihedral : 17.953 178.987 6154 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.34 % Allowed : 15.33 % Favored : 83.33 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.59 (0.14), residues: 1151 sheet: 0.47 (0.42), residues: 124 loop : 0.23 (0.23), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP D 44 HIS 0.006 0.001 HIS C 254 PHE 0.021 0.002 PHE C 227 TYR 0.020 0.002 TYR D 179 ARG 0.003 0.000 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.15420 ( 871) hydrogen bonds : angle 6.51691 ( 2571) covalent geometry : bond 0.00554 (16386) covalent geometry : angle 0.74027 (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 901 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 878 time to evaluate : 1.858 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: A 29 ASP cc_start: 0.8173 (t0) cc_final: 0.7972 (t70) REVERT: A 37 PHE cc_start: 0.6567 (m-80) cc_final: 0.6202 (m-10) REVERT: A 41 ILE cc_start: 0.8350 (mm) cc_final: 0.8046 (mm) REVERT: A 101 TYR cc_start: 0.7570 (m-80) cc_final: 0.7215 (m-10) REVERT: A 119 GLU cc_start: 0.7561 (mp0) cc_final: 0.6802 (mp0) REVERT: A 143 LEU cc_start: 0.8762 (tp) cc_final: 0.8409 (tp) REVERT: A 168 VAL cc_start: 0.8904 (t) cc_final: 0.8652 (t) REVERT: A 181 ASP cc_start: 0.8597 (m-30) cc_final: 0.8166 (m-30) REVERT: A 191 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7457 (mm110) REVERT: A 258 ILE cc_start: 0.8700 (tp) cc_final: 0.8365 (tp) REVERT: A 264 THR cc_start: 0.8998 (p) cc_final: 0.8793 (m) REVERT: A 278 LEU cc_start: 0.8386 (tp) cc_final: 0.8153 (tp) REVERT: A 322 MET cc_start: 0.7510 (mmp) cc_final: 0.6585 (mmm) REVERT: A 362 ASP cc_start: 0.5877 (m-30) cc_final: 0.4691 (m-30) REVERT: A 425 ILE cc_start: 0.9125 (mt) cc_final: 0.8809 (mt) REVERT: A 431 LEU cc_start: 0.9210 (mt) cc_final: 0.8859 (mm) REVERT: A 436 LEU cc_start: 0.9165 (mt) cc_final: 0.8802 (mt) REVERT: A 447 ASN cc_start: 0.7619 (m-40) cc_final: 0.6964 (m110) REVERT: A 493 MET cc_start: 0.7567 (tmm) cc_final: 0.7048 (tmm) REVERT: A 494 MET cc_start: 0.7764 (mtp) cc_final: 0.7311 (mtp) REVERT: A 500 ILE cc_start: 0.9352 (mt) cc_final: 0.9030 (mt) REVERT: A 522 TYR cc_start: 0.7435 (m-80) cc_final: 0.6466 (m-10) REVERT: A 531 TYR cc_start: 0.6454 (m-80) cc_final: 0.6044 (m-80) REVERT: A 558 TRP cc_start: 0.8229 (m100) cc_final: 0.6944 (m100) REVERT: A 561 LEU cc_start: 0.8853 (tp) cc_final: 0.8632 (tp) REVERT: A 565 VAL cc_start: 0.8965 (t) cc_final: 0.8734 (t) REVERT: A 571 TYR cc_start: 0.6916 (t80) cc_final: 0.6600 (t80) REVERT: A 575 ARG cc_start: 0.8503 (mtm110) cc_final: 0.7988 (ptp90) REVERT: A 655 THR cc_start: 0.8855 (m) cc_final: 0.8496 (t) REVERT: A 684 TYR cc_start: 0.5726 (m-80) cc_final: 0.4280 (m-80) REVERT: B 41 ILE cc_start: 0.8888 (mm) cc_final: 0.8445 (mm) REVERT: B 51 LEU cc_start: 0.8225 (tp) cc_final: 0.7885 (tp) REVERT: B 78 LYS cc_start: 0.8360 (tttp) cc_final: 0.8120 (tttt) REVERT: B 95 MET cc_start: 0.6966 (tpp) cc_final: 0.6650 (tpp) REVERT: B 99 LYS cc_start: 0.8995 (mmtt) cc_final: 0.8743 (mmtt) REVERT: B 101 TYR cc_start: 0.7746 (m-80) cc_final: 0.7545 (m-80) REVERT: B 121 ARG cc_start: 0.8271 (tpm170) cc_final: 0.7574 (tpp-160) REVERT: B 122 ILE cc_start: 0.9011 (mt) cc_final: 0.8377 (mt) REVERT: B 147 GLN cc_start: 0.8114 (mt0) cc_final: 0.5856 (mt0) REVERT: B 157 LEU cc_start: 0.8161 (tp) cc_final: 0.7916 (tp) REVERT: B 172 LEU cc_start: 0.9041 (mp) cc_final: 0.8740 (mp) REVERT: B 181 ASP cc_start: 0.8259 (m-30) cc_final: 0.7793 (m-30) REVERT: B 191 GLN cc_start: 0.8218 (mm-40) cc_final: 0.7848 (mm-40) REVERT: B 204 SER cc_start: 0.8945 (m) cc_final: 0.8452 (p) REVERT: B 258 ILE cc_start: 0.8950 (tp) cc_final: 0.8705 (tp) REVERT: B 291 LEU cc_start: 0.9105 (mt) cc_final: 0.8869 (mt) REVERT: B 319 MET cc_start: 0.7375 (tpp) cc_final: 0.7026 (mmp) REVERT: B 322 MET cc_start: 0.7547 (mmm) cc_final: 0.6396 (mmm) REVERT: B 418 ASN cc_start: 0.7391 (m-40) cc_final: 0.6754 (m-40) REVERT: B 469 HIS cc_start: 0.8278 (t-170) cc_final: 0.7984 (t70) REVERT: B 500 ILE cc_start: 0.9212 (mt) cc_final: 0.8849 (mt) REVERT: B 515 ASP cc_start: 0.8433 (m-30) cc_final: 0.8185 (m-30) REVERT: B 522 TYR cc_start: 0.7414 (m-80) cc_final: 0.6990 (m-10) REVERT: B 561 LEU cc_start: 0.8672 (tp) cc_final: 0.8434 (tp) REVERT: B 570 MET cc_start: 0.6615 (mtm) cc_final: 0.5997 (mtm) REVERT: B 587 VAL cc_start: 0.8980 (t) cc_final: 0.8624 (t) REVERT: B 588 GLN cc_start: 0.7762 (mm-40) cc_final: 0.6703 (mm-40) REVERT: B 589 SER cc_start: 0.8503 (m) cc_final: 0.7966 (p) REVERT: B 627 LYS cc_start: 0.8225 (tttt) cc_final: 0.8024 (tttt) REVERT: B 631 ASP cc_start: 0.7629 (m-30) cc_final: 0.7336 (t0) REVERT: B 644 ILE cc_start: 0.8499 (mt) cc_final: 0.8213 (mt) REVERT: B 655 THR cc_start: 0.9341 (m) cc_final: 0.8573 (t) REVERT: C 56 MET cc_start: -0.0066 (mmm) cc_final: -0.0494 (ttp) REVERT: C 90 LEU cc_start: 0.5964 (mt) cc_final: 0.5480 (mt) REVERT: C 95 MET cc_start: 0.5795 (tmm) cc_final: 0.5483 (tmm) REVERT: D 185 MET cc_start: 0.2872 (mmm) cc_final: 0.0385 (mpp) outliers start: 23 outliers final: 6 residues processed: 887 average time/residue: 0.3122 time to fit residues: 391.8601 Evaluate side-chains 613 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 607 time to evaluate : 1.685 ------------------------------------------------------------------------------- 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: 8.9990 chunk 145 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 112 optimal weight: 0.9980 chunk 174 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 242 GLN A 320 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN A 645 GLN B 150 GLN B 218 ASN ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 GLN B 645 GLN B 676 HIS C 24 GLN C 28 GLN C 186 GLN C 238 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.142174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.095749 restraints weight = 42649.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.099048 restraints weight = 26116.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.101143 restraints weight = 18335.319| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 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 = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16386 Z= 0.180 Angle : 0.635 9.003 22134 Z= 0.336 Chirality : 0.042 0.229 2360 Planarity : 0.004 0.060 2818 Dihedral : 11.414 179.944 2242 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 16.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 0.12 % Allowed : 2.68 % Favored : 97.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.53 (0.19), residues: 1932 helix: 1.54 (0.15), residues: 1121 sheet: -0.26 (0.40), residues: 148 loop : 0.62 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 30 HIS 0.009 0.001 HIS A 304 PHE 0.033 0.002 PHE D 320 TYR 0.061 0.002 TYR A 612 ARG 0.005 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04670 ( 871) hydrogen bonds : angle 5.03577 ( 2571) covalent geometry : bond 0.00384 (16386) covalent geometry : angle 0.63523 (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 735 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 733 time to evaluate : 1.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9315 (t0) cc_final: 0.9050 (t70) REVERT: A 40 TYR cc_start: 0.9129 (t80) cc_final: 0.8817 (t80) REVERT: A 51 LEU cc_start: 0.9386 (tp) cc_final: 0.9035 (tp) REVERT: A 89 PHE cc_start: 0.8876 (t80) cc_final: 0.8162 (t80) REVERT: A 119 GLU cc_start: 0.9191 (mp0) cc_final: 0.8440 (tm-30) REVERT: A 120 ASP cc_start: 0.9149 (m-30) cc_final: 0.8699 (m-30) REVERT: A 143 LEU cc_start: 0.9404 (tp) cc_final: 0.8949 (tp) REVERT: A 148 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8504 (mt-10) REVERT: A 181 ASP cc_start: 0.9108 (m-30) cc_final: 0.8884 (m-30) REVERT: A 195 LEU cc_start: 0.9574 (mt) cc_final: 0.9319 (mt) REVERT: A 227 MET cc_start: 0.9253 (mtm) cc_final: 0.9002 (mtm) REVERT: A 235 ARG cc_start: 0.8754 (mtm110) cc_final: 0.8470 (mtm110) REVERT: A 239 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.7246 (tt0) REVERT: A 252 ASN cc_start: 0.9370 (t0) cc_final: 0.8905 (t0) REVERT: A 286 ASP cc_start: 0.8985 (m-30) cc_final: 0.8183 (m-30) REVERT: A 307 TYR cc_start: 0.9553 (t80) cc_final: 0.9352 (t80) REVERT: A 322 MET cc_start: 0.9078 (mmp) cc_final: 0.8835 (mmm) REVERT: A 350 ARG cc_start: 0.8464 (mmm-85) cc_final: 0.8018 (mmm-85) REVERT: A 370 ASN cc_start: 0.9403 (m-40) cc_final: 0.9041 (m110) REVERT: A 402 GLU cc_start: 0.8534 (mp0) cc_final: 0.8236 (mp0) REVERT: A 459 LYS cc_start: 0.9056 (mttp) cc_final: 0.8592 (mtmt) REVERT: A 468 LEU cc_start: 0.9796 (tp) cc_final: 0.9513 (tp) REVERT: A 472 LEU cc_start: 0.9732 (mt) cc_final: 0.9444 (mt) REVERT: A 500 ILE cc_start: 0.9650 (mt) cc_final: 0.9435 (mt) REVERT: A 522 TYR cc_start: 0.9244 (m-80) cc_final: 0.8819 (m-10) REVERT: A 570 MET cc_start: 0.9038 (mtp) cc_final: 0.7807 (mtp) REVERT: A 575 ARG cc_start: 0.9113 (mtm110) cc_final: 0.8777 (ptp90) REVERT: A 598 MET cc_start: 0.9214 (mtp) cc_final: 0.8518 (mmt) REVERT: A 615 MET cc_start: 0.8734 (mmp) cc_final: 0.8309 (mmp) REVERT: A 632 MET cc_start: 0.8888 (mtp) cc_final: 0.8445 (mtm) REVERT: A 645 GLN cc_start: 0.8786 (tp40) cc_final: 0.8563 (tp-100) REVERT: A 650 GLN cc_start: 0.8745 (mt0) cc_final: 0.8161 (mt0) REVERT: A 657 PHE cc_start: 0.8470 (m-80) cc_final: 0.7625 (m-80) REVERT: B 17 MET cc_start: 0.8944 (mpp) cc_final: 0.8726 (mpp) REVERT: B 51 LEU cc_start: 0.9259 (tp) cc_final: 0.8865 (tp) REVERT: B 62 GLN cc_start: 0.9648 (mp-120) cc_final: 0.8977 (mp10) REVERT: B 95 MET cc_start: 0.9178 (tpp) cc_final: 0.8601 (tpp) REVERT: B 99 LYS cc_start: 0.9516 (mmmt) cc_final: 0.9049 (mmmt) REVERT: B 115 LEU cc_start: 0.9451 (mt) cc_final: 0.9184 (mt) REVERT: B 117 ARG cc_start: 0.9023 (ttm110) cc_final: 0.8778 (ttm110) REVERT: B 119 GLU cc_start: 0.9283 (mp0) cc_final: 0.8875 (mp0) REVERT: B 144 MET cc_start: 0.9299 (mtm) cc_final: 0.8908 (mtm) REVERT: B 147 GLN cc_start: 0.9042 (mt0) cc_final: 0.8618 (mt0) REVERT: B 205 LYS cc_start: 0.9430 (mmmt) cc_final: 0.8971 (mmmm) REVERT: B 211 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8135 (mm-30) REVERT: B 227 MET cc_start: 0.9392 (mtp) cc_final: 0.9158 (mtp) REVERT: B 236 TYR cc_start: 0.8976 (t80) cc_final: 0.8660 (t80) REVERT: B 251 LEU cc_start: 0.9489 (tp) cc_final: 0.9189 (tp) REVERT: B 252 ASN cc_start: 0.9337 (t0) cc_final: 0.9043 (t0) REVERT: B 286 ASP cc_start: 0.8753 (m-30) cc_final: 0.8188 (m-30) REVERT: B 288 PHE cc_start: 0.9438 (t80) cc_final: 0.9200 (t80) REVERT: B 291 LEU cc_start: 0.9610 (mt) cc_final: 0.9316 (mt) REVERT: B 322 MET cc_start: 0.9314 (mmm) cc_final: 0.8715 (mmm) REVERT: B 342 LEU cc_start: 0.9682 (tp) cc_final: 0.9336 (tp) REVERT: B 345 LYS cc_start: 0.9456 (tttt) cc_final: 0.9199 (tttt) REVERT: B 348 MET cc_start: 0.9264 (tpp) cc_final: 0.8647 (tpp) REVERT: B 362 ASP cc_start: 0.8996 (m-30) cc_final: 0.8120 (m-30) REVERT: B 393 SER cc_start: 0.9710 (t) cc_final: 0.9062 (p) REVERT: B 398 ASP cc_start: 0.8691 (t70) cc_final: 0.8405 (t70) REVERT: B 403 ILE cc_start: 0.9356 (mp) cc_final: 0.9051 (tp) REVERT: B 427 LYS cc_start: 0.9588 (ptpp) cc_final: 0.9237 (ptpp) REVERT: B 430 LYS cc_start: 0.9137 (ptpp) cc_final: 0.8871 (mtmm) REVERT: B 444 ASP cc_start: 0.8047 (t70) cc_final: 0.7802 (t0) REVERT: B 458 MET cc_start: 0.9409 (mmm) cc_final: 0.8859 (mmm) REVERT: B 494 MET cc_start: 0.9485 (mtt) cc_final: 0.9139 (mtt) REVERT: B 500 ILE cc_start: 0.9793 (mt) cc_final: 0.9486 (mt) REVERT: B 522 TYR cc_start: 0.9122 (m-80) cc_final: 0.8852 (m-10) REVERT: B 547 PHE cc_start: 0.8844 (m-80) cc_final: 0.8610 (m-80) REVERT: B 548 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8643 (mt-10) REVERT: B 570 MET cc_start: 0.9498 (mtp) cc_final: 0.8623 (mtp) REVERT: B 585 SER cc_start: 0.9070 (p) cc_final: 0.8526 (t) REVERT: B 591 THR cc_start: 0.9245 (p) cc_final: 0.9019 (p) REVERT: B 603 GLU cc_start: 0.8892 (tm-30) cc_final: 0.8088 (tm-30) REVERT: B 615 MET cc_start: 0.8795 (mmp) cc_final: 0.8300 (mmt) REVERT: B 631 ASP cc_start: 0.9369 (m-30) cc_final: 0.9031 (t0) REVERT: B 648 ILE cc_start: 0.9570 (mm) cc_final: 0.9347 (mm) REVERT: B 667 LEU cc_start: 0.9057 (tp) cc_final: 0.8701 (tp) REVERT: B 668 ASN cc_start: 0.9390 (m-40) cc_final: 0.8920 (m-40) REVERT: B 677 ARG cc_start: 0.9626 (mmm160) cc_final: 0.9225 (mmm-85) REVERT: C 95 MET cc_start: 0.8536 (tmm) cc_final: 0.8194 (tmm) REVERT: C 100 VAL cc_start: 0.8966 (t) cc_final: 0.8346 (t) REVERT: C 136 GLN cc_start: 0.0145 (mt0) cc_final: -0.0214 (tp40) REVERT: C 185 MET cc_start: 0.2108 (tmm) cc_final: 0.1491 (mmm) REVERT: C 227 PHE cc_start: 0.8893 (t80) cc_final: 0.8602 (t80) REVERT: D 17 PHE cc_start: 0.4674 (m-80) cc_final: 0.4376 (m-80) REVERT: D 96 MET cc_start: 0.9026 (mmm) cc_final: 0.8808 (mmt) REVERT: D 167 LEU cc_start: 0.9345 (mt) cc_final: 0.9144 (mt) REVERT: D 169 TYR cc_start: 0.8525 (m-80) cc_final: 0.8207 (m-80) REVERT: D 179 TYR cc_start: 0.6552 (t80) cc_final: 0.6050 (t80) REVERT: D 185 MET cc_start: 0.1549 (mmm) cc_final: 0.0900 (mpp) REVERT: D 197 ASP cc_start: 0.9339 (t70) cc_final: 0.9049 (t70) REVERT: D 201 HIS cc_start: 0.5460 (m170) cc_final: 0.4807 (m170) REVERT: D 212 ILE cc_start: 0.8694 (pt) cc_final: 0.8472 (pt) outliers start: 2 outliers final: 0 residues processed: 734 average time/residue: 0.3026 time to fit residues: 322.1075 Evaluate side-chains 596 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 595 time to evaluate : 1.758 ------------------------------------------------------------------------------- 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: 1.9990 chunk 168 optimal weight: 7.9990 chunk 175 optimal weight: 0.8980 chunk 34 optimal weight: 7.9990 chunk 47 optimal weight: 2.9990 chunk 191 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 189 optimal weight: 0.0010 chunk 141 optimal weight: 9.9990 overall best weight: 1.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 147 GLN A 180 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 GLN B 150 GLN B 191 GLN B 304 HIS B 418 ASN ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN C 52 GLN C 127 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.135614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.090848 restraints weight = 44671.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.094082 restraints weight = 26882.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.096299 restraints weight = 18129.089| |-----------------------------------------------------------------------------| r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3219 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16386 Z= 0.167 Angle : 0.613 7.938 22134 Z= 0.324 Chirality : 0.042 0.173 2360 Planarity : 0.004 0.113 2818 Dihedral : 11.234 173.626 2242 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.06 % Allowed : 2.68 % Favored : 97.26 % 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: 1.35 (0.19), residues: 1932 helix: 1.51 (0.15), residues: 1103 sheet: -0.47 (0.39), residues: 152 loop : 0.37 (0.24), residues: 677 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 124 HIS 0.007 0.001 HIS B 304 PHE 0.021 0.002 PHE A 129 TYR 0.042 0.002 TYR A 612 ARG 0.015 0.001 ARG A 669 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 871) hydrogen bonds : angle 4.91173 ( 2571) covalent geometry : bond 0.00359 (16386) covalent geometry : angle 0.61316 (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 689 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 688 time to evaluate : 1.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9382 (t0) cc_final: 0.9023 (t70) REVERT: A 81 PHE cc_start: 0.9464 (m-80) cc_final: 0.9246 (m-80) REVERT: A 88 LYS cc_start: 0.9497 (mptt) cc_final: 0.9198 (mmtt) REVERT: A 89 PHE cc_start: 0.9031 (t80) cc_final: 0.8649 (t80) REVERT: A 119 GLU cc_start: 0.9191 (mp0) cc_final: 0.8180 (tm-30) REVERT: A 143 LEU cc_start: 0.9376 (tp) cc_final: 0.8928 (tp) REVERT: A 147 GLN cc_start: 0.9111 (mm-40) cc_final: 0.8823 (mm-40) REVERT: A 148 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8374 (mt-10) REVERT: A 181 ASP cc_start: 0.9123 (m-30) cc_final: 0.8815 (m-30) REVERT: A 191 GLN cc_start: 0.9292 (mm-40) cc_final: 0.9048 (mm110) REVERT: A 195 LEU cc_start: 0.9555 (mt) cc_final: 0.9336 (mt) REVERT: A 227 MET cc_start: 0.9338 (mtm) cc_final: 0.9076 (mtm) REVERT: A 252 ASN cc_start: 0.9400 (t0) cc_final: 0.8945 (t0) REVERT: A 307 TYR cc_start: 0.9537 (t80) cc_final: 0.9172 (t80) REVERT: A 322 MET cc_start: 0.9188 (mmp) cc_final: 0.8686 (mmm) REVERT: A 370 ASN cc_start: 0.9444 (m-40) cc_final: 0.9157 (m110) REVERT: A 421 GLU cc_start: 0.9296 (tm-30) cc_final: 0.9039 (tm-30) REVERT: A 459 LYS cc_start: 0.9200 (mttp) cc_final: 0.8617 (mtmm) REVERT: A 468 LEU cc_start: 0.9802 (tp) cc_final: 0.9514 (tp) REVERT: A 472 LEU cc_start: 0.9734 (mt) cc_final: 0.9473 (mt) REVERT: A 494 MET cc_start: 0.9568 (mtp) cc_final: 0.9168 (mtp) REVERT: A 500 ILE cc_start: 0.9660 (mt) cc_final: 0.9263 (mt) REVERT: A 515 ASP cc_start: 0.9294 (m-30) cc_final: 0.8982 (m-30) REVERT: A 522 TYR cc_start: 0.9322 (m-80) cc_final: 0.8726 (m-10) REVERT: A 570 MET cc_start: 0.9283 (mtp) cc_final: 0.8096 (mtp) REVERT: A 575 ARG cc_start: 0.9238 (mtm110) cc_final: 0.8913 (mtm-85) REVERT: A 598 MET cc_start: 0.9349 (mtp) cc_final: 0.8723 (mmm) REVERT: A 641 ILE cc_start: 0.9885 (mm) cc_final: 0.9674 (mm) REVERT: A 650 GLN cc_start: 0.8782 (mt0) cc_final: 0.7934 (mt0) REVERT: A 657 PHE cc_start: 0.8478 (m-80) cc_final: 0.8166 (m-80) REVERT: B 15 GLU cc_start: 0.9174 (tp30) cc_final: 0.8778 (tp30) REVERT: B 51 LEU cc_start: 0.9292 (tp) cc_final: 0.8904 (tp) REVERT: B 95 MET cc_start: 0.9078 (tpp) cc_final: 0.8481 (mmm) REVERT: B 99 LYS cc_start: 0.9545 (mmmt) cc_final: 0.9028 (mmmt) REVERT: B 115 LEU cc_start: 0.9541 (mt) cc_final: 0.9237 (mt) REVERT: B 139 GLU cc_start: 0.9463 (mp0) cc_final: 0.9171 (mp0) REVERT: B 144 MET cc_start: 0.9277 (mtm) cc_final: 0.8804 (mtm) REVERT: B 147 GLN cc_start: 0.9046 (mt0) cc_final: 0.7719 (mt0) REVERT: B 158 ASN cc_start: 0.9645 (m110) cc_final: 0.9092 (p0) REVERT: B 161 ARG cc_start: 0.8798 (ttm110) cc_final: 0.8156 (mtp85) REVERT: B 164 ARG cc_start: 0.8806 (ttp80) cc_final: 0.8597 (ttp80) REVERT: B 191 GLN cc_start: 0.9287 (mm110) cc_final: 0.8993 (mm110) REVERT: B 211 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8331 (mm-30) REVERT: B 217 GLU cc_start: 0.9168 (pp20) cc_final: 0.8945 (tm-30) REVERT: B 218 ASN cc_start: 0.9662 (t0) cc_final: 0.9398 (t0) REVERT: B 227 MET cc_start: 0.9373 (mtp) cc_final: 0.9132 (mtp) REVERT: B 236 TYR cc_start: 0.8914 (t80) cc_final: 0.8540 (t80) REVERT: B 251 LEU cc_start: 0.9468 (tp) cc_final: 0.9176 (tp) REVERT: B 286 ASP cc_start: 0.8784 (m-30) cc_final: 0.8220 (m-30) REVERT: B 290 GLU cc_start: 0.9282 (pp20) cc_final: 0.9011 (pp20) REVERT: B 312 GLN cc_start: 0.9084 (pm20) cc_final: 0.8730 (pm20) REVERT: B 318 ASP cc_start: 0.9453 (t0) cc_final: 0.9248 (p0) REVERT: B 322 MET cc_start: 0.9178 (mmm) cc_final: 0.8488 (mmm) REVERT: B 342 LEU cc_start: 0.9728 (tp) cc_final: 0.9427 (tp) REVERT: B 345 LYS cc_start: 0.9537 (tttt) cc_final: 0.9201 (tttt) REVERT: B 357 TYR cc_start: 0.8713 (m-80) cc_final: 0.8512 (m-80) REVERT: B 362 ASP cc_start: 0.9082 (m-30) cc_final: 0.8160 (m-30) REVERT: B 375 LYS cc_start: 0.9177 (mmtm) cc_final: 0.8772 (mmtm) REVERT: B 386 LEU cc_start: 0.9142 (mt) cc_final: 0.8535 (mt) REVERT: B 393 SER cc_start: 0.9554 (t) cc_final: 0.9025 (t) REVERT: B 398 ASP cc_start: 0.8858 (t70) cc_final: 0.8646 (t70) REVERT: B 402 GLU cc_start: 0.8577 (mp0) cc_final: 0.8221 (mp0) REVERT: B 403 ILE cc_start: 0.9390 (mp) cc_final: 0.9032 (tp) REVERT: B 415 ASN cc_start: 0.9653 (t0) cc_final: 0.9398 (t0) REVERT: B 427 LYS cc_start: 0.9536 (ptpp) cc_final: 0.9309 (ptpp) REVERT: B 430 LYS cc_start: 0.9189 (ptpp) cc_final: 0.8981 (mtmm) REVERT: B 445 ILE cc_start: 0.8121 (mm) cc_final: 0.7857 (mm) REVERT: B 456 LYS cc_start: 0.9599 (mmmm) cc_final: 0.9393 (mtmt) REVERT: B 458 MET cc_start: 0.9426 (mmm) cc_final: 0.9101 (mmm) REVERT: B 494 MET cc_start: 0.9551 (mtt) cc_final: 0.9214 (mtt) REVERT: B 542 LYS cc_start: 0.9581 (mppt) cc_final: 0.9281 (mtmm) REVERT: B 570 MET cc_start: 0.9502 (mtp) cc_final: 0.8814 (mtp) REVERT: B 585 SER cc_start: 0.9128 (p) cc_final: 0.8654 (t) REVERT: B 588 GLN cc_start: 0.9571 (mm110) cc_final: 0.8701 (mm110) REVERT: B 591 THR cc_start: 0.9295 (p) cc_final: 0.9075 (p) REVERT: B 603 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8273 (tm-30) REVERT: B 615 MET cc_start: 0.8803 (mmp) cc_final: 0.8389 (mmp) REVERT: B 631 ASP cc_start: 0.9381 (m-30) cc_final: 0.9021 (t0) REVERT: B 645 GLN cc_start: 0.9114 (tp40) cc_final: 0.8910 (tp-100) REVERT: B 656 LEU cc_start: 0.9738 (mt) cc_final: 0.9482 (mt) REVERT: B 668 ASN cc_start: 0.9401 (m-40) cc_final: 0.8925 (m-40) REVERT: B 677 ARG cc_start: 0.9646 (mmm160) cc_final: 0.9273 (mmm-85) REVERT: C 56 MET cc_start: -0.0942 (ttp) cc_final: -0.1153 (ttp) REVERT: C 95 MET cc_start: 0.8696 (tmm) cc_final: 0.8405 (tmm) REVERT: C 100 VAL cc_start: 0.9113 (t) cc_final: 0.8836 (t) REVERT: C 101 HIS cc_start: 0.8057 (m90) cc_final: 0.7785 (m90) REVERT: C 124 TRP cc_start: 0.7661 (t60) cc_final: 0.7068 (t60) REVERT: D 22 TYR cc_start: 0.5104 (t80) cc_final: 0.4843 (t80) REVERT: D 69 GLN cc_start: 0.8955 (tp40) cc_final: 0.8488 (tm-30) REVERT: D 179 TYR cc_start: 0.6791 (t80) cc_final: 0.6421 (t80) REVERT: D 185 MET cc_start: 0.1811 (mmm) cc_final: 0.1235 (mpp) outliers start: 1 outliers final: 0 residues processed: 688 average time/residue: 0.2939 time to fit residues: 295.9185 Evaluate side-chains 595 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 595 time to evaluate : 1.881 ------------------------------------------------------------------------------- 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: 20.0000 chunk 99 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 50 optimal weight: 0.9990 chunk 69 optimal weight: 0.0570 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 overall best weight: 0.9504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 HIS ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN A 675 HIS B 150 GLN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN C 52 GLN C 238 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.136985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.091641 restraints weight = 44427.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.094932 restraints weight = 26599.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.096936 restraints weight = 18006.232| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16386 Z= 0.129 Angle : 0.585 7.289 22134 Z= 0.310 Chirality : 0.041 0.240 2360 Planarity : 0.004 0.081 2818 Dihedral : 10.794 167.084 2242 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 0.06 % Allowed : 1.92 % Favored : 98.02 % 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: 1.18 (0.19), residues: 1932 helix: 1.38 (0.15), residues: 1117 sheet: -0.48 (0.39), residues: 154 loop : 0.24 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 124 HIS 0.005 0.001 HIS B 438 PHE 0.033 0.002 PHE B 81 TYR 0.030 0.002 TYR B 574 ARG 0.009 0.001 ARG B 117 Details of bonding type rmsd hydrogen bonds : bond 0.03847 ( 871) hydrogen bonds : angle 4.77708 ( 2571) covalent geometry : bond 0.00277 (16386) covalent geometry : angle 0.58502 (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 673 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 672 time to evaluate : 1.823 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: A 29 ASP cc_start: 0.9470 (t0) cc_final: 0.9082 (t70) REVERT: A 67 GLU cc_start: 0.9474 (mp0) cc_final: 0.9265 (pm20) REVERT: A 88 LYS cc_start: 0.9514 (mptt) cc_final: 0.9285 (mmtt) REVERT: A 89 PHE cc_start: 0.9011 (t80) cc_final: 0.8650 (t80) REVERT: A 95 MET cc_start: 0.8652 (mmm) cc_final: 0.8293 (mmm) REVERT: A 119 GLU cc_start: 0.9117 (mp0) cc_final: 0.8130 (tm-30) REVERT: A 139 GLU cc_start: 0.9215 (mt-10) cc_final: 0.8770 (pt0) REVERT: A 143 LEU cc_start: 0.9367 (tp) cc_final: 0.9151 (tp) REVERT: A 147 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8679 (mm-40) REVERT: A 172 LEU cc_start: 0.9311 (mp) cc_final: 0.8816 (mp) REVERT: A 175 VAL cc_start: 0.9379 (t) cc_final: 0.9167 (t) REVERT: A 195 LEU cc_start: 0.9547 (mt) cc_final: 0.9325 (mt) REVERT: A 226 VAL cc_start: 0.9641 (t) cc_final: 0.9438 (t) REVERT: A 252 ASN cc_start: 0.9263 (t0) cc_final: 0.8851 (t0) REVERT: A 266 LYS cc_start: 0.9117 (mttp) cc_final: 0.8901 (mttp) REVERT: A 307 TYR cc_start: 0.9600 (t80) cc_final: 0.9143 (t80) REVERT: A 342 LEU cc_start: 0.9605 (tp) cc_final: 0.9265 (tp) REVERT: A 348 MET cc_start: 0.9390 (ptp) cc_final: 0.9159 (ptp) REVERT: A 350 ARG cc_start: 0.8810 (mmm-85) cc_final: 0.8171 (mmm-85) REVERT: A 370 ASN cc_start: 0.9527 (m-40) cc_final: 0.9204 (m110) REVERT: A 394 TYR cc_start: 0.9254 (m-80) cc_final: 0.8800 (m-80) REVERT: A 403 ILE cc_start: 0.9127 (tp) cc_final: 0.8918 (tp) REVERT: A 406 ASP cc_start: 0.8892 (m-30) cc_final: 0.8544 (m-30) REVERT: A 407 ILE cc_start: 0.9116 (mt) cc_final: 0.8866 (mt) REVERT: A 418 ASN cc_start: 0.9496 (m-40) cc_final: 0.8902 (m-40) REVERT: A 421 GLU cc_start: 0.9272 (tm-30) cc_final: 0.9061 (tm-30) REVERT: A 459 LYS cc_start: 0.9180 (mttp) cc_final: 0.8596 (mtmm) REVERT: A 468 LEU cc_start: 0.9775 (tp) cc_final: 0.9541 (tp) REVERT: A 472 LEU cc_start: 0.9721 (mt) cc_final: 0.9511 (mt) REVERT: A 493 MET cc_start: 0.9274 (tmm) cc_final: 0.8594 (tmm) REVERT: A 494 MET cc_start: 0.9504 (mtp) cc_final: 0.9101 (mtp) REVERT: A 500 ILE cc_start: 0.9628 (mt) cc_final: 0.9287 (mt) REVERT: A 515 ASP cc_start: 0.9303 (m-30) cc_final: 0.9028 (m-30) REVERT: A 522 TYR cc_start: 0.9365 (m-80) cc_final: 0.8923 (m-10) REVERT: A 531 TYR cc_start: 0.8276 (m-80) cc_final: 0.7922 (m-80) REVERT: A 570 MET cc_start: 0.9427 (mtp) cc_final: 0.8342 (mtp) REVERT: A 598 MET cc_start: 0.9258 (mtp) cc_final: 0.8859 (mmm) REVERT: A 599 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8833 (mt-10) REVERT: A 612 TYR cc_start: 0.8626 (m-80) cc_final: 0.8086 (m-80) REVERT: A 615 MET cc_start: 0.8572 (mmp) cc_final: 0.8360 (mmp) REVERT: A 645 GLN cc_start: 0.8983 (tp40) cc_final: 0.8741 (tp-100) REVERT: B 15 GLU cc_start: 0.9245 (tp30) cc_final: 0.8891 (tp30) REVERT: B 17 MET cc_start: 0.8971 (mpp) cc_final: 0.8697 (mpp) REVERT: B 51 LEU cc_start: 0.9408 (tp) cc_final: 0.8945 (tp) REVERT: B 95 MET cc_start: 0.9061 (tpp) cc_final: 0.8473 (tpp) REVERT: B 99 LYS cc_start: 0.9490 (mmmt) cc_final: 0.9021 (mmmt) REVERT: B 107 LYS cc_start: 0.9637 (mptt) cc_final: 0.9308 (mptt) REVERT: B 115 LEU cc_start: 0.9580 (mt) cc_final: 0.9360 (mt) REVERT: B 122 ILE cc_start: 0.9721 (mt) cc_final: 0.9494 (mt) REVERT: B 139 GLU cc_start: 0.9502 (mp0) cc_final: 0.9227 (mp0) REVERT: B 144 MET cc_start: 0.9127 (mtm) cc_final: 0.8667 (mtm) REVERT: B 147 GLN cc_start: 0.9232 (mt0) cc_final: 0.8574 (mm-40) REVERT: B 157 LEU cc_start: 0.9646 (tp) cc_final: 0.9153 (tp) REVERT: B 158 ASN cc_start: 0.9605 (m110) cc_final: 0.9098 (p0) REVERT: B 161 ARG cc_start: 0.8670 (ttm110) cc_final: 0.8127 (mtt180) REVERT: B 176 ASN cc_start: 0.8911 (t0) cc_final: 0.8698 (t0) REVERT: B 191 GLN cc_start: 0.9050 (mm110) cc_final: 0.8683 (mm110) REVERT: B 211 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8513 (mm-30) REVERT: B 217 GLU cc_start: 0.9141 (pp20) cc_final: 0.8921 (tm-30) REVERT: B 218 ASN cc_start: 0.9614 (t0) cc_final: 0.9339 (m-40) REVERT: B 227 MET cc_start: 0.9387 (mtp) cc_final: 0.9141 (mtp) REVERT: B 236 TYR cc_start: 0.8788 (t80) cc_final: 0.8258 (t80) REVERT: B 251 LEU cc_start: 0.9510 (tp) cc_final: 0.9240 (tp) REVERT: B 286 ASP cc_start: 0.8809 (m-30) cc_final: 0.8196 (m-30) REVERT: B 296 LYS cc_start: 0.8859 (mmpt) cc_final: 0.8513 (mtmm) REVERT: B 312 GLN cc_start: 0.9145 (pm20) cc_final: 0.8248 (pm20) REVERT: B 333 LYS cc_start: 0.9418 (ttmm) cc_final: 0.9150 (ttmm) REVERT: B 335 GLU cc_start: 0.8998 (pt0) cc_final: 0.8695 (pt0) REVERT: B 342 LEU cc_start: 0.9715 (tp) cc_final: 0.9458 (tp) REVERT: B 345 LYS cc_start: 0.9573 (tttt) cc_final: 0.9198 (tttt) REVERT: B 350 ARG cc_start: 0.8651 (mtp85) cc_final: 0.8377 (mtp85) REVERT: B 362 ASP cc_start: 0.9122 (m-30) cc_final: 0.8178 (m-30) REVERT: B 375 LYS cc_start: 0.9141 (mmtm) cc_final: 0.8916 (mmtm) REVERT: B 390 GLN cc_start: 0.9321 (mt0) cc_final: 0.9045 (mt0) REVERT: B 393 SER cc_start: 0.9567 (t) cc_final: 0.9071 (t) REVERT: B 398 ASP cc_start: 0.8882 (t70) cc_final: 0.8574 (t70) REVERT: B 399 GLU cc_start: 0.8908 (mp0) cc_final: 0.8695 (mp0) REVERT: B 402 GLU cc_start: 0.8646 (mp0) cc_final: 0.8314 (mp0) REVERT: B 403 ILE cc_start: 0.9339 (mp) cc_final: 0.8977 (tp) REVERT: B 427 LYS cc_start: 0.9593 (ptpp) cc_final: 0.9324 (ptpp) REVERT: B 447 ASN cc_start: 0.8411 (m-40) cc_final: 0.8087 (t0) REVERT: B 458 MET cc_start: 0.9433 (mmm) cc_final: 0.9136 (mmm) REVERT: B 494 MET cc_start: 0.9518 (mtt) cc_final: 0.9228 (mtt) REVERT: B 501 GLN cc_start: 0.9505 (mt0) cc_final: 0.8836 (mt0) REVERT: B 558 TRP cc_start: 0.9175 (m100) cc_final: 0.8926 (m100) REVERT: B 570 MET cc_start: 0.9432 (mtp) cc_final: 0.8997 (mtp) REVERT: B 585 SER cc_start: 0.9120 (p) cc_final: 0.8712 (t) REVERT: B 597 ILE cc_start: 0.9291 (pt) cc_final: 0.9077 (pt) REVERT: B 615 MET cc_start: 0.8975 (mmp) cc_final: 0.8502 (mmp) REVERT: B 631 ASP cc_start: 0.9536 (m-30) cc_final: 0.9157 (t0) REVERT: B 632 MET cc_start: 0.8742 (mmm) cc_final: 0.8291 (mmm) REVERT: B 650 GLN cc_start: 0.7905 (mm-40) cc_final: 0.6981 (mm-40) REVERT: B 667 LEU cc_start: 0.9224 (tp) cc_final: 0.8912 (tp) REVERT: B 668 ASN cc_start: 0.9336 (m-40) cc_final: 0.8952 (m-40) REVERT: B 677 ARG cc_start: 0.9624 (mmm160) cc_final: 0.9246 (mmm-85) REVERT: C 95 MET cc_start: 0.8855 (tmm) cc_final: 0.8580 (tmm) REVERT: C 101 HIS cc_start: 0.7580 (m90) cc_final: 0.7192 (m90) REVERT: C 124 TRP cc_start: 0.7635 (t60) cc_final: 0.7323 (t60) REVERT: C 185 MET cc_start: 0.3036 (tmm) cc_final: 0.2407 (mmm) REVERT: C 261 ARG cc_start: 0.5831 (mtm110) cc_final: 0.5489 (ptp90) REVERT: C 315 LEU cc_start: 0.8480 (mm) cc_final: 0.8242 (mm) REVERT: D 69 GLN cc_start: 0.8969 (tp40) cc_final: 0.8430 (tm-30) REVERT: D 97 GLU cc_start: 0.2145 (mp0) cc_final: 0.0691 (mp0) REVERT: D 179 TYR cc_start: 0.6903 (t80) cc_final: 0.6546 (t80) REVERT: D 185 MET cc_start: 0.2021 (mmm) cc_final: 0.1647 (mpp) REVERT: D 201 HIS cc_start: 0.5846 (m170) cc_final: 0.5349 (m90) outliers start: 1 outliers final: 0 residues processed: 672 average time/residue: 0.3050 time to fit residues: 304.5092 Evaluate side-chains 575 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 575 time to evaluate : 1.746 ------------------------------------------------------------------------------- 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: 3.9990 chunk 41 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 51 optimal weight: 0.0030 chunk 175 optimal weight: 7.9990 chunk 182 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 242 GLN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN ** B 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.141447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.095311 restraints weight = 45100.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.098677 restraints weight = 26400.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.100876 restraints weight = 17708.137| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.5949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16386 Z= 0.122 Angle : 0.577 7.666 22134 Z= 0.302 Chirality : 0.041 0.189 2360 Planarity : 0.004 0.062 2818 Dihedral : 10.431 163.591 2242 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % 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: 1.33 (0.15), residues: 1119 sheet: -0.64 (0.38), residues: 154 loop : 0.20 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 124 HIS 0.005 0.001 HIS B 469 PHE 0.020 0.002 PHE B 81 TYR 0.023 0.001 TYR B 574 ARG 0.009 0.001 ARG B 117 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 871) hydrogen bonds : angle 4.79231 ( 2571) covalent geometry : bond 0.00266 (16386) covalent geometry : angle 0.57699 (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 653 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 653 time to evaluate : 1.750 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: A 29 ASP cc_start: 0.9485 (t0) cc_final: 0.9046 (t70) REVERT: A 67 GLU cc_start: 0.9475 (mp0) cc_final: 0.9264 (pm20) REVERT: A 89 PHE cc_start: 0.8986 (t80) cc_final: 0.8606 (t80) REVERT: A 95 MET cc_start: 0.8688 (mmm) cc_final: 0.8391 (mmm) REVERT: A 119 GLU cc_start: 0.9105 (mp0) cc_final: 0.7983 (tm-30) REVERT: A 143 LEU cc_start: 0.9500 (tp) cc_final: 0.9102 (tp) REVERT: A 147 GLN cc_start: 0.9172 (mm-40) cc_final: 0.8713 (mm110) REVERT: A 164 ARG cc_start: 0.8192 (ptm-80) cc_final: 0.7741 (ptm-80) REVERT: A 172 LEU cc_start: 0.9287 (mp) cc_final: 0.8848 (mp) REVERT: A 175 VAL cc_start: 0.9389 (t) cc_final: 0.9187 (t) REVERT: A 195 LEU cc_start: 0.9557 (mt) cc_final: 0.9342 (mt) REVERT: A 204 SER cc_start: 0.9400 (m) cc_final: 0.9192 (m) REVERT: A 252 ASN cc_start: 0.9352 (t0) cc_final: 0.8841 (t0) REVERT: A 307 TYR cc_start: 0.9586 (t80) cc_final: 0.9129 (t80) REVERT: A 335 GLU cc_start: 0.8592 (mm-30) cc_final: 0.8165 (mp0) REVERT: A 350 ARG cc_start: 0.8831 (mmm-85) cc_final: 0.8166 (mmm-85) REVERT: A 361 GLN cc_start: 0.9434 (tt0) cc_final: 0.9134 (tp40) REVERT: A 370 ASN cc_start: 0.9509 (m-40) cc_final: 0.9207 (m110) REVERT: A 394 TYR cc_start: 0.9255 (m-80) cc_final: 0.8737 (m-80) REVERT: A 406 ASP cc_start: 0.8964 (m-30) cc_final: 0.8636 (m-30) REVERT: A 407 ILE cc_start: 0.9096 (mt) cc_final: 0.8855 (mt) REVERT: A 415 ASN cc_start: 0.9188 (t0) cc_final: 0.8848 (t0) REVERT: A 417 LEU cc_start: 0.9787 (tt) cc_final: 0.9583 (tt) REVERT: A 418 ASN cc_start: 0.9508 (m-40) cc_final: 0.8938 (m-40) REVERT: A 421 GLU cc_start: 0.9303 (tm-30) cc_final: 0.9073 (tm-30) REVERT: A 468 LEU cc_start: 0.9727 (tp) cc_final: 0.9380 (tp) REVERT: A 479 TYR cc_start: 0.9174 (t80) cc_final: 0.8862 (t80) REVERT: A 493 MET cc_start: 0.9276 (tmm) cc_final: 0.9044 (tmm) REVERT: A 494 MET cc_start: 0.9516 (mtp) cc_final: 0.9078 (mtp) REVERT: A 500 ILE cc_start: 0.9630 (mt) cc_final: 0.8937 (mt) REVERT: A 522 TYR cc_start: 0.9351 (m-80) cc_final: 0.9041 (m-10) REVERT: A 558 TRP cc_start: 0.9298 (m100) cc_final: 0.9005 (m100) REVERT: A 570 MET cc_start: 0.9400 (mtp) cc_final: 0.8309 (mtp) REVERT: A 575 ARG cc_start: 0.9268 (mtm-85) cc_final: 0.8952 (mpp80) REVERT: A 598 MET cc_start: 0.9290 (mtp) cc_final: 0.8960 (mmm) REVERT: A 603 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8794 (tp30) REVERT: A 615 MET cc_start: 0.8587 (mmp) cc_final: 0.8346 (mmp) REVERT: A 640 MET cc_start: 0.9162 (tpp) cc_final: 0.8942 (tpp) REVERT: A 641 ILE cc_start: 0.9873 (mm) cc_final: 0.9662 (mm) REVERT: A 645 GLN cc_start: 0.9054 (tp40) cc_final: 0.8830 (tp-100) REVERT: A 650 GLN cc_start: 0.8890 (mt0) cc_final: 0.7949 (mt0) REVERT: A 654 PHE cc_start: 0.9370 (t80) cc_final: 0.9057 (t80) REVERT: B 15 GLU cc_start: 0.9278 (tp30) cc_final: 0.8892 (tp30) REVERT: B 17 MET cc_start: 0.8932 (mpp) cc_final: 0.8649 (mpp) REVERT: B 51 LEU cc_start: 0.9402 (tp) cc_final: 0.9071 (tp) REVERT: B 87 LYS cc_start: 0.9110 (tttt) cc_final: 0.8839 (mtpt) REVERT: B 95 MET cc_start: 0.9089 (tpp) cc_final: 0.8554 (tpp) REVERT: B 99 LYS cc_start: 0.9539 (mmmt) cc_final: 0.9033 (mmmt) REVERT: B 100 PHE cc_start: 0.9574 (t80) cc_final: 0.9362 (t80) REVERT: B 101 TYR cc_start: 0.9425 (m-10) cc_final: 0.8911 (m-10) REVERT: B 115 LEU cc_start: 0.9627 (mt) cc_final: 0.9379 (mt) REVERT: B 136 LYS cc_start: 0.9615 (mmtp) cc_final: 0.9394 (mmmm) REVERT: B 143 LEU cc_start: 0.9431 (tp) cc_final: 0.9095 (tp) REVERT: B 145 ILE cc_start: 0.9700 (tp) cc_final: 0.9466 (tp) REVERT: B 147 GLN cc_start: 0.9077 (mt0) cc_final: 0.8826 (mt0) REVERT: B 157 LEU cc_start: 0.9549 (tp) cc_final: 0.9218 (tp) REVERT: B 158 ASN cc_start: 0.9512 (m110) cc_final: 0.9149 (p0) REVERT: B 161 ARG cc_start: 0.8764 (ttm110) cc_final: 0.8163 (mtt180) REVERT: B 164 ARG cc_start: 0.9280 (ttp80) cc_final: 0.8703 (tmm-80) REVERT: B 191 GLN cc_start: 0.9066 (mm110) cc_final: 0.8865 (mm110) REVERT: B 211 GLU cc_start: 0.8894 (mm-30) cc_final: 0.8458 (mm-30) REVERT: B 217 GLU cc_start: 0.9180 (pp20) cc_final: 0.8933 (tm-30) REVERT: B 218 ASN cc_start: 0.9601 (t0) cc_final: 0.9307 (m-40) REVERT: B 227 MET cc_start: 0.9381 (mtp) cc_final: 0.9105 (mtp) REVERT: B 236 TYR cc_start: 0.8616 (t80) cc_final: 0.8333 (t80) REVERT: B 251 LEU cc_start: 0.9546 (tp) cc_final: 0.9287 (tp) REVERT: B 286 ASP cc_start: 0.8800 (m-30) cc_final: 0.8223 (m-30) REVERT: B 290 GLU cc_start: 0.9239 (pp20) cc_final: 0.8642 (pp20) REVERT: B 291 LEU cc_start: 0.9598 (mt) cc_final: 0.9336 (mt) REVERT: B 296 LYS cc_start: 0.8914 (mmpt) cc_final: 0.8527 (mtmm) REVERT: B 316 GLU cc_start: 0.9378 (pt0) cc_final: 0.9116 (pp20) REVERT: B 321 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8526 (tm-30) REVERT: B 322 MET cc_start: 0.9068 (mmm) cc_final: 0.8171 (mmm) REVERT: B 333 LYS cc_start: 0.9573 (ttmm) cc_final: 0.9265 (ttmm) REVERT: B 335 GLU cc_start: 0.9011 (pt0) cc_final: 0.8724 (pt0) REVERT: B 345 LYS cc_start: 0.9630 (tttt) cc_final: 0.9304 (tttt) REVERT: B 350 ARG cc_start: 0.8593 (mtp85) cc_final: 0.8319 (mtp85) REVERT: B 362 ASP cc_start: 0.9139 (m-30) cc_final: 0.8129 (m-30) REVERT: B 373 ILE cc_start: 0.9522 (tp) cc_final: 0.9213 (tp) REVERT: B 375 LYS cc_start: 0.9151 (mmtm) cc_final: 0.8923 (mmtm) REVERT: B 390 GLN cc_start: 0.9363 (mt0) cc_final: 0.9034 (mt0) REVERT: B 393 SER cc_start: 0.9590 (t) cc_final: 0.9122 (t) REVERT: B 396 ASP cc_start: 0.8488 (m-30) cc_final: 0.8162 (m-30) REVERT: B 402 GLU cc_start: 0.8618 (mp0) cc_final: 0.8284 (mp0) REVERT: B 403 ILE cc_start: 0.9337 (mp) cc_final: 0.9019 (tp) REVERT: B 421 GLU cc_start: 0.9513 (tm-30) cc_final: 0.9265 (tm-30) REVERT: B 458 MET cc_start: 0.9412 (mmm) cc_final: 0.9076 (mmm) REVERT: B 493 MET cc_start: 0.9407 (tmm) cc_final: 0.9065 (tmm) REVERT: B 500 ILE cc_start: 0.9690 (mt) cc_final: 0.9197 (mt) REVERT: B 501 GLN cc_start: 0.9531 (mt0) cc_final: 0.8890 (mt0) REVERT: B 510 LYS cc_start: 0.9009 (mmtm) cc_final: 0.8809 (mmtm) REVERT: B 558 TRP cc_start: 0.9313 (m100) cc_final: 0.8885 (m100) REVERT: B 570 MET cc_start: 0.9395 (mtp) cc_final: 0.8878 (mtp) REVERT: B 585 SER cc_start: 0.9102 (p) cc_final: 0.8663 (t) REVERT: B 591 THR cc_start: 0.9053 (p) cc_final: 0.8674 (p) REVERT: B 599 GLU cc_start: 0.8763 (pm20) cc_final: 0.8528 (pm20) REVERT: B 615 MET cc_start: 0.9090 (mmp) cc_final: 0.8576 (mmp) REVERT: B 627 LYS cc_start: 0.9171 (tttt) cc_final: 0.8801 (ttpp) REVERT: B 631 ASP cc_start: 0.9587 (m-30) cc_final: 0.9256 (t0) REVERT: B 632 MET cc_start: 0.8647 (mmm) cc_final: 0.8205 (mmm) REVERT: B 650 GLN cc_start: 0.7862 (mm-40) cc_final: 0.6941 (mm-40) REVERT: B 667 LEU cc_start: 0.9308 (tp) cc_final: 0.8907 (tp) REVERT: B 668 ASN cc_start: 0.9357 (m-40) cc_final: 0.8938 (m-40) REVERT: B 677 ARG cc_start: 0.9627 (mmm160) cc_final: 0.9264 (mmm-85) REVERT: C 95 MET cc_start: 0.8735 (tmm) cc_final: 0.8500 (tmm) REVERT: C 98 ASN cc_start: 0.6631 (p0) cc_final: 0.6412 (p0) REVERT: C 124 TRP cc_start: 0.7755 (t60) cc_final: 0.7527 (t60) REVERT: C 136 GLN cc_start: -0.0411 (mt0) cc_final: -0.0724 (tp40) REVERT: C 261 ARG cc_start: 0.5751 (mtm110) cc_final: 0.5445 (ptp90) REVERT: C 315 LEU cc_start: 0.8470 (mm) cc_final: 0.8207 (mm) REVERT: D 53 ASP cc_start: 0.6297 (m-30) cc_final: 0.5435 (t70) REVERT: D 69 GLN cc_start: 0.8995 (tp40) cc_final: 0.8637 (tm-30) REVERT: D 97 GLU cc_start: 0.2137 (mp0) cc_final: 0.1758 (mp0) REVERT: D 179 TYR cc_start: 0.6949 (t80) cc_final: 0.6589 (t80) REVERT: D 185 MET cc_start: 0.2517 (mmm) cc_final: 0.2253 (mpp) outliers start: 0 outliers final: 0 residues processed: 653 average time/residue: 0.2757 time to fit residues: 265.9143 Evaluate side-chains 588 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 588 time to evaluate : 1.707 ------------------------------------------------------------------------------- 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: 5.9990 chunk 126 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 156 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 115 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 25 GLN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 608 ASN B 44 ASN B 191 GLN ** B 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 127 GLN C 132 GLN ** C 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.123360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.082347 restraints weight = 49290.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.085185 restraints weight = 28924.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.087147 restraints weight = 19452.703| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3039 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3039 r_free = 0.3039 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.6826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.048 16386 Z= 0.399 Angle : 0.841 14.574 22134 Z= 0.442 Chirality : 0.046 0.230 2360 Planarity : 0.005 0.066 2818 Dihedral : 11.521 179.498 2242 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 23.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.06 % Allowed : 2.80 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.18), residues: 1932 helix: 0.74 (0.15), residues: 1133 sheet: -0.86 (0.39), residues: 142 loop : -0.02 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 623 HIS 0.010 0.002 HIS B 675 PHE 0.030 0.003 PHE B 657 TYR 0.041 0.003 TYR B 574 ARG 0.011 0.001 ARG B 117 Details of bonding type rmsd hydrogen bonds : bond 0.04556 ( 871) hydrogen bonds : angle 5.45274 ( 2571) covalent geometry : bond 0.00801 (16386) covalent geometry : angle 0.84074 (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 627 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 626 time to evaluate : 1.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9469 (t0) cc_final: 0.9162 (t70) REVERT: A 95 MET cc_start: 0.8874 (mmm) cc_final: 0.8577 (tpt) REVERT: A 116 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8702 (tt0) REVERT: A 143 LEU cc_start: 0.9528 (tp) cc_final: 0.9136 (tp) REVERT: A 147 GLN cc_start: 0.9423 (mm-40) cc_final: 0.8879 (mm110) REVERT: A 148 GLU cc_start: 0.8964 (mt-10) cc_final: 0.8706 (mt-10) REVERT: A 164 ARG cc_start: 0.8313 (ptm-80) cc_final: 0.7320 (ptm-80) REVERT: A 172 LEU cc_start: 0.9279 (mp) cc_final: 0.9041 (mp) REVERT: A 195 LEU cc_start: 0.9718 (mt) cc_final: 0.9453 (mt) REVERT: A 251 LEU cc_start: 0.9567 (tp) cc_final: 0.9204 (tp) REVERT: A 252 ASN cc_start: 0.9557 (t0) cc_final: 0.8998 (t0) REVERT: A 260 ASP cc_start: 0.9645 (m-30) cc_final: 0.9315 (m-30) REVERT: A 350 ARG cc_start: 0.8864 (mmm-85) cc_final: 0.7962 (mmm-85) REVERT: A 377 LYS cc_start: 0.8909 (mttt) cc_final: 0.8694 (mtmt) REVERT: A 385 VAL cc_start: 0.9442 (t) cc_final: 0.9195 (t) REVERT: A 394 TYR cc_start: 0.9262 (m-80) cc_final: 0.8795 (m-80) REVERT: A 406 ASP cc_start: 0.8949 (m-30) cc_final: 0.8683 (m-30) REVERT: A 415 ASN cc_start: 0.9443 (t0) cc_final: 0.8966 (t0) REVERT: A 418 ASN cc_start: 0.9497 (m-40) cc_final: 0.8959 (m-40) REVERT: A 421 GLU cc_start: 0.9335 (tm-30) cc_final: 0.9050 (tm-30) REVERT: A 468 LEU cc_start: 0.9748 (tp) cc_final: 0.9484 (tp) REVERT: A 472 LEU cc_start: 0.9747 (mt) cc_final: 0.9454 (mt) REVERT: A 493 MET cc_start: 0.9200 (tmm) cc_final: 0.8936 (tmm) REVERT: A 496 ASN cc_start: 0.9557 (t0) cc_final: 0.8752 (t0) REVERT: A 515 ASP cc_start: 0.9414 (m-30) cc_final: 0.9072 (m-30) REVERT: A 570 MET cc_start: 0.9186 (mtp) cc_final: 0.8213 (mtp) REVERT: A 575 ARG cc_start: 0.9246 (mtm-85) cc_final: 0.8630 (mpp80) REVERT: A 598 MET cc_start: 0.9171 (mtp) cc_final: 0.8883 (mtp) REVERT: A 603 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8977 (tp30) REVERT: A 639 ASP cc_start: 0.9337 (m-30) cc_final: 0.9107 (m-30) REVERT: A 645 GLN cc_start: 0.9173 (tp40) cc_final: 0.8958 (tp-100) REVERT: A 650 GLN cc_start: 0.8795 (mt0) cc_final: 0.8098 (mt0) REVERT: A 682 ILE cc_start: 0.9521 (mp) cc_final: 0.9234 (mp) REVERT: B 15 GLU cc_start: 0.9286 (tp30) cc_final: 0.9083 (tp30) REVERT: B 55 LEU cc_start: 0.9676 (mt) cc_final: 0.9430 (mt) REVERT: B 77 ILE cc_start: 0.9573 (mt) cc_final: 0.9312 (mt) REVERT: B 81 PHE cc_start: 0.9286 (m-10) cc_final: 0.9085 (m-10) REVERT: B 99 LYS cc_start: 0.9618 (mmmt) cc_final: 0.9350 (mmmm) REVERT: B 104 TYR cc_start: 0.9246 (m-10) cc_final: 0.8927 (m-80) REVERT: B 115 LEU cc_start: 0.9670 (mt) cc_final: 0.9380 (mt) REVERT: B 117 ARG cc_start: 0.9446 (ttm110) cc_final: 0.9223 (ttm-80) REVERT: B 136 LYS cc_start: 0.9642 (mmtp) cc_final: 0.9353 (mmmm) REVERT: B 144 MET cc_start: 0.9264 (mmp) cc_final: 0.8765 (mmp) REVERT: B 158 ASN cc_start: 0.9610 (m110) cc_final: 0.9174 (p0) REVERT: B 191 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8768 (mm-40) REVERT: B 211 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8002 (mm-30) REVERT: B 227 MET cc_start: 0.9313 (mtp) cc_final: 0.9109 (mtp) REVERT: B 236 TYR cc_start: 0.8915 (t80) cc_final: 0.8543 (t80) REVERT: B 251 LEU cc_start: 0.9545 (tp) cc_final: 0.9229 (tp) REVERT: B 258 ILE cc_start: 0.9434 (tp) cc_final: 0.9183 (tp) REVERT: B 282 VAL cc_start: 0.9651 (t) cc_final: 0.9429 (m) REVERT: B 286 ASP cc_start: 0.8889 (m-30) cc_final: 0.8204 (m-30) REVERT: B 296 LYS cc_start: 0.9154 (mmpt) cc_final: 0.8841 (mtmm) REVERT: B 322 MET cc_start: 0.9077 (mmm) cc_final: 0.8743 (mmm) REVERT: B 333 LYS cc_start: 0.9504 (ttmm) cc_final: 0.9180 (ttmm) REVERT: B 335 GLU cc_start: 0.9138 (pt0) cc_final: 0.8887 (pt0) REVERT: B 342 LEU cc_start: 0.9820 (tp) cc_final: 0.9547 (tp) REVERT: B 345 LYS cc_start: 0.9652 (tttt) cc_final: 0.9450 (tttt) REVERT: B 346 LEU cc_start: 0.9736 (mt) cc_final: 0.9518 (mt) REVERT: B 350 ARG cc_start: 0.8850 (mtp85) cc_final: 0.7987 (mtp85) REVERT: B 362 ASP cc_start: 0.9142 (m-30) cc_final: 0.8098 (m-30) REVERT: B 370 ASN cc_start: 0.9513 (m-40) cc_final: 0.9050 (m110) REVERT: B 373 ILE cc_start: 0.9707 (tp) cc_final: 0.9497 (tp) REVERT: B 375 LYS cc_start: 0.9252 (mmtm) cc_final: 0.8841 (mmtm) REVERT: B 390 GLN cc_start: 0.9293 (mt0) cc_final: 0.9086 (mm-40) REVERT: B 413 SER cc_start: 0.9335 (m) cc_final: 0.9084 (m) REVERT: B 418 ASN cc_start: 0.9330 (m-40) cc_final: 0.9122 (t0) REVERT: B 447 ASN cc_start: 0.7803 (t0) cc_final: 0.6693 (t0) REVERT: B 471 TYR cc_start: 0.9499 (t80) cc_final: 0.9248 (t80) REVERT: B 501 GLN cc_start: 0.9544 (mt0) cc_final: 0.9327 (mt0) REVERT: B 588 GLN cc_start: 0.9606 (mm110) cc_final: 0.9334 (mm-40) REVERT: B 599 GLU cc_start: 0.8921 (pm20) cc_final: 0.8666 (pm20) REVERT: B 615 MET cc_start: 0.9128 (mmp) cc_final: 0.8641 (mmm) REVERT: B 634 MET cc_start: 0.9339 (mmm) cc_final: 0.9133 (mmp) REVERT: B 648 ILE cc_start: 0.9657 (mm) cc_final: 0.9445 (mm) REVERT: B 650 GLN cc_start: 0.8050 (mm-40) cc_final: 0.7291 (mm-40) REVERT: B 655 THR cc_start: 0.9299 (m) cc_final: 0.9028 (t) REVERT: B 656 LEU cc_start: 0.9724 (mt) cc_final: 0.9511 (mt) REVERT: B 668 ASN cc_start: 0.9475 (m-40) cc_final: 0.8963 (m-40) REVERT: C 98 ASN cc_start: 0.8095 (p0) cc_final: 0.7831 (p0) REVERT: C 100 VAL cc_start: 0.8629 (t) cc_final: 0.8305 (p) REVERT: C 105 TYR cc_start: 0.7849 (m-80) cc_final: 0.7648 (m-80) REVERT: C 124 TRP cc_start: 0.7740 (t60) cc_final: 0.7297 (t60) REVERT: D 18 THR cc_start: 0.5611 (m) cc_final: 0.5410 (t) REVERT: D 22 TYR cc_start: 0.5644 (t80) cc_final: 0.5395 (t80) REVERT: D 25 ASN cc_start: 0.8312 (m-40) cc_final: 0.7987 (m-40) REVERT: D 69 GLN cc_start: 0.9383 (tp40) cc_final: 0.8945 (tp40) REVERT: D 74 MET cc_start: 0.8606 (mmp) cc_final: 0.8388 (mmp) REVERT: D 91 ASN cc_start: 0.8622 (m110) cc_final: 0.8134 (m110) REVERT: D 100 VAL cc_start: 0.5001 (t) cc_final: 0.4309 (p) REVERT: D 185 MET cc_start: 0.2583 (mmm) cc_final: 0.2217 (mpp) outliers start: 1 outliers final: 0 residues processed: 627 average time/residue: 0.2824 time to fit residues: 261.4119 Evaluate side-chains 548 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 548 time to evaluate : 1.902 ------------------------------------------------------------------------------- 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: 1.9990 chunk 85 optimal weight: 0.9980 chunk 161 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 146 optimal weight: 8.9990 chunk 184 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 175 optimal weight: 9.9990 chunk 24 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 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 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 410 ASN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.130860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.087575 restraints weight = 46753.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.090516 restraints weight = 27430.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.092603 restraints weight = 18354.120| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.7002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16386 Z= 0.176 Angle : 0.653 9.769 22134 Z= 0.345 Chirality : 0.044 0.265 2360 Planarity : 0.004 0.066 2818 Dihedral : 11.043 173.353 2242 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % 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: 1.02 (0.15), residues: 1114 sheet: -0.61 (0.39), residues: 140 loop : 0.06 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 623 HIS 0.015 0.001 HIS D 201 PHE 0.027 0.002 PHE A 378 TYR 0.042 0.002 TYR C 142 ARG 0.011 0.001 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 871) hydrogen bonds : angle 5.16045 ( 2571) covalent geometry : bond 0.00373 (16386) covalent geometry : angle 0.65293 (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 634 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 634 time to evaluate : 1.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9480 (t0) cc_final: 0.9238 (t70) REVERT: A 95 MET cc_start: 0.8825 (mmm) cc_final: 0.8366 (tpt) REVERT: A 119 GLU cc_start: 0.9309 (mp0) cc_final: 0.8143 (tm-30) REVERT: A 143 LEU cc_start: 0.9590 (tp) cc_final: 0.9212 (tp) REVERT: A 147 GLN cc_start: 0.9370 (mm-40) cc_final: 0.9095 (mm110) REVERT: A 148 GLU cc_start: 0.8958 (mt-10) cc_final: 0.8745 (mt-10) REVERT: A 164 ARG cc_start: 0.8312 (ptm-80) cc_final: 0.6777 (ptm-80) REVERT: A 172 LEU cc_start: 0.9378 (mp) cc_final: 0.8893 (mp) REVERT: A 173 LEU cc_start: 0.9533 (mt) cc_final: 0.9309 (mt) REVERT: A 180 ASN cc_start: 0.9009 (m-40) cc_final: 0.8685 (t0) REVERT: A 195 LEU cc_start: 0.9653 (mt) cc_final: 0.9430 (mt) REVERT: A 204 SER cc_start: 0.9381 (m) cc_final: 0.8991 (p) REVERT: A 251 LEU cc_start: 0.9473 (tp) cc_final: 0.9263 (tp) REVERT: A 252 ASN cc_start: 0.9526 (t0) cc_final: 0.8904 (t0) REVERT: A 313 HIS cc_start: 0.9034 (m170) cc_final: 0.8639 (m-70) REVERT: A 350 ARG cc_start: 0.8907 (mmm-85) cc_final: 0.8178 (mmm-85) REVERT: A 370 ASN cc_start: 0.9611 (m-40) cc_final: 0.9324 (m110) REVERT: A 387 GLN cc_start: 0.9141 (mt0) cc_final: 0.8767 (mp10) REVERT: A 394 TYR cc_start: 0.9291 (m-80) cc_final: 0.8781 (m-80) REVERT: A 406 ASP cc_start: 0.8982 (m-30) cc_final: 0.8583 (m-30) REVERT: A 407 ILE cc_start: 0.9104 (mt) cc_final: 0.8660 (mt) REVERT: A 415 ASN cc_start: 0.9490 (t0) cc_final: 0.8866 (t0) REVERT: A 418 ASN cc_start: 0.9509 (m-40) cc_final: 0.8720 (m-40) REVERT: A 468 LEU cc_start: 0.9687 (tp) cc_final: 0.9461 (tp) REVERT: A 472 LEU cc_start: 0.9735 (mt) cc_final: 0.9443 (mt) REVERT: A 493 MET cc_start: 0.9195 (tmm) cc_final: 0.8824 (tmm) REVERT: A 496 ASN cc_start: 0.9561 (t0) cc_final: 0.8326 (t0) REVERT: A 500 ILE cc_start: 0.9662 (mt) cc_final: 0.8684 (mt) REVERT: A 508 LYS cc_start: 0.9728 (tttt) cc_final: 0.9482 (tttp) REVERT: A 515 ASP cc_start: 0.9333 (m-30) cc_final: 0.8962 (m-30) REVERT: A 516 GLN cc_start: 0.9149 (tt0) cc_final: 0.8846 (tt0) REVERT: A 570 MET cc_start: 0.9186 (mtp) cc_final: 0.8093 (mtp) REVERT: A 575 ARG cc_start: 0.9305 (mtm-85) cc_final: 0.8646 (mpp80) REVERT: A 599 GLU cc_start: 0.8840 (tp30) cc_final: 0.8602 (tp30) REVERT: A 601 ILE cc_start: 0.9325 (tt) cc_final: 0.9058 (tt) REVERT: A 603 GLU cc_start: 0.9246 (mm-30) cc_final: 0.9032 (tp30) REVERT: A 639 ASP cc_start: 0.9305 (m-30) cc_final: 0.8984 (m-30) REVERT: A 640 MET cc_start: 0.9146 (tpp) cc_final: 0.8885 (tpp) REVERT: A 645 GLN cc_start: 0.9398 (tp40) cc_final: 0.9106 (tp-100) REVERT: A 650 GLN cc_start: 0.8922 (mt0) cc_final: 0.8115 (mt0) REVERT: A 682 ILE cc_start: 0.9446 (mp) cc_final: 0.9186 (mp) REVERT: B 15 GLU cc_start: 0.9329 (tp30) cc_final: 0.9128 (tp30) REVERT: B 51 LEU cc_start: 0.9434 (tp) cc_final: 0.9139 (tp) REVERT: B 99 LYS cc_start: 0.9685 (mmmt) cc_final: 0.9297 (mmmm) REVERT: B 115 LEU cc_start: 0.9582 (mt) cc_final: 0.9345 (mt) REVERT: B 120 ASP cc_start: 0.9362 (m-30) cc_final: 0.9116 (m-30) REVERT: B 136 LYS cc_start: 0.9683 (mmtp) cc_final: 0.9392 (mmmm) REVERT: B 139 GLU cc_start: 0.9546 (mp0) cc_final: 0.9251 (mp0) REVERT: B 144 MET cc_start: 0.9240 (mmp) cc_final: 0.8657 (mmp) REVERT: B 145 ILE cc_start: 0.9706 (tp) cc_final: 0.9257 (tp) REVERT: B 147 GLN cc_start: 0.9526 (mt0) cc_final: 0.8909 (mt0) REVERT: B 158 ASN cc_start: 0.9607 (m110) cc_final: 0.9107 (p0) REVERT: B 161 ARG cc_start: 0.8935 (ttm110) cc_final: 0.8599 (mtp85) REVERT: B 200 SER cc_start: 0.9119 (t) cc_final: 0.8917 (t) REVERT: B 211 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8254 (mm-30) REVERT: B 227 MET cc_start: 0.9345 (mtp) cc_final: 0.9111 (mtp) REVERT: B 251 LEU cc_start: 0.9478 (tp) cc_final: 0.9236 (tp) REVERT: B 286 ASP cc_start: 0.8775 (m-30) cc_final: 0.8008 (m-30) REVERT: B 296 LYS cc_start: 0.9032 (mmpt) cc_final: 0.8673 (mtmm) REVERT: B 322 MET cc_start: 0.9136 (mmm) cc_final: 0.8767 (mmm) REVERT: B 333 LYS cc_start: 0.9551 (ttmm) cc_final: 0.9231 (ttmm) REVERT: B 335 GLU cc_start: 0.9134 (pt0) cc_final: 0.8806 (pt0) REVERT: B 350 ARG cc_start: 0.8773 (mtp85) cc_final: 0.8051 (mtp85) REVERT: B 362 ASP cc_start: 0.9175 (m-30) cc_final: 0.8211 (m-30) REVERT: B 373 ILE cc_start: 0.9579 (tp) cc_final: 0.9308 (tp) REVERT: B 375 LYS cc_start: 0.9282 (mmtm) cc_final: 0.8859 (mmtm) REVERT: B 393 SER cc_start: 0.9534 (t) cc_final: 0.9014 (t) REVERT: B 402 GLU cc_start: 0.8638 (mp0) cc_final: 0.8323 (mp0) REVERT: B 413 SER cc_start: 0.9521 (m) cc_final: 0.9044 (t) REVERT: B 418 ASN cc_start: 0.9530 (m-40) cc_final: 0.9194 (t0) REVERT: B 447 ASN cc_start: 0.7753 (t0) cc_final: 0.6929 (t0) REVERT: B 458 MET cc_start: 0.9550 (mmm) cc_final: 0.9217 (mmm) REVERT: B 467 ASN cc_start: 0.9432 (m-40) cc_final: 0.9101 (m-40) REVERT: B 471 TYR cc_start: 0.9322 (t80) cc_final: 0.9012 (t80) REVERT: B 501 GLN cc_start: 0.9507 (mt0) cc_final: 0.8956 (mt0) REVERT: B 606 TYR cc_start: 0.8791 (m-10) cc_final: 0.8422 (m-10) REVERT: B 615 MET cc_start: 0.9190 (mmp) cc_final: 0.8802 (mmm) REVERT: B 634 MET cc_start: 0.9449 (mmm) cc_final: 0.9168 (mmp) REVERT: B 646 GLN cc_start: 0.9610 (pt0) cc_final: 0.9325 (pm20) REVERT: B 667 LEU cc_start: 0.9324 (tt) cc_final: 0.9020 (tt) REVERT: B 668 ASN cc_start: 0.9474 (m-40) cc_final: 0.8985 (m-40) REVERT: C 95 MET cc_start: 0.9105 (tmm) cc_final: 0.8849 (tmm) REVERT: C 98 ASN cc_start: 0.7834 (p0) cc_final: 0.7622 (p0) REVERT: C 101 HIS cc_start: 0.8560 (m90) cc_final: 0.8114 (m90) REVERT: C 261 ARG cc_start: 0.5273 (mtm110) cc_final: 0.4967 (ptp90) REVERT: D 25 ASN cc_start: 0.8222 (m-40) cc_final: 0.7956 (m-40) REVERT: D 69 GLN cc_start: 0.9360 (tp40) cc_final: 0.8850 (tp40) REVERT: D 91 ASN cc_start: 0.8374 (m110) cc_final: 0.8108 (m-40) REVERT: D 100 VAL cc_start: 0.4811 (t) cc_final: 0.4105 (p) REVERT: D 205 VAL cc_start: 0.9358 (t) cc_final: 0.9050 (p) outliers start: 0 outliers final: 0 residues processed: 634 average time/residue: 0.2877 time to fit residues: 269.5851 Evaluate side-chains 566 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 566 time to evaluate : 1.880 ------------------------------------------------------------------------------- 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: 8.9990 chunk 51 optimal weight: 5.9990 chunk 159 optimal weight: 20.0000 chunk 72 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 183 optimal weight: 10.0000 chunk 52 optimal weight: 5.9990 chunk 180 optimal weight: 10.0000 chunk 108 optimal weight: 9.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 338 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 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 52 GLN D 186 GLN D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.132273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.089189 restraints weight = 47117.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.092141 restraints weight = 27521.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.094205 restraints weight = 18306.961| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3122 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3122 r_free = 0.3122 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3122 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.7327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 16386 Z= 0.194 Angle : 0.667 9.550 22134 Z= 0.355 Chirality : 0.045 0.235 2360 Planarity : 0.004 0.049 2818 Dihedral : 10.975 168.718 2242 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.61 (0.19), residues: 1932 helix: 0.88 (0.15), residues: 1126 sheet: -0.65 (0.41), residues: 132 loop : 0.02 (0.23), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 558 HIS 0.011 0.001 HIS D 201 PHE 0.032 0.002 PHE A 171 TYR 0.051 0.002 TYR B 684 ARG 0.010 0.001 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.03920 ( 871) hydrogen bonds : angle 5.15315 ( 2571) covalent geometry : bond 0.00411 (16386) covalent geometry : angle 0.66738 (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 617 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 617 time to evaluate : 1.751 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: A 29 ASP cc_start: 0.9428 (t0) cc_final: 0.9124 (t70) REVERT: A 95 MET cc_start: 0.8821 (mmm) cc_final: 0.8460 (tpt) REVERT: A 119 GLU cc_start: 0.9154 (mp0) cc_final: 0.8686 (mt-10) REVERT: A 139 GLU cc_start: 0.9238 (mt-10) cc_final: 0.8993 (pt0) REVERT: A 143 LEU cc_start: 0.9598 (tp) cc_final: 0.9283 (tp) REVERT: A 147 GLN cc_start: 0.9354 (mm-40) cc_final: 0.9097 (mm110) REVERT: A 164 ARG cc_start: 0.8312 (ptm-80) cc_final: 0.6819 (ptm-80) REVERT: A 172 LEU cc_start: 0.9405 (mp) cc_final: 0.8912 (mp) REVERT: A 173 LEU cc_start: 0.9554 (mt) cc_final: 0.9323 (mt) REVERT: A 190 MET cc_start: 0.9655 (mmm) cc_final: 0.9004 (mmm) REVERT: A 195 LEU cc_start: 0.9621 (mt) cc_final: 0.9412 (mt) REVERT: A 204 SER cc_start: 0.9410 (m) cc_final: 0.9004 (p) REVERT: A 236 TYR cc_start: 0.8939 (t80) cc_final: 0.8705 (t80) REVERT: A 251 LEU cc_start: 0.9580 (tp) cc_final: 0.9326 (tp) REVERT: A 252 ASN cc_start: 0.9485 (t0) cc_final: 0.8964 (t0) REVERT: A 350 ARG cc_start: 0.8960 (mmm-85) cc_final: 0.8427 (mmm-85) REVERT: A 370 ASN cc_start: 0.9557 (m-40) cc_final: 0.9273 (m110) REVERT: A 373 ILE cc_start: 0.9501 (mt) cc_final: 0.9169 (mt) REVERT: A 394 TYR cc_start: 0.9302 (m-80) cc_final: 0.8796 (m-80) REVERT: A 406 ASP cc_start: 0.9071 (m-30) cc_final: 0.8713 (m-30) REVERT: A 407 ILE cc_start: 0.9221 (mt) cc_final: 0.8749 (mt) REVERT: A 415 ASN cc_start: 0.9535 (t0) cc_final: 0.8957 (t0) REVERT: A 418 ASN cc_start: 0.9523 (m-40) cc_final: 0.8945 (m-40) REVERT: A 421 GLU cc_start: 0.9253 (tm-30) cc_final: 0.9039 (tm-30) REVERT: A 427 LYS cc_start: 0.9710 (ptmm) cc_final: 0.9486 (ptpp) REVERT: A 472 LEU cc_start: 0.9762 (mt) cc_final: 0.9541 (mt) REVERT: A 493 MET cc_start: 0.9159 (tmm) cc_final: 0.8774 (tmm) REVERT: A 496 ASN cc_start: 0.9571 (t0) cc_final: 0.8441 (t0) REVERT: A 500 ILE cc_start: 0.9628 (mt) cc_final: 0.8672 (mt) REVERT: A 515 ASP cc_start: 0.9338 (m-30) cc_final: 0.8982 (m-30) REVERT: A 516 GLN cc_start: 0.9108 (tt0) cc_final: 0.8866 (tt0) REVERT: A 570 MET cc_start: 0.8801 (mtp) cc_final: 0.8336 (ttm) REVERT: A 575 ARG cc_start: 0.9285 (mtm-85) cc_final: 0.8623 (mpp80) REVERT: A 586 TYR cc_start: 0.9410 (m-10) cc_final: 0.9093 (m-10) REVERT: A 603 GLU cc_start: 0.9208 (mm-30) cc_final: 0.9001 (tp30) REVERT: A 615 MET cc_start: 0.8878 (mmp) cc_final: 0.8047 (mmp) REVERT: A 639 ASP cc_start: 0.9259 (m-30) cc_final: 0.8963 (m-30) REVERT: A 640 MET cc_start: 0.9148 (tpp) cc_final: 0.8761 (tpp) REVERT: A 645 GLN cc_start: 0.9371 (tp40) cc_final: 0.9149 (tp-100) REVERT: A 655 THR cc_start: 0.8864 (m) cc_final: 0.8635 (m) REVERT: A 657 PHE cc_start: 0.8702 (m-80) cc_final: 0.8320 (m-80) REVERT: A 682 ILE cc_start: 0.9496 (mp) cc_final: 0.9194 (mp) REVERT: A 686 ARG cc_start: 0.8890 (mmt180) cc_final: 0.8488 (mmt180) REVERT: B 51 LEU cc_start: 0.9556 (tp) cc_final: 0.9335 (tp) REVERT: B 99 LYS cc_start: 0.9653 (mmmt) cc_final: 0.9395 (mmmm) REVERT: B 115 LEU cc_start: 0.9541 (mt) cc_final: 0.9336 (mt) REVERT: B 128 PHE cc_start: 0.9680 (t80) cc_final: 0.9396 (t80) REVERT: B 136 LYS cc_start: 0.9683 (mmtp) cc_final: 0.9394 (mmmm) REVERT: B 144 MET cc_start: 0.9168 (mmp) cc_final: 0.8531 (mmp) REVERT: B 147 GLN cc_start: 0.9553 (mt0) cc_final: 0.8940 (mt0) REVERT: B 157 LEU cc_start: 0.9567 (tp) cc_final: 0.9340 (tp) REVERT: B 158 ASN cc_start: 0.9612 (m110) cc_final: 0.9103 (p0) REVERT: B 161 ARG cc_start: 0.8924 (ttm110) cc_final: 0.8566 (mtp85) REVERT: B 200 SER cc_start: 0.9127 (t) cc_final: 0.8919 (t) REVERT: B 211 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8271 (mm-30) REVERT: B 227 MET cc_start: 0.9331 (mtp) cc_final: 0.9080 (mtp) REVERT: B 232 ASN cc_start: 0.9202 (m110) cc_final: 0.8932 (m110) REVERT: B 251 LEU cc_start: 0.9511 (tp) cc_final: 0.9281 (tp) REVERT: B 286 ASP cc_start: 0.8733 (m-30) cc_final: 0.8095 (m-30) REVERT: B 294 GLU cc_start: 0.9571 (mp0) cc_final: 0.9365 (mp0) REVERT: B 296 LYS cc_start: 0.9156 (mmpt) cc_final: 0.8824 (mtmm) REVERT: B 322 MET cc_start: 0.9172 (mmm) cc_final: 0.8784 (mmm) REVERT: B 333 LYS cc_start: 0.9559 (ttmm) cc_final: 0.9218 (ttmm) REVERT: B 335 GLU cc_start: 0.9205 (pt0) cc_final: 0.8873 (pt0) REVERT: B 350 ARG cc_start: 0.8814 (mtp85) cc_final: 0.8050 (mtp85) REVERT: B 362 ASP cc_start: 0.9128 (m-30) cc_final: 0.8165 (m-30) REVERT: B 393 SER cc_start: 0.9490 (t) cc_final: 0.8921 (t) REVERT: B 396 ASP cc_start: 0.8699 (m-30) cc_final: 0.8434 (m-30) REVERT: B 402 GLU cc_start: 0.8600 (mp0) cc_final: 0.8259 (mp0) REVERT: B 413 SER cc_start: 0.9487 (m) cc_final: 0.9028 (t) REVERT: B 447 ASN cc_start: 0.7883 (t0) cc_final: 0.7160 (t0) REVERT: B 458 MET cc_start: 0.9551 (mmm) cc_final: 0.9214 (mmm) REVERT: B 467 ASN cc_start: 0.9444 (m-40) cc_final: 0.9143 (m-40) REVERT: B 471 TYR cc_start: 0.9351 (t80) cc_final: 0.9036 (t80) REVERT: B 615 MET cc_start: 0.9241 (mmp) cc_final: 0.8904 (mmm) REVERT: B 631 ASP cc_start: 0.9579 (m-30) cc_final: 0.9361 (m-30) REVERT: B 634 MET cc_start: 0.9473 (mmm) cc_final: 0.9217 (mmp) REVERT: B 646 GLN cc_start: 0.9613 (pt0) cc_final: 0.9322 (pm20) REVERT: B 667 LEU cc_start: 0.9332 (tt) cc_final: 0.9004 (tt) REVERT: B 668 ASN cc_start: 0.9418 (m-40) cc_final: 0.8991 (m-40) REVERT: B 683 TYR cc_start: 0.8131 (t80) cc_final: 0.7914 (t80) REVERT: C 100 VAL cc_start: 0.8698 (t) cc_final: 0.8391 (p) REVERT: C 133 LYS cc_start: 0.8237 (mtmm) cc_final: 0.7861 (ptmt) REVERT: C 261 ARG cc_start: 0.5016 (mtm110) cc_final: 0.4668 (ptp90) REVERT: D 68 GLU cc_start: 0.8419 (mp0) cc_final: 0.8156 (mp0) REVERT: D 69 GLN cc_start: 0.9394 (tp40) cc_final: 0.9083 (tp40) outliers start: 0 outliers final: 0 residues processed: 617 average time/residue: 0.2797 time to fit residues: 256.5560 Evaluate side-chains 553 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 553 time to evaluate : 1.863 ------------------------------------------------------------------------------- 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: 2.9990 chunk 102 optimal weight: 1.9990 chunk 182 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 115 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 188 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 50 optimal weight: 8.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 HIS ** B 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN C 52 GLN C 186 GLN D 69 GLN D 216 GLN D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.136721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.092523 restraints weight = 46111.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.095588 restraints weight = 27029.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.097694 restraints weight = 18092.099| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 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 = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.7512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16386 Z= 0.140 Angle : 0.645 8.569 22134 Z= 0.341 Chirality : 0.044 0.212 2360 Planarity : 0.004 0.049 2818 Dihedral : 10.869 179.138 2242 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % 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: 0.77 (0.19), residues: 1932 helix: 1.02 (0.15), residues: 1126 sheet: -0.03 (0.45), residues: 110 loop : -0.06 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 124 HIS 0.009 0.001 HIS D 201 PHE 0.028 0.002 PHE B 360 TYR 0.043 0.002 TYR A 683 ARG 0.008 0.001 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 871) hydrogen bonds : angle 5.06985 ( 2571) covalent geometry : bond 0.00307 (16386) covalent geometry : angle 0.64531 (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 627 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 627 time to evaluate : 1.772 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: A 29 ASP cc_start: 0.9444 (t0) cc_final: 0.9130 (t70) REVERT: A 95 MET cc_start: 0.8834 (mmm) cc_final: 0.8426 (tpt) REVERT: A 116 GLU cc_start: 0.9129 (tt0) cc_final: 0.8620 (tt0) REVERT: A 119 GLU cc_start: 0.9023 (mp0) cc_final: 0.8753 (mt-10) REVERT: A 143 LEU cc_start: 0.9603 (tp) cc_final: 0.9273 (tp) REVERT: A 147 GLN cc_start: 0.9336 (mm-40) cc_final: 0.9122 (mm110) REVERT: A 164 ARG cc_start: 0.8323 (ptm-80) cc_final: 0.7453 (ptm-80) REVERT: A 172 LEU cc_start: 0.9402 (mp) cc_final: 0.8906 (mp) REVERT: A 173 LEU cc_start: 0.9569 (mt) cc_final: 0.9353 (mt) REVERT: A 190 MET cc_start: 0.9660 (mmm) cc_final: 0.9306 (mmm) REVERT: A 204 SER cc_start: 0.9395 (m) cc_final: 0.8978 (p) REVERT: A 252 ASN cc_start: 0.9476 (t0) cc_final: 0.8945 (t0) REVERT: A 301 PHE cc_start: 0.9254 (m-80) cc_final: 0.9046 (m-10) REVERT: A 307 TYR cc_start: 0.9616 (t80) cc_final: 0.9072 (t80) REVERT: A 322 MET cc_start: 0.9120 (tpt) cc_final: 0.8815 (mmm) REVERT: A 350 ARG cc_start: 0.8960 (mmm-85) cc_final: 0.8454 (mmm-85) REVERT: A 370 ASN cc_start: 0.9501 (m-40) cc_final: 0.9249 (m-40) REVERT: A 373 ILE cc_start: 0.9474 (mt) cc_final: 0.9105 (mt) REVERT: A 387 GLN cc_start: 0.9121 (mt0) cc_final: 0.8518 (mp10) REVERT: A 394 TYR cc_start: 0.9236 (m-80) cc_final: 0.8291 (m-80) REVERT: A 406 ASP cc_start: 0.9039 (m-30) cc_final: 0.8682 (m-30) REVERT: A 407 ILE cc_start: 0.9235 (mt) cc_final: 0.8819 (mt) REVERT: A 421 GLU cc_start: 0.9235 (tm-30) cc_final: 0.9034 (tm-30) REVERT: A 466 MET cc_start: 0.9666 (ptt) cc_final: 0.9411 (ptt) REVERT: A 472 LEU cc_start: 0.9750 (mt) cc_final: 0.9540 (mt) REVERT: A 493 MET cc_start: 0.9129 (tmm) cc_final: 0.8767 (tmm) REVERT: A 496 ASN cc_start: 0.9543 (t0) cc_final: 0.8350 (t0) REVERT: A 500 ILE cc_start: 0.9640 (mt) cc_final: 0.8692 (mt) REVERT: A 515 ASP cc_start: 0.9315 (m-30) cc_final: 0.9013 (m-30) REVERT: A 516 GLN cc_start: 0.9133 (tt0) cc_final: 0.8890 (tt0) REVERT: A 541 GLU cc_start: 0.8913 (pm20) cc_final: 0.8667 (pm20) REVERT: A 575 ARG cc_start: 0.9216 (mtm-85) cc_final: 0.8438 (mpp80) REVERT: A 586 TYR cc_start: 0.9126 (m-10) cc_final: 0.8882 (m-10) REVERT: A 602 GLU cc_start: 0.8397 (pm20) cc_final: 0.7986 (pm20) REVERT: A 615 MET cc_start: 0.9038 (mmp) cc_final: 0.8523 (mmp) REVERT: A 639 ASP cc_start: 0.9255 (m-30) cc_final: 0.8854 (m-30) REVERT: A 640 MET cc_start: 0.8993 (tpp) cc_final: 0.8714 (tpp) REVERT: A 645 GLN cc_start: 0.9374 (tp40) cc_final: 0.9143 (tp-100) REVERT: A 650 GLN cc_start: 0.8812 (mt0) cc_final: 0.7263 (mt0) REVERT: A 655 THR cc_start: 0.8762 (m) cc_final: 0.8507 (m) REVERT: A 657 PHE cc_start: 0.8725 (m-80) cc_final: 0.8344 (m-80) REVERT: A 682 ILE cc_start: 0.9454 (mp) cc_final: 0.9196 (mp) REVERT: B 29 ASP cc_start: 0.9471 (t70) cc_final: 0.9215 (t70) REVERT: B 99 LYS cc_start: 0.9636 (mmmt) cc_final: 0.9412 (mmmm) REVERT: B 128 PHE cc_start: 0.9668 (t80) cc_final: 0.9407 (t80) REVERT: B 136 LYS cc_start: 0.9672 (mmtp) cc_final: 0.9363 (mmmm) REVERT: B 144 MET cc_start: 0.9147 (mmp) cc_final: 0.8775 (mmp) REVERT: B 145 ILE cc_start: 0.9666 (tp) cc_final: 0.9357 (tp) REVERT: B 147 GLN cc_start: 0.9397 (mt0) cc_final: 0.8705 (mt0) REVERT: B 158 ASN cc_start: 0.9556 (m110) cc_final: 0.8865 (p0) REVERT: B 161 ARG cc_start: 0.8801 (ttm110) cc_final: 0.7749 (mtp85) REVERT: B 164 ARG cc_start: 0.9282 (ttp80) cc_final: 0.8413 (ttm110) REVERT: B 200 SER cc_start: 0.9113 (t) cc_final: 0.8828 (t) REVERT: B 211 GLU cc_start: 0.8895 (mm-30) cc_final: 0.8401 (mm-30) REVERT: B 227 MET cc_start: 0.9300 (mtp) cc_final: 0.9069 (mtp) REVERT: B 229 LEU cc_start: 0.9679 (mt) cc_final: 0.9395 (mt) REVERT: B 232 ASN cc_start: 0.9256 (m110) cc_final: 0.8956 (p0) REVERT: B 251 LEU cc_start: 0.9538 (tp) cc_final: 0.9265 (tp) REVERT: B 286 ASP cc_start: 0.8716 (m-30) cc_final: 0.8010 (m-30) REVERT: B 290 GLU cc_start: 0.9245 (pp20) cc_final: 0.8647 (pp20) REVERT: B 291 LEU cc_start: 0.9605 (mt) cc_final: 0.9360 (mt) REVERT: B 296 LYS cc_start: 0.9043 (mmpt) cc_final: 0.8700 (mtmm) REVERT: B 321 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8558 (tm-30) REVERT: B 322 MET cc_start: 0.9178 (mmm) cc_final: 0.8297 (mmm) REVERT: B 333 LYS cc_start: 0.9574 (ttmm) cc_final: 0.9261 (ttmm) REVERT: B 335 GLU cc_start: 0.9159 (pt0) cc_final: 0.8831 (pt0) REVERT: B 342 LEU cc_start: 0.9754 (tp) cc_final: 0.9474 (tp) REVERT: B 350 ARG cc_start: 0.8623 (mtp85) cc_final: 0.7897 (mtp85) REVERT: B 362 ASP cc_start: 0.9087 (m-30) cc_final: 0.8113 (m-30) REVERT: B 375 LYS cc_start: 0.9233 (mmtm) cc_final: 0.8867 (mmtm) REVERT: B 393 SER cc_start: 0.9491 (t) cc_final: 0.8934 (t) REVERT: B 396 ASP cc_start: 0.8658 (m-30) cc_final: 0.8382 (m-30) REVERT: B 402 GLU cc_start: 0.8637 (mp0) cc_final: 0.8298 (mp0) REVERT: B 413 SER cc_start: 0.9530 (m) cc_final: 0.9145 (t) REVERT: B 415 ASN cc_start: 0.9677 (t0) cc_final: 0.9236 (t0) REVERT: B 417 LEU cc_start: 0.9730 (tt) cc_final: 0.9405 (tt) REVERT: B 418 ASN cc_start: 0.9372 (m110) cc_final: 0.8922 (m-40) REVERT: B 421 GLU cc_start: 0.9406 (tm-30) cc_final: 0.9175 (tm-30) REVERT: B 443 THR cc_start: 0.9331 (m) cc_final: 0.9108 (t) REVERT: B 458 MET cc_start: 0.9520 (mmm) cc_final: 0.9166 (mmm) REVERT: B 467 ASN cc_start: 0.9375 (m-40) cc_final: 0.9140 (m110) REVERT: B 471 TYR cc_start: 0.9298 (t80) cc_final: 0.8878 (t80) REVERT: B 494 MET cc_start: 0.9543 (mtt) cc_final: 0.8921 (mtt) REVERT: B 501 GLN cc_start: 0.9528 (mt0) cc_final: 0.8964 (mt0) REVERT: B 615 MET cc_start: 0.9178 (mmp) cc_final: 0.8724 (mmm) REVERT: B 631 ASP cc_start: 0.9516 (m-30) cc_final: 0.9312 (m-30) REVERT: B 634 MET cc_start: 0.9492 (mmm) cc_final: 0.9246 (mmp) REVERT: B 636 LYS cc_start: 0.9681 (mptt) cc_final: 0.9430 (mmmt) REVERT: B 639 ASP cc_start: 0.9341 (m-30) cc_final: 0.8990 (m-30) REVERT: B 667 LEU cc_start: 0.9360 (tt) cc_final: 0.9036 (tt) REVERT: B 668 ASN cc_start: 0.9375 (m-40) cc_final: 0.8938 (m-40) REVERT: B 683 TYR cc_start: 0.8154 (t80) cc_final: 0.7879 (t80) REVERT: C 98 ASN cc_start: 0.7383 (p0) cc_final: 0.7157 (p0) REVERT: C 100 VAL cc_start: 0.8337 (t) cc_final: 0.7969 (p) REVERT: C 133 LYS cc_start: 0.8278 (mtmm) cc_final: 0.7936 (ptmt) REVERT: C 261 ARG cc_start: 0.4997 (mtm110) cc_final: 0.4665 (ptp90) REVERT: D 69 GLN cc_start: 0.9384 (tp-100) cc_final: 0.8881 (tp-100) REVERT: D 74 MET cc_start: 0.8841 (mmp) cc_final: 0.8628 (mmp) outliers start: 0 outliers final: 0 residues processed: 627 average time/residue: 0.2772 time to fit residues: 257.9912 Evaluate side-chains 545 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 545 time to evaluate : 1.820 ------------------------------------------------------------------------------- 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: 0.8980 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 0.4980 chunk 160 optimal weight: 8.9990 chunk 106 optimal weight: 5.9990 chunk 120 optimal weight: 0.0030 chunk 135 optimal weight: 0.9990 chunk 148 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- 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 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** B 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 HIS B 645 GLN C 52 GLN D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.138494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.094935 restraints weight = 46390.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.097996 restraints weight = 27216.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.100094 restraints weight = 18018.066| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.7716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16386 Z= 0.135 Angle : 0.653 7.806 22134 Z= 0.346 Chirality : 0.044 0.205 2360 Planarity : 0.004 0.048 2818 Dihedral : 10.744 176.285 2242 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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: 0.69 (0.19), residues: 1932 helix: 0.95 (0.15), residues: 1140 sheet: 0.02 (0.46), residues: 110 loop : -0.13 (0.23), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 124 HIS 0.006 0.001 HIS D 201 PHE 0.025 0.002 PHE A 171 TYR 0.038 0.002 TYR A 683 ARG 0.008 0.001 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.03745 ( 871) hydrogen bonds : angle 5.09660 ( 2571) covalent geometry : bond 0.00298 (16386) covalent geometry : angle 0.65317 (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 627 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 627 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 MET cc_start: 0.9088 (mpp) cc_final: 0.8774 (mpp) REVERT: A 95 MET cc_start: 0.8842 (mmm) cc_final: 0.8345 (tpt) REVERT: A 119 GLU cc_start: 0.8951 (mp0) cc_final: 0.8474 (mt-10) REVERT: A 143 LEU cc_start: 0.9617 (tp) cc_final: 0.9297 (tp) REVERT: A 147 GLN cc_start: 0.9324 (mm-40) cc_final: 0.8938 (mm110) REVERT: A 172 LEU cc_start: 0.9383 (mp) cc_final: 0.8872 (mp) REVERT: A 173 LEU cc_start: 0.9547 (mt) cc_final: 0.9277 (mt) REVERT: A 190 MET cc_start: 0.9631 (mmm) cc_final: 0.9296 (mmm) REVERT: A 195 LEU cc_start: 0.9570 (mt) cc_final: 0.9349 (mt) REVERT: A 235 ARG cc_start: 0.9044 (ptp90) cc_final: 0.8535 (mtm110) REVERT: A 252 ASN cc_start: 0.9461 (t0) cc_final: 0.9024 (t0) REVERT: A 307 TYR cc_start: 0.9633 (t80) cc_final: 0.9113 (t80) REVERT: A 322 MET cc_start: 0.9102 (tpt) cc_final: 0.8799 (mmm) REVERT: A 350 ARG cc_start: 0.8930 (mmm-85) cc_final: 0.8454 (mmm-85) REVERT: A 370 ASN cc_start: 0.9452 (m-40) cc_final: 0.9050 (m-40) REVERT: A 373 ILE cc_start: 0.9405 (mt) cc_final: 0.9165 (mt) REVERT: A 406 ASP cc_start: 0.9037 (m-30) cc_final: 0.8678 (m-30) REVERT: A 407 ILE cc_start: 0.9245 (mt) cc_final: 0.8782 (mt) REVERT: A 415 ASN cc_start: 0.9407 (t0) cc_final: 0.8886 (t0) REVERT: A 418 ASN cc_start: 0.9456 (m110) cc_final: 0.8970 (m-40) REVERT: A 421 GLU cc_start: 0.9190 (tm-30) cc_final: 0.8971 (tm-30) REVERT: A 447 ASN cc_start: 0.7829 (m-40) cc_final: 0.5972 (m-40) REVERT: A 466 MET cc_start: 0.9667 (ptt) cc_final: 0.9405 (ptt) REVERT: A 472 LEU cc_start: 0.9775 (mt) cc_final: 0.9572 (mt) REVERT: A 493 MET cc_start: 0.9100 (tmm) cc_final: 0.8758 (tmm) REVERT: A 496 ASN cc_start: 0.9541 (t0) cc_final: 0.8313 (t0) REVERT: A 500 ILE cc_start: 0.9672 (mt) cc_final: 0.8695 (mt) REVERT: A 515 ASP cc_start: 0.9302 (m-30) cc_final: 0.8964 (m-30) REVERT: A 516 GLN cc_start: 0.9110 (tt0) cc_final: 0.8795 (tt0) REVERT: A 570 MET cc_start: 0.7951 (ttm) cc_final: 0.7529 (ttm) REVERT: A 575 ARG cc_start: 0.9196 (mtm-85) cc_final: 0.8440 (mpp80) REVERT: A 586 TYR cc_start: 0.9108 (m-10) cc_final: 0.8865 (m-10) REVERT: A 601 ILE cc_start: 0.9456 (tt) cc_final: 0.9239 (tt) REVERT: A 602 GLU cc_start: 0.8263 (pm20) cc_final: 0.8005 (pm20) REVERT: A 612 TYR cc_start: 0.8692 (m-80) cc_final: 0.8304 (m-80) REVERT: A 615 MET cc_start: 0.9041 (mmp) cc_final: 0.8582 (mmp) REVERT: A 639 ASP cc_start: 0.9273 (m-30) cc_final: 0.8899 (m-30) REVERT: A 640 MET cc_start: 0.9000 (tpp) cc_final: 0.8723 (tpp) REVERT: A 645 GLN cc_start: 0.9405 (tp40) cc_final: 0.9196 (tp-100) REVERT: A 682 ILE cc_start: 0.9468 (mp) cc_final: 0.9193 (mp) REVERT: B 15 GLU cc_start: 0.9022 (tp30) cc_final: 0.8785 (tp30) REVERT: B 29 ASP cc_start: 0.9484 (t70) cc_final: 0.9183 (t70) REVERT: B 51 LEU cc_start: 0.9422 (tp) cc_final: 0.9206 (tp) REVERT: B 99 LYS cc_start: 0.9592 (mmmt) cc_final: 0.8904 (mmmt) REVERT: B 136 LYS cc_start: 0.9661 (mmtp) cc_final: 0.9342 (mmmm) REVERT: B 161 ARG cc_start: 0.8736 (ttm110) cc_final: 0.7607 (mtp85) REVERT: B 164 ARG cc_start: 0.9271 (ttp80) cc_final: 0.8621 (ttm110) REVERT: B 200 SER cc_start: 0.9106 (t) cc_final: 0.8825 (t) REVERT: B 211 GLU cc_start: 0.8868 (mm-30) cc_final: 0.8506 (mm-30) REVERT: B 218 ASN cc_start: 0.9465 (m110) cc_final: 0.8257 (m110) REVERT: B 227 MET cc_start: 0.9288 (mtp) cc_final: 0.9042 (mtp) REVERT: B 229 LEU cc_start: 0.9664 (mt) cc_final: 0.9383 (mt) REVERT: B 232 ASN cc_start: 0.9212 (m110) cc_final: 0.8986 (p0) REVERT: B 251 LEU cc_start: 0.9483 (tp) cc_final: 0.9244 (tp) REVERT: B 286 ASP cc_start: 0.8717 (m-30) cc_final: 0.8181 (m-30) REVERT: B 290 GLU cc_start: 0.9276 (pp20) cc_final: 0.8686 (pp20) REVERT: B 291 LEU cc_start: 0.9593 (mt) cc_final: 0.9338 (mt) REVERT: B 296 LYS cc_start: 0.8940 (mmpt) cc_final: 0.8596 (mtmm) REVERT: B 321 GLU cc_start: 0.9065 (tm-30) cc_final: 0.8621 (tm-30) REVERT: B 322 MET cc_start: 0.9197 (mmm) cc_final: 0.8248 (mmm) REVERT: B 333 LYS cc_start: 0.9555 (ttmm) cc_final: 0.9228 (ttmm) REVERT: B 335 GLU cc_start: 0.9161 (pt0) cc_final: 0.8820 (pt0) REVERT: B 344 GLU cc_start: 0.9235 (mm-30) cc_final: 0.8946 (mm-30) REVERT: B 350 ARG cc_start: 0.8589 (mtp85) cc_final: 0.7953 (mtp85) REVERT: B 362 ASP cc_start: 0.9020 (m-30) cc_final: 0.8029 (m-30) REVERT: B 393 SER cc_start: 0.9470 (t) cc_final: 0.8931 (t) REVERT: B 396 ASP cc_start: 0.8718 (m-30) cc_final: 0.8331 (m-30) REVERT: B 402 GLU cc_start: 0.8620 (mp0) cc_final: 0.8290 (mp0) REVERT: B 413 SER cc_start: 0.9476 (m) cc_final: 0.9122 (t) REVERT: B 415 ASN cc_start: 0.9587 (t0) cc_final: 0.8973 (t0) REVERT: B 417 LEU cc_start: 0.9726 (tt) cc_final: 0.9351 (tt) REVERT: B 418 ASN cc_start: 0.9202 (m110) cc_final: 0.8772 (m-40) REVERT: B 421 GLU cc_start: 0.9404 (tm-30) cc_final: 0.9139 (tm-30) REVERT: B 441 GLU cc_start: 0.9166 (pm20) cc_final: 0.8944 (pm20) REVERT: B 458 MET cc_start: 0.9463 (mmm) cc_final: 0.8921 (mmm) REVERT: B 459 LYS cc_start: 0.9259 (mppt) cc_final: 0.8426 (mptt) REVERT: B 467 ASN cc_start: 0.9320 (m-40) cc_final: 0.9077 (m110) REVERT: B 471 TYR cc_start: 0.9126 (t80) cc_final: 0.8736 (t80) REVERT: B 480 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7014 (mt-10) REVERT: B 494 MET cc_start: 0.9525 (mtt) cc_final: 0.8915 (mtt) REVERT: B 501 GLN cc_start: 0.9529 (mt0) cc_final: 0.8959 (mt0) REVERT: B 634 MET cc_start: 0.9536 (mmm) cc_final: 0.9329 (mmp) REVERT: B 646 GLN cc_start: 0.9598 (pt0) cc_final: 0.9051 (pm20) REVERT: B 648 ILE cc_start: 0.9494 (mm) cc_final: 0.9281 (mm) REVERT: B 667 LEU cc_start: 0.9363 (tt) cc_final: 0.9056 (tt) REVERT: B 668 ASN cc_start: 0.9308 (m-40) cc_final: 0.8834 (m-40) REVERT: B 680 LYS cc_start: 0.9030 (mttt) cc_final: 0.8737 (mttt) REVERT: B 683 TYR cc_start: 0.8240 (t80) cc_final: 0.7840 (t80) REVERT: C 95 MET cc_start: 0.9072 (tmm) cc_final: 0.8836 (tmm) REVERT: C 98 ASN cc_start: 0.7356 (p0) cc_final: 0.7099 (p0) REVERT: C 100 VAL cc_start: 0.8492 (t) cc_final: 0.8221 (p) REVERT: C 101 HIS cc_start: 0.8484 (m90) cc_final: 0.7912 (m90) REVERT: C 133 LYS cc_start: 0.8302 (mtmm) cc_final: 0.7965 (ptmt) REVERT: C 261 ARG cc_start: 0.4981 (mtm110) cc_final: 0.4611 (ptp-170) REVERT: D 69 GLN cc_start: 0.9361 (tp-100) cc_final: 0.8866 (tp-100) REVERT: D 74 MET cc_start: 0.8732 (mmp) cc_final: 0.8530 (mmp) REVERT: D 91 ASN cc_start: 0.8228 (m110) cc_final: 0.8028 (m110) REVERT: D 158 VAL cc_start: 0.9252 (t) cc_final: 0.8957 (m) REVERT: D 205 VAL cc_start: 0.9298 (t) cc_final: 0.9091 (p) outliers start: 0 outliers final: 0 residues processed: 627 average time/residue: 0.2693 time to fit residues: 251.4538 Evaluate side-chains 557 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 557 time to evaluate : 1.672 ------------------------------------------------------------------------------- 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: 4.9990 chunk 16 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 chunk 179 optimal weight: 0.0970 chunk 190 optimal weight: 20.0000 chunk 58 optimal weight: 1.9990 chunk 180 optimal weight: 0.8980 chunk 108 optimal weight: 0.2980 chunk 43 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN D 234 GLN ** D 238 ASN ** 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 = 0.3844 r_free = 0.3844 target = 0.143215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.099214 restraints weight = 45982.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.102566 restraints weight = 26875.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.104876 restraints weight = 17670.008| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3247 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3247 r_free = 0.3247 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3247 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.7899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16386 Z= 0.135 Angle : 0.657 9.851 22134 Z= 0.347 Chirality : 0.044 0.210 2360 Planarity : 0.004 0.045 2818 Dihedral : 10.586 167.889 2242 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 14.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.19), residues: 1932 helix: 1.00 (0.15), residues: 1124 sheet: -0.11 (0.45), residues: 110 loop : -0.16 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 124 HIS 0.007 0.001 HIS D 201 PHE 0.024 0.002 PHE A 171 TYR 0.041 0.002 TYR A 683 ARG 0.012 0.001 ARG B 604 Details of bonding type rmsd hydrogen bonds : bond 0.03780 ( 871) hydrogen bonds : angle 5.14048 ( 2571) covalent geometry : bond 0.00297 (16386) covalent geometry : angle 0.65722 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7210.20 seconds wall clock time: 126 minutes 13.36 seconds (7573.36 seconds total)