Starting phenix.real_space_refine on Sat May 17 16:27:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bzf_45066/05_2025/9bzf_45066_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bzf_45066/05_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_45066/05_2025/9bzf_45066.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bzf_45066/05_2025/9bzf_45066.map" model { file = "/net/cci-nas-00/data/ceres_data/9bzf_45066/05_2025/9bzf_45066_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bzf_45066/05_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16038 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "D" Number of atoms: 2374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2374 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 7, 'TRANS': 281} Chain breaks: 1 Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 9.91, per 1000 atoms: 0.62 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: 4.66 Conformation dependent library (CDL) restraints added in 2.2 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: 1.82 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: 5.67 Time building geometry restraints manager: 5.42 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: 0.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 40.240 Find NCS groups from input model: 0.970 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: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.860 ------------------------------------------------------------------------------- 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 : 1.726 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: 0.7973 (t70) REVERT: A 37 PHE cc_start: 0.6567 (m-80) cc_final: 0.6200 (m-10) REVERT: A 41 ILE cc_start: 0.8350 (mm) cc_final: 0.8047 (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: 0.8411 (tp) REVERT: A 168 VAL cc_start: 0.8904 (t) cc_final: 0.8653 (t) REVERT: A 181 ASP cc_start: 0.8597 (m-30) cc_final: 0.8164 (m-30) REVERT: A 191 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7445 (mm110) REVERT: A 258 ILE cc_start: 0.8700 (tp) cc_final: 0.8366 (tp) REVERT: A 264 THR cc_start: 0.8998 (p) cc_final: 0.8792 (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: 0.6586 (mmm) REVERT: A 362 ASP cc_start: 0.5877 (m-30) cc_final: 0.4692 (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: 0.8860 (mm) REVERT: A 436 LEU cc_start: 0.9165 (mt) cc_final: 0.8798 (mt) REVERT: A 447 ASN cc_start: 0.7619 (m-40) cc_final: 0.6965 (m110) REVERT: A 493 MET cc_start: 0.7567 (tmm) cc_final: 0.7049 (tmm) REVERT: A 494 MET cc_start: 0.7764 (mtp) cc_final: 0.7312 (mtp) REVERT: A 500 ILE cc_start: 0.9352 (mt) cc_final: 0.9031 (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: 0.6045 (m-80) REVERT: A 558 TRP cc_start: 0.8229 (m100) cc_final: 0.6943 (m100) REVERT: A 561 LEU cc_start: 0.8853 (tp) cc_final: 0.8634 (tp) REVERT: A 565 VAL cc_start: 0.8965 (t) cc_final: 0.8733 (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: 0.7987 (ptp90) REVERT: A 655 THR cc_start: 0.8855 (m) cc_final: 0.8497 (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: 0.8446 (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: 0.8119 (tttt) REVERT: B 95 MET cc_start: 0.6966 (tpp) cc_final: 0.6649 (tpp) REVERT: B 99 LYS cc_start: 0.8995 (mmtt) cc_final: 0.8742 (mmtt) REVERT: B 101 TYR cc_start: 0.7746 (m-80) cc_final: 0.7546 (m-80) REVERT: B 121 ARG cc_start: 0.8271 (tpm170) cc_final: 0.7575 (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: 0.7915 (tp) REVERT: B 172 LEU cc_start: 0.9041 (mp) cc_final: 0.8738 (mp) REVERT: B 181 ASP cc_start: 0.8259 (m-30) cc_final: 0.7789 (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: 0.8458 (p) REVERT: B 258 ILE cc_start: 0.8950 (tp) cc_final: 0.8707 (tp) REVERT: B 291 LEU cc_start: 0.9105 (mt) cc_final: 0.8870 (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: 0.6394 (mmm) REVERT: B 418 ASN cc_start: 0.7391 (m-40) cc_final: 0.6755 (m-40) REVERT: B 469 HIS cc_start: 0.8278 (t-170) cc_final: 0.7983 (t70) REVERT: B 500 ILE cc_start: 0.9212 (mt) cc_final: 0.8848 (mt) REVERT: B 515 ASP cc_start: 0.8433 (m-30) cc_final: 0.8186 (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: 0.8623 (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: 0.7967 (p) REVERT: B 631 ASP cc_start: 0.7629 (m-30) cc_final: 0.7338 (t0) REVERT: B 644 ILE cc_start: 0.8499 (mt) cc_final: 0.8212 (mt) REVERT: B 655 THR cc_start: 0.9341 (m) cc_final: 0.8575 (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: 0.3089 time to fit residues: 386.6616 Evaluate side-chains 614 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 608 time to evaluate : 1.744 ------------------------------------------------------------------------------- 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 645 GLN B 218 ASN B 304 HIS B 313 HIS ** B 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN C 24 GLN C 28 GLN C 186 GLN C 238 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 234 GLN ** D 263 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.140495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.094303 restraints weight = 43833.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.097807 restraints weight = 26227.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.100024 restraints weight = 17576.018| |-----------------------------------------------------------------------------| r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3228 r_free = 0.3228 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3228 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.4307 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= 0.174 Angle : 0.634 8.982 22134 Z= 0.337 Chirality : 0.042 0.211 2360 Planarity : 0.004 0.045 2818 Dihedral : 11.462 179.764 2242 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.17 % Allowed : 2.74 % Favored : 97.09 % 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: 1.46 (0.19), residues: 1932 helix: 1.48 (0.15), residues: 1121 sheet: -0.32 (0.39), residues: 148 loop : 0.60 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 30 HIS 0.009 0.001 HIS A 304 PHE 0.033 0.002 PHE D 320 TYR 0.065 0.002 TYR A 612 ARG 0.006 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.04418 ( 871) hydrogen bonds : angle 5.02331 ( 2571) covalent geometry : bond 0.00363 (16386) covalent geometry : angle 0.63440 (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 740 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 737 time to evaluate : 1.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9331 (t0) cc_final: 0.9039 (t70) REVERT: A 40 TYR cc_start: 0.9169 (t80) cc_final: 0.8873 (t80) REVERT: A 89 PHE cc_start: 0.8879 (t80) cc_final: 0.8205 (t80) REVERT: A 119 GLU cc_start: 0.9196 (mp0) cc_final: 0.8416 (tm-30) REVERT: A 120 ASP cc_start: 0.9214 (m-30) cc_final: 0.8759 (m-30) REVERT: A 143 LEU cc_start: 0.9373 (tp) cc_final: 0.8928 (tp) REVERT: A 148 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8374 (mt-10) REVERT: A 181 ASP cc_start: 0.9114 (m-30) cc_final: 0.8890 (m-30) REVERT: A 195 LEU cc_start: 0.9563 (mt) cc_final: 0.9299 (mt) REVERT: A 227 MET cc_start: 0.9247 (mtm) cc_final: 0.9021 (mtm) REVERT: A 235 ARG cc_start: 0.8759 (mtm110) cc_final: 0.8471 (mtm110) REVERT: A 239 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7302 (tt0) REVERT: A 252 ASN cc_start: 0.9392 (t0) cc_final: 0.8917 (t0) REVERT: A 286 ASP cc_start: 0.9000 (m-30) cc_final: 0.8236 (m-30) REVERT: A 307 TYR cc_start: 0.9556 (t80) cc_final: 0.9338 (t80) REVERT: A 314 MET cc_start: 0.9162 (ttp) cc_final: 0.8951 (ttt) REVERT: A 322 MET cc_start: 0.9108 (mmp) cc_final: 0.8641 (mmm) REVERT: A 335 GLU cc_start: 0.8499 (mm-30) cc_final: 0.7745 (mm-30) REVERT: A 350 ARG cc_start: 0.8622 (mmm-85) cc_final: 0.8156 (mmm-85) REVERT: A 370 ASN cc_start: 0.9375 (m-40) cc_final: 0.9023 (m110) REVERT: A 402 GLU cc_start: 0.8540 (mp0) cc_final: 0.8237 (mp0) REVERT: A 415 ASN cc_start: 0.9494 (t0) cc_final: 0.8873 (t0) REVERT: A 418 ASN cc_start: 0.9362 (m-40) cc_final: 0.8735 (m-40) REVERT: A 459 LYS cc_start: 0.9145 (mttp) cc_final: 0.8625 (mtmt) REVERT: A 468 LEU cc_start: 0.9783 (tp) cc_final: 0.9485 (tp) REVERT: A 472 LEU cc_start: 0.9735 (mt) cc_final: 0.9481 (mt) REVERT: A 500 ILE cc_start: 0.9662 (mt) cc_final: 0.9458 (mt) REVERT: A 515 ASP cc_start: 0.9269 (m-30) cc_final: 0.8951 (m-30) REVERT: A 522 TYR cc_start: 0.9218 (m-80) cc_final: 0.8799 (m-10) REVERT: A 570 MET cc_start: 0.9057 (mtp) cc_final: 0.7751 (mtp) REVERT: A 575 ARG cc_start: 0.9131 (mtm110) cc_final: 0.8786 (ptp90) REVERT: A 598 MET cc_start: 0.9292 (mtp) cc_final: 0.8685 (mmt) REVERT: A 615 MET cc_start: 0.8808 (mmp) cc_final: 0.8399 (mmp) REVERT: A 632 MET cc_start: 0.8905 (mtp) cc_final: 0.8307 (mtt) REVERT: A 650 GLN cc_start: 0.8777 (mt0) cc_final: 0.8134 (mt0) REVERT: A 657 PHE cc_start: 0.8500 (m-80) cc_final: 0.7828 (m-80) REVERT: B 15 GLU cc_start: 0.9211 (tp30) cc_final: 0.8716 (tp30) REVERT: B 17 MET cc_start: 0.8979 (mpp) cc_final: 0.8777 (mpp) REVERT: B 51 LEU cc_start: 0.9228 (tp) cc_final: 0.8830 (tp) REVERT: B 62 GLN cc_start: 0.9649 (mp-120) cc_final: 0.8974 (mp10) REVERT: B 95 MET cc_start: 0.9168 (tpp) cc_final: 0.8604 (tpp) REVERT: B 99 LYS cc_start: 0.9528 (mmmt) cc_final: 0.9089 (mmmt) REVERT: B 115 LEU cc_start: 0.9445 (mt) cc_final: 0.9136 (mt) REVERT: B 117 ARG cc_start: 0.9124 (ttm110) cc_final: 0.8863 (ttm110) REVERT: B 119 GLU cc_start: 0.9289 (mp0) cc_final: 0.8849 (mp0) REVERT: B 122 ILE cc_start: 0.9759 (mt) cc_final: 0.9485 (mt) REVERT: B 144 MET cc_start: 0.9344 (mtm) cc_final: 0.8990 (mtm) REVERT: B 147 GLN cc_start: 0.9061 (mt0) cc_final: 0.8731 (mt0) REVERT: B 205 LYS cc_start: 0.9437 (mmmt) cc_final: 0.8976 (mmmm) REVERT: B 218 ASN cc_start: 0.9722 (t0) cc_final: 0.9432 (t0) REVERT: B 227 MET cc_start: 0.9439 (mtp) cc_final: 0.9195 (mtp) REVERT: B 236 TYR cc_start: 0.9010 (t80) cc_final: 0.8633 (t80) REVERT: B 251 LEU cc_start: 0.9496 (tp) cc_final: 0.9178 (tp) REVERT: B 252 ASN cc_start: 0.9392 (t0) cc_final: 0.9080 (t0) REVERT: B 286 ASP cc_start: 0.8771 (m-30) cc_final: 0.8284 (m-30) REVERT: B 288 PHE cc_start: 0.9374 (t80) cc_final: 0.9150 (t80) REVERT: B 291 LEU cc_start: 0.9600 (mt) cc_final: 0.9289 (mt) REVERT: B 314 MET cc_start: 0.8385 (tmm) cc_final: 0.8177 (tmm) REVERT: B 322 MET cc_start: 0.9309 (mmm) cc_final: 0.8707 (mmm) REVERT: B 342 LEU cc_start: 0.9693 (tp) cc_final: 0.9356 (tp) REVERT: B 345 LYS cc_start: 0.9508 (tttt) cc_final: 0.9256 (tttt) REVERT: B 348 MET cc_start: 0.9296 (tpp) cc_final: 0.8424 (tpp) REVERT: B 362 ASP cc_start: 0.8990 (m-30) cc_final: 0.8099 (m-30) REVERT: B 373 ILE cc_start: 0.9663 (mt) cc_final: 0.9341 (tp) REVERT: B 375 LYS cc_start: 0.9229 (mmtm) cc_final: 0.8811 (mmtm) REVERT: B 393 SER cc_start: 0.9704 (t) cc_final: 0.9039 (p) REVERT: B 398 ASP cc_start: 0.8716 (t70) cc_final: 0.8416 (t70) REVERT: B 403 ILE cc_start: 0.9344 (mp) cc_final: 0.9014 (tp) REVERT: B 430 LYS cc_start: 0.9144 (ptpp) cc_final: 0.8893 (mtmm) REVERT: B 458 MET cc_start: 0.9417 (mmm) cc_final: 0.8836 (mmm) REVERT: B 494 MET cc_start: 0.9488 (mtt) cc_final: 0.9192 (mtt) REVERT: B 500 ILE cc_start: 0.9794 (mt) cc_final: 0.9480 (mt) REVERT: B 515 ASP cc_start: 0.9071 (m-30) cc_final: 0.8864 (m-30) REVERT: B 548 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8542 (mt-10) REVERT: B 570 MET cc_start: 0.9563 (mtp) cc_final: 0.8931 (mtp) REVERT: B 585 SER cc_start: 0.9111 (p) cc_final: 0.8574 (t) REVERT: B 591 THR cc_start: 0.9259 (p) cc_final: 0.9045 (p) REVERT: B 603 GLU cc_start: 0.8890 (tm-30) cc_final: 0.8131 (tm-30) REVERT: B 615 MET cc_start: 0.8780 (mmp) cc_final: 0.8431 (mmp) REVERT: B 648 ILE cc_start: 0.9598 (mm) cc_final: 0.9365 (mm) REVERT: B 667 LEU cc_start: 0.9064 (tp) cc_final: 0.8707 (tp) REVERT: B 668 ASN cc_start: 0.9401 (m-40) cc_final: 0.8936 (m-40) REVERT: B 677 ARG cc_start: 0.9646 (mmm160) cc_final: 0.9330 (mmm-85) REVERT: C 100 VAL cc_start: 0.9061 (t) cc_final: 0.8638 (t) REVERT: C 101 HIS cc_start: 0.8128 (m90) cc_final: 0.7855 (m90) REVERT: D 169 TYR cc_start: 0.8584 (m-80) cc_final: 0.8230 (m-80) REVERT: D 179 TYR cc_start: 0.6525 (t80) cc_final: 0.6109 (t80) REVERT: D 185 MET cc_start: 0.1494 (mmm) cc_final: 0.0928 (mpp) REVERT: D 197 ASP cc_start: 0.9427 (t70) cc_final: 0.9095 (t70) REVERT: D 201 HIS cc_start: 0.5530 (m170) cc_final: 0.4859 (m170) outliers start: 3 outliers final: 0 residues processed: 738 average time/residue: 0.2932 time to fit residues: 312.0492 Evaluate side-chains 589 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 588 time to evaluate : 1.737 ------------------------------------------------------------------------------- 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: 6.9990 chunk 168 optimal weight: 8.9990 chunk 175 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 191 optimal weight: 20.0000 chunk 57 optimal weight: 4.9990 chunk 52 optimal weight: 6.9990 chunk 171 optimal weight: 6.9990 chunk 189 optimal weight: 0.0570 chunk 141 optimal weight: 8.9990 overall best weight: 3.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN B 158 ASN ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 HIS B 645 GLN C 127 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 181 GLN D 233 ASN D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.129702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.086047 restraints weight = 46008.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.089249 restraints weight = 27576.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.091346 restraints weight = 18416.013| |-----------------------------------------------------------------------------| r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.5444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16386 Z= 0.229 Angle : 0.663 9.913 22134 Z= 0.351 Chirality : 0.042 0.150 2360 Planarity : 0.005 0.158 2818 Dihedral : 11.431 170.547 2242 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 2.86 % 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: 1.21 (0.19), residues: 1932 helix: 1.37 (0.15), residues: 1108 sheet: -0.53 (0.39), residues: 152 loop : 0.37 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 124 HIS 0.008 0.002 HIS B 438 PHE 0.022 0.002 PHE D 320 TYR 0.044 0.002 TYR A 612 ARG 0.009 0.001 ARG B 164 Details of bonding type rmsd hydrogen bonds : bond 0.04186 ( 871) hydrogen bonds : angle 4.96555 ( 2571) covalent geometry : bond 0.00472 (16386) covalent geometry : angle 0.66296 (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 660 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 660 time to evaluate : 1.723 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9492 (t0) cc_final: 0.9278 (t70) REVERT: A 81 PHE cc_start: 0.9397 (m-80) cc_final: 0.9196 (m-80) REVERT: A 89 PHE cc_start: 0.9214 (t80) cc_final: 0.8829 (t80) REVERT: A 116 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8571 (tt0) REVERT: A 119 GLU cc_start: 0.9254 (mp0) cc_final: 0.8183 (tm-30) REVERT: A 143 LEU cc_start: 0.9413 (tp) cc_final: 0.8954 (tp) REVERT: A 147 GLN cc_start: 0.9270 (mm110) cc_final: 0.8903 (mm-40) REVERT: A 148 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8361 (mt-10) REVERT: A 172 LEU cc_start: 0.9293 (mp) cc_final: 0.8896 (mp) REVERT: A 181 ASP cc_start: 0.9152 (m-30) cc_final: 0.8816 (m-30) REVERT: A 195 LEU cc_start: 0.9623 (mt) cc_final: 0.9392 (mt) REVERT: A 204 SER cc_start: 0.9409 (m) cc_final: 0.9185 (m) REVERT: A 227 MET cc_start: 0.9353 (mtm) cc_final: 0.9097 (mtm) REVERT: A 250 TYR cc_start: 0.8711 (m-80) cc_final: 0.8252 (m-80) REVERT: A 252 ASN cc_start: 0.9460 (t0) cc_final: 0.8882 (t0) REVERT: A 307 TYR cc_start: 0.9544 (t80) cc_final: 0.9140 (t80) REVERT: A 342 LEU cc_start: 0.9564 (tp) cc_final: 0.9319 (tp) REVERT: A 348 MET cc_start: 0.9366 (ptp) cc_final: 0.9164 (ptp) REVERT: A 370 ASN cc_start: 0.9578 (m-40) cc_final: 0.9317 (m110) REVERT: A 387 GLN cc_start: 0.8968 (mt0) cc_final: 0.8536 (mp10) REVERT: A 394 TYR cc_start: 0.9316 (m-80) cc_final: 0.9024 (m-80) REVERT: A 406 ASP cc_start: 0.8885 (m-30) cc_final: 0.8568 (m-30) REVERT: A 421 GLU cc_start: 0.9298 (tm-30) cc_final: 0.9085 (tm-30) REVERT: A 459 LYS cc_start: 0.9297 (mttp) cc_final: 0.8855 (mtmm) REVERT: A 468 LEU cc_start: 0.9812 (tp) cc_final: 0.9458 (tp) REVERT: A 472 LEU cc_start: 0.9741 (mt) cc_final: 0.9455 (mt) REVERT: A 494 MET cc_start: 0.9495 (mtp) cc_final: 0.9058 (mtp) REVERT: A 499 SER cc_start: 0.9950 (t) cc_final: 0.9708 (p) REVERT: A 515 ASP cc_start: 0.9345 (m-30) cc_final: 0.9083 (m-30) REVERT: A 522 TYR cc_start: 0.9332 (m-80) cc_final: 0.8651 (m-10) REVERT: A 570 MET cc_start: 0.9314 (mtp) cc_final: 0.7821 (mtp) REVERT: A 575 ARG cc_start: 0.9297 (mtm110) cc_final: 0.8613 (ptp90) REVERT: A 598 MET cc_start: 0.9275 (mtp) cc_final: 0.8634 (mmm) REVERT: A 599 GLU cc_start: 0.9068 (mt-10) cc_final: 0.8728 (mt-10) REVERT: A 602 GLU cc_start: 0.8382 (pt0) cc_final: 0.7747 (pt0) REVERT: A 615 MET cc_start: 0.8838 (mmp) cc_final: 0.8626 (mmp) REVERT: A 650 GLN cc_start: 0.8600 (mt0) cc_final: 0.7466 (mt0) REVERT: A 686 ARG cc_start: 0.8930 (mmt180) cc_final: 0.8650 (mmt180) REVERT: B 15 GLU cc_start: 0.9197 (tp30) cc_final: 0.8807 (tp30) REVERT: B 51 LEU cc_start: 0.9365 (tp) cc_final: 0.9088 (tp) REVERT: B 95 MET cc_start: 0.9271 (tpp) cc_final: 0.8731 (tpp) REVERT: B 99 LYS cc_start: 0.9581 (mmmt) cc_final: 0.9067 (mmmt) REVERT: B 107 LYS cc_start: 0.9579 (mptt) cc_final: 0.9256 (mptt) REVERT: B 115 LEU cc_start: 0.9556 (mt) cc_final: 0.9313 (mt) REVERT: B 139 GLU cc_start: 0.9512 (mp0) cc_final: 0.9235 (mp0) REVERT: B 144 MET cc_start: 0.9237 (mtm) cc_final: 0.8850 (mtm) REVERT: B 147 GLN cc_start: 0.9026 (mt0) cc_final: 0.8798 (mt0) REVERT: B 157 LEU cc_start: 0.9584 (tp) cc_final: 0.9078 (tp) REVERT: B 158 ASN cc_start: 0.9545 (m-40) cc_final: 0.9018 (m-40) REVERT: B 161 ARG cc_start: 0.9136 (ttm110) cc_final: 0.8297 (mtt180) REVERT: B 227 MET cc_start: 0.9430 (mtp) cc_final: 0.9144 (mtp) REVERT: B 251 LEU cc_start: 0.9492 (tp) cc_final: 0.9221 (tp) REVERT: B 286 ASP cc_start: 0.8839 (m-30) cc_final: 0.8364 (m-30) REVERT: B 290 GLU cc_start: 0.9394 (pp20) cc_final: 0.8905 (pp20) REVERT: B 291 LEU cc_start: 0.9564 (mt) cc_final: 0.9198 (mt) REVERT: B 301 PHE cc_start: 0.9216 (m-80) cc_final: 0.9003 (m-10) REVERT: B 312 GLN cc_start: 0.9182 (pm20) cc_final: 0.8719 (pm20) REVERT: B 322 MET cc_start: 0.9179 (mmm) cc_final: 0.8526 (mmm) REVERT: B 342 LEU cc_start: 0.9779 (tp) cc_final: 0.9553 (tp) REVERT: B 345 LYS cc_start: 0.9573 (tttt) cc_final: 0.9248 (tttt) REVERT: B 350 ARG cc_start: 0.8748 (mtp85) cc_final: 0.8272 (mtp85) REVERT: B 362 ASP cc_start: 0.9107 (m-30) cc_final: 0.8120 (m-30) REVERT: B 370 ASN cc_start: 0.9625 (m-40) cc_final: 0.9227 (m110) REVERT: B 375 LYS cc_start: 0.9230 (mmtm) cc_final: 0.8768 (mmtm) REVERT: B 386 LEU cc_start: 0.9249 (mt) cc_final: 0.8498 (mt) REVERT: B 398 ASP cc_start: 0.8980 (t70) cc_final: 0.8778 (t70) REVERT: B 403 ILE cc_start: 0.9408 (mp) cc_final: 0.8962 (tp) REVERT: B 427 LYS cc_start: 0.9550 (ptpp) cc_final: 0.9276 (ptpp) REVERT: B 494 MET cc_start: 0.9583 (mtt) cc_final: 0.9154 (mtt) REVERT: B 501 GLN cc_start: 0.9432 (mt0) cc_final: 0.9160 (mt0) REVERT: B 515 ASP cc_start: 0.9488 (m-30) cc_final: 0.9170 (m-30) REVERT: B 547 PHE cc_start: 0.8985 (m-80) cc_final: 0.8428 (m-80) REVERT: B 570 MET cc_start: 0.9418 (mtp) cc_final: 0.9133 (mtp) REVERT: B 574 TYR cc_start: 0.8865 (m-10) cc_final: 0.8600 (m-10) REVERT: B 585 SER cc_start: 0.9105 (p) cc_final: 0.8631 (t) REVERT: B 606 TYR cc_start: 0.8575 (m-80) cc_final: 0.8334 (m-80) REVERT: B 615 MET cc_start: 0.8901 (mmp) cc_final: 0.8693 (mmp) REVERT: B 626 TYR cc_start: 0.8967 (m-80) cc_final: 0.8760 (m-80) REVERT: B 631 ASP cc_start: 0.9255 (t0) cc_final: 0.9003 (t0) REVERT: B 646 GLN cc_start: 0.9504 (pt0) cc_final: 0.9138 (pm20) REVERT: B 655 THR cc_start: 0.9223 (m) cc_final: 0.8841 (t) REVERT: B 668 ASN cc_start: 0.9420 (m-40) cc_final: 0.9048 (m-40) REVERT: B 677 ARG cc_start: 0.9667 (mmm160) cc_final: 0.9291 (mmm-85) REVERT: C 56 MET cc_start: -0.1272 (ttp) cc_final: -0.1509 (ttp) REVERT: C 100 VAL cc_start: 0.9034 (t) cc_final: 0.8796 (t) REVERT: C 101 HIS cc_start: 0.7909 (m90) cc_final: 0.7490 (m90) REVERT: C 124 TRP cc_start: 0.7756 (t60) cc_final: 0.7209 (t60) REVERT: C 185 MET cc_start: 0.2880 (tmm) cc_final: 0.2368 (mmm) REVERT: C 261 ARG cc_start: 0.5647 (mtm110) cc_final: 0.5357 (ptp90) REVERT: D 69 GLN cc_start: 0.9232 (tp40) cc_final: 0.8434 (tm-30) REVERT: D 146 GLN cc_start: 0.9198 (mt0) cc_final: 0.8963 (tm-30) REVERT: D 179 TYR cc_start: 0.7232 (t80) cc_final: 0.6850 (t80) REVERT: D 185 MET cc_start: 0.2077 (mmm) cc_final: 0.1540 (mpp) outliers start: 0 outliers final: 0 residues processed: 660 average time/residue: 0.2698 time to fit residues: 262.6723 Evaluate side-chains 555 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 555 time to evaluate : 1.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 180 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 150 GLN A 313 HIS ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN A 675 HIS ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 191 GLN B 410 ASN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN B 645 GLN C 132 GLN C 201 HIS D 69 GLN D 234 GLN ** D 238 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 = 0.3720 r_free = 0.3720 target = 0.127223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.083977 restraints weight = 47269.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.087052 restraints weight = 28167.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.089102 restraints weight = 18678.056| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 7 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.6204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16386 Z= 0.241 Angle : 0.664 10.051 22134 Z= 0.353 Chirality : 0.042 0.150 2360 Planarity : 0.004 0.089 2818 Dihedral : 11.370 175.268 2242 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 2.74 % 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: 0.97 (0.19), residues: 1932 helix: 1.17 (0.15), residues: 1125 sheet: -0.46 (0.39), residues: 140 loop : 0.19 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 124 HIS 0.007 0.001 HIS A 372 PHE 0.035 0.002 PHE B 81 TYR 0.047 0.002 TYR A 612 ARG 0.009 0.001 ARG B 117 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 871) hydrogen bonds : angle 5.09337 ( 2571) covalent geometry : bond 0.00490 (16386) covalent geometry : angle 0.66367 (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 639 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 639 time to evaluate : 1.964 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: 0.9497 (t0) cc_final: 0.9172 (t70) REVERT: A 95 MET cc_start: 0.9102 (tpp) cc_final: 0.8718 (tpt) REVERT: A 116 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8683 (tt0) REVERT: A 119 GLU cc_start: 0.9301 (mp0) cc_final: 0.8375 (tm-30) REVERT: A 164 ARG cc_start: 0.8279 (ptm-80) cc_final: 0.7410 (ptm-80) REVERT: A 172 LEU cc_start: 0.9314 (mp) cc_final: 0.9047 (mp) REVERT: A 195 LEU cc_start: 0.9654 (mt) cc_final: 0.9401 (mt) REVERT: A 204 SER cc_start: 0.9437 (m) cc_final: 0.9171 (m) REVERT: A 217 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8757 (tm-30) REVERT: A 227 MET cc_start: 0.9338 (mtm) cc_final: 0.9067 (mtm) REVERT: A 251 LEU cc_start: 0.9587 (tp) cc_final: 0.9255 (tp) REVERT: A 252 ASN cc_start: 0.9542 (t0) cc_final: 0.9069 (t0) REVERT: A 255 HIS cc_start: 0.8926 (t-90) cc_final: 0.8521 (t-90) REVERT: A 307 TYR cc_start: 0.9658 (t80) cc_final: 0.9219 (t80) REVERT: A 322 MET cc_start: 0.9047 (tpt) cc_final: 0.8813 (tpp) REVERT: A 337 ILE cc_start: 0.9449 (mp) cc_final: 0.9138 (mp) REVERT: A 348 MET cc_start: 0.9354 (ptp) cc_final: 0.9126 (ptp) REVERT: A 350 ARG cc_start: 0.8858 (mmm-85) cc_final: 0.8400 (mmm-85) REVERT: A 361 GLN cc_start: 0.9527 (tt0) cc_final: 0.9207 (tp40) REVERT: A 387 GLN cc_start: 0.9034 (mt0) cc_final: 0.8499 (mp10) REVERT: A 394 TYR cc_start: 0.9311 (m-80) cc_final: 0.8528 (m-80) REVERT: A 406 ASP cc_start: 0.8983 (m-30) cc_final: 0.8745 (m-30) REVERT: A 415 ASN cc_start: 0.9495 (t0) cc_final: 0.9000 (t0) REVERT: A 417 LEU cc_start: 0.9796 (tt) cc_final: 0.9589 (tt) REVERT: A 418 ASN cc_start: 0.9484 (m110) cc_final: 0.8829 (m-40) REVERT: A 421 GLU cc_start: 0.9358 (tm-30) cc_final: 0.9150 (tm-30) REVERT: A 425 ILE cc_start: 0.9526 (mp) cc_final: 0.9279 (mp) REVERT: A 459 LYS cc_start: 0.9350 (mttp) cc_final: 0.8942 (mtmm) REVERT: A 468 LEU cc_start: 0.9668 (tp) cc_final: 0.9444 (tp) REVERT: A 472 LEU cc_start: 0.9770 (mt) cc_final: 0.9532 (mt) REVERT: A 493 MET cc_start: 0.9221 (tmm) cc_final: 0.8925 (tmm) REVERT: A 494 MET cc_start: 0.9439 (mtp) cc_final: 0.9122 (mtp) REVERT: A 499 SER cc_start: 0.9943 (t) cc_final: 0.9675 (p) REVERT: A 515 ASP cc_start: 0.9368 (m-30) cc_final: 0.9085 (m-30) REVERT: A 522 TYR cc_start: 0.9348 (m-80) cc_final: 0.8838 (m-10) REVERT: A 558 TRP cc_start: 0.9284 (m100) cc_final: 0.8771 (m100) REVERT: A 570 MET cc_start: 0.9406 (mtp) cc_final: 0.7868 (mtp) REVERT: A 575 ARG cc_start: 0.9391 (mtm110) cc_final: 0.8393 (ptp90) REVERT: A 576 LEU cc_start: 0.9335 (mt) cc_final: 0.9094 (mt) REVERT: A 613 TYR cc_start: 0.8875 (t80) cc_final: 0.8157 (t80) REVERT: A 615 MET cc_start: 0.8939 (mmp) cc_final: 0.8098 (mmp) REVERT: A 650 GLN cc_start: 0.8712 (mt0) cc_final: 0.7502 (mt0) REVERT: B 51 LEU cc_start: 0.9497 (tp) cc_final: 0.9162 (tp) REVERT: B 95 MET cc_start: 0.9350 (tpp) cc_final: 0.8900 (tpp) REVERT: B 99 LYS cc_start: 0.9551 (mmmt) cc_final: 0.9096 (mmmt) REVERT: B 107 LYS cc_start: 0.9604 (mptt) cc_final: 0.9311 (mmtt) REVERT: B 115 LEU cc_start: 0.9587 (mt) cc_final: 0.9360 (mt) REVERT: B 136 LYS cc_start: 0.9657 (mmtp) cc_final: 0.9426 (mmmm) REVERT: B 139 GLU cc_start: 0.9513 (mp0) cc_final: 0.9303 (mp0) REVERT: B 147 GLN cc_start: 0.9028 (mt0) cc_final: 0.8766 (mt0) REVERT: B 157 LEU cc_start: 0.9543 (tp) cc_final: 0.9059 (tp) REVERT: B 158 ASN cc_start: 0.9547 (m-40) cc_final: 0.9283 (p0) REVERT: B 161 ARG cc_start: 0.9115 (ttm110) cc_final: 0.8447 (mtt180) REVERT: B 251 LEU cc_start: 0.9436 (tp) cc_final: 0.9127 (tp) REVERT: B 286 ASP cc_start: 0.8881 (m-30) cc_final: 0.8225 (m-30) REVERT: B 296 LYS cc_start: 0.8956 (mmpt) cc_final: 0.8597 (mtmm) REVERT: B 322 MET cc_start: 0.9098 (mmm) cc_final: 0.8318 (mmm) REVERT: B 345 LYS cc_start: 0.9629 (tttt) cc_final: 0.9322 (tttt) REVERT: B 350 ARG cc_start: 0.8832 (mtp85) cc_final: 0.8129 (mtp85) REVERT: B 362 ASP cc_start: 0.9199 (m-30) cc_final: 0.8201 (m-30) REVERT: B 373 ILE cc_start: 0.9648 (tp) cc_final: 0.9316 (tp) REVERT: B 407 ILE cc_start: 0.8882 (mt) cc_final: 0.8630 (mt) REVERT: B 413 SER cc_start: 0.9473 (m) cc_final: 0.9027 (t) REVERT: B 420 MET cc_start: 0.9058 (tpt) cc_final: 0.8795 (tpp) REVERT: B 494 MET cc_start: 0.9571 (mtt) cc_final: 0.8969 (mtt) REVERT: B 570 MET cc_start: 0.9432 (mtp) cc_final: 0.8863 (mtp) REVERT: B 606 TYR cc_start: 0.8523 (m-80) cc_final: 0.8101 (m-10) REVERT: B 615 MET cc_start: 0.8952 (mmp) cc_final: 0.8666 (mmp) REVERT: B 646 GLN cc_start: 0.9574 (pt0) cc_final: 0.9252 (pm20) REVERT: B 658 LEU cc_start: 0.9596 (mm) cc_final: 0.9263 (mm) REVERT: B 667 LEU cc_start: 0.9384 (tp) cc_final: 0.9076 (tp) REVERT: B 668 ASN cc_start: 0.9428 (m-40) cc_final: 0.8666 (m110) REVERT: B 677 ARG cc_start: 0.9656 (mmm160) cc_final: 0.9307 (mmm-85) REVERT: B 683 TYR cc_start: 0.9002 (t80) cc_final: 0.8704 (t80) REVERT: C 93 MET cc_start: 0.9411 (mtm) cc_final: 0.9179 (tpt) REVERT: C 100 VAL cc_start: 0.9117 (t) cc_final: 0.8842 (t) REVERT: C 101 HIS cc_start: 0.8458 (m90) cc_final: 0.8177 (m90) REVERT: C 130 TYR cc_start: 0.7304 (m-80) cc_final: 0.6995 (m-80) REVERT: C 155 LYS cc_start: 0.8966 (ttpp) cc_final: 0.8695 (ttpp) REVERT: C 261 ARG cc_start: 0.5572 (mtm110) cc_final: 0.5082 (ptp90) REVERT: D 25 ASN cc_start: 0.8251 (m-40) cc_final: 0.8001 (m-40) REVERT: D 69 GLN cc_start: 0.9340 (tp-100) cc_final: 0.9114 (tp40) REVERT: D 100 VAL cc_start: 0.4886 (t) cc_final: 0.4275 (p) REVERT: D 179 TYR cc_start: 0.6990 (t80) cc_final: 0.6779 (t80) REVERT: D 185 MET cc_start: 0.2448 (mmm) cc_final: 0.1893 (mpp) outliers start: 0 outliers final: 0 residues processed: 639 average time/residue: 0.2748 time to fit residues: 257.2669 Evaluate side-chains 558 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 558 time to evaluate : 1.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 67 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 175 optimal weight: 1.9990 chunk 182 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 338 ASN ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 447 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN ** B 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN C 24 GLN ** D 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 214 ASN D 234 GLN ** D 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.132330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.088389 restraints weight = 46411.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.091651 restraints weight = 27386.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.093790 restraints weight = 17954.720| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 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 = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.6504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16386 Z= 0.143 Angle : 0.597 8.609 22134 Z= 0.314 Chirality : 0.042 0.231 2360 Planarity : 0.004 0.067 2818 Dihedral : 11.134 176.942 2242 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.06 % Allowed : 1.40 % Favored : 98.54 % 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: 1.07 (0.19), residues: 1932 helix: 1.26 (0.15), residues: 1140 sheet: -0.56 (0.39), residues: 140 loop : 0.21 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP C 124 HIS 0.017 0.001 HIS C 201 PHE 0.019 0.002 PHE B 81 TYR 0.040 0.002 TYR A 683 ARG 0.004 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.03811 ( 871) hydrogen bonds : angle 4.91554 ( 2571) covalent geometry : bond 0.00309 (16386) covalent geometry : angle 0.59655 (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 654 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 653 time to evaluate : 1.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9520 (t0) cc_final: 0.9101 (t70) REVERT: A 88 LYS cc_start: 0.9416 (mptt) cc_final: 0.9212 (mmtt) REVERT: A 89 PHE cc_start: 0.9047 (t80) cc_final: 0.8768 (t80) REVERT: A 95 MET cc_start: 0.8860 (tpp) cc_final: 0.8459 (tpt) REVERT: A 116 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8479 (tt0) REVERT: A 139 GLU cc_start: 0.9235 (mt-10) cc_final: 0.8956 (pt0) REVERT: A 143 LEU cc_start: 0.9581 (tp) cc_final: 0.9228 (tp) REVERT: A 158 ASN cc_start: 0.9545 (m-40) cc_final: 0.9264 (m-40) REVERT: A 164 ARG cc_start: 0.8425 (ptm-80) cc_final: 0.7608 (ptm-80) REVERT: A 172 LEU cc_start: 0.9233 (mp) cc_final: 0.8952 (mp) REVERT: A 195 LEU cc_start: 0.9628 (mt) cc_final: 0.9411 (mt) REVERT: A 204 SER cc_start: 0.9421 (m) cc_final: 0.9145 (m) REVERT: A 227 MET cc_start: 0.9346 (mtm) cc_final: 0.9060 (mtm) REVERT: A 252 ASN cc_start: 0.9359 (t0) cc_final: 0.8828 (t0) REVERT: A 255 HIS cc_start: 0.8771 (t-90) cc_final: 0.8482 (t-90) REVERT: A 307 TYR cc_start: 0.9643 (t80) cc_final: 0.9158 (t80) REVERT: A 322 MET cc_start: 0.9133 (tpt) cc_final: 0.8880 (mmm) REVERT: A 348 MET cc_start: 0.9342 (ptp) cc_final: 0.9053 (ptp) REVERT: A 350 ARG cc_start: 0.8879 (mmm-85) cc_final: 0.8403 (mmm-85) REVERT: A 361 GLN cc_start: 0.9468 (tt0) cc_final: 0.9232 (tp40) REVERT: A 370 ASN cc_start: 0.9590 (m-40) cc_final: 0.9328 (m110) REVERT: A 387 GLN cc_start: 0.8977 (mt0) cc_final: 0.8543 (mp10) REVERT: A 394 TYR cc_start: 0.9299 (m-80) cc_final: 0.8525 (m-80) REVERT: A 406 ASP cc_start: 0.8987 (m-30) cc_final: 0.8738 (m-30) REVERT: A 407 ILE cc_start: 0.9106 (mt) cc_final: 0.8685 (mt) REVERT: A 421 GLU cc_start: 0.9289 (tm-30) cc_final: 0.9022 (tm-30) REVERT: A 459 LYS cc_start: 0.9232 (mttp) cc_final: 0.8272 (mtmm) REVERT: A 468 LEU cc_start: 0.9574 (tp) cc_final: 0.9300 (tp) REVERT: A 472 LEU cc_start: 0.9746 (mt) cc_final: 0.9504 (mt) REVERT: A 493 MET cc_start: 0.9200 (tmm) cc_final: 0.8861 (tmm) REVERT: A 494 MET cc_start: 0.9415 (mtp) cc_final: 0.9116 (mtp) REVERT: A 496 ASN cc_start: 0.9687 (t0) cc_final: 0.9150 (t0) REVERT: A 499 SER cc_start: 0.9942 (t) cc_final: 0.9724 (p) REVERT: A 500 ILE cc_start: 0.9742 (mt) cc_final: 0.9369 (mt) REVERT: A 515 ASP cc_start: 0.9298 (m-30) cc_final: 0.9026 (m-30) REVERT: A 522 TYR cc_start: 0.9360 (m-80) cc_final: 0.8729 (m-10) REVERT: A 570 MET cc_start: 0.9477 (mtp) cc_final: 0.7919 (mtp) REVERT: A 575 ARG cc_start: 0.9424 (mtm110) cc_final: 0.8964 (ptp90) REVERT: A 586 TYR cc_start: 0.9318 (m-10) cc_final: 0.8998 (m-10) REVERT: A 613 TYR cc_start: 0.8951 (t80) cc_final: 0.7541 (t80) REVERT: A 615 MET cc_start: 0.8825 (mmp) cc_final: 0.8097 (mmp) REVERT: A 639 ASP cc_start: 0.9285 (m-30) cc_final: 0.9017 (m-30) REVERT: A 650 GLN cc_start: 0.8684 (mt0) cc_final: 0.7531 (mt0) REVERT: B 15 GLU cc_start: 0.9118 (tp30) cc_final: 0.8894 (tp30) REVERT: B 17 MET cc_start: 0.8860 (mpp) cc_final: 0.8466 (mpp) REVERT: B 51 LEU cc_start: 0.9417 (tp) cc_final: 0.9157 (tp) REVERT: B 87 LYS cc_start: 0.9125 (tttt) cc_final: 0.8849 (ttpt) REVERT: B 95 MET cc_start: 0.9200 (tpp) cc_final: 0.8719 (tpp) REVERT: B 99 LYS cc_start: 0.9555 (mmmt) cc_final: 0.9079 (mmmt) REVERT: B 107 LYS cc_start: 0.9656 (mptt) cc_final: 0.9382 (mmtt) REVERT: B 115 LEU cc_start: 0.9611 (mt) cc_final: 0.9309 (mt) REVERT: B 119 GLU cc_start: 0.9243 (mp0) cc_final: 0.8931 (tm-30) REVERT: B 120 ASP cc_start: 0.9399 (m-30) cc_final: 0.8825 (m-30) REVERT: B 136 LYS cc_start: 0.9649 (mmtp) cc_final: 0.9363 (mmmm) REVERT: B 144 MET cc_start: 0.9130 (mtm) cc_final: 0.8906 (mtm) REVERT: B 145 ILE cc_start: 0.9707 (tp) cc_final: 0.9485 (tp) REVERT: B 147 GLN cc_start: 0.9227 (mt0) cc_final: 0.8531 (mt0) REVERT: B 158 ASN cc_start: 0.9572 (m-40) cc_final: 0.9353 (p0) REVERT: B 211 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7498 (mm-30) REVERT: B 227 MET cc_start: 0.9345 (mtm) cc_final: 0.9110 (mtm) REVERT: B 251 LEU cc_start: 0.9456 (tp) cc_final: 0.9193 (tp) REVERT: B 286 ASP cc_start: 0.8854 (m-30) cc_final: 0.8048 (m-30) REVERT: B 296 LYS cc_start: 0.8968 (mmpt) cc_final: 0.8644 (mtmm) REVERT: B 321 GLU cc_start: 0.8895 (tm-30) cc_final: 0.8515 (tm-30) REVERT: B 322 MET cc_start: 0.9091 (mmm) cc_final: 0.8124 (mmm) REVERT: B 345 LYS cc_start: 0.9680 (tttt) cc_final: 0.9434 (tttt) REVERT: B 350 ARG cc_start: 0.8775 (mtp85) cc_final: 0.8279 (mtp85) REVERT: B 355 TYR cc_start: 0.9328 (m-10) cc_final: 0.9075 (m-10) REVERT: B 362 ASP cc_start: 0.9266 (m-30) cc_final: 0.8324 (m-30) REVERT: B 375 LYS cc_start: 0.9168 (mmtm) cc_final: 0.8702 (mmtm) REVERT: B 393 SER cc_start: 0.9488 (t) cc_final: 0.8908 (t) REVERT: B 398 ASP cc_start: 0.9031 (t70) cc_final: 0.8615 (t70) REVERT: B 402 GLU cc_start: 0.8599 (mp0) cc_final: 0.8246 (mp0) REVERT: B 440 SER cc_start: 0.9703 (t) cc_final: 0.9427 (p) REVERT: B 494 MET cc_start: 0.9520 (mtt) cc_final: 0.8906 (mtt) REVERT: B 606 TYR cc_start: 0.8442 (m-80) cc_final: 0.8093 (m-10) REVERT: B 615 MET cc_start: 0.8992 (mmp) cc_final: 0.8621 (mmp) REVERT: B 636 LYS cc_start: 0.9688 (mptt) cc_final: 0.9443 (mmmt) REVERT: B 639 ASP cc_start: 0.9341 (m-30) cc_final: 0.9042 (m-30) REVERT: B 646 GLN cc_start: 0.9544 (pt0) cc_final: 0.9252 (pm20) REVERT: B 667 LEU cc_start: 0.9370 (tp) cc_final: 0.9070 (tt) REVERT: B 668 ASN cc_start: 0.9398 (m-40) cc_final: 0.9036 (m-40) REVERT: B 677 ARG cc_start: 0.9623 (mmm160) cc_final: 0.9350 (mmm-85) REVERT: B 679 ILE cc_start: 0.9704 (mm) cc_final: 0.9497 (mm) REVERT: C 203 VAL cc_start: 0.7980 (p) cc_final: 0.7751 (m) REVERT: C 261 ARG cc_start: 0.5236 (mtm110) cc_final: 0.4826 (ptp90) REVERT: D 22 TYR cc_start: 0.5339 (t80) cc_final: 0.4978 (t80) REVERT: D 69 GLN cc_start: 0.9327 (tp-100) cc_final: 0.8961 (tm-30) REVERT: D 100 VAL cc_start: 0.5230 (t) cc_final: 0.4866 (t) REVERT: D 201 HIS cc_start: 0.7596 (m90) cc_final: 0.7325 (m90) outliers start: 1 outliers final: 0 residues processed: 653 average time/residue: 0.2889 time to fit residues: 277.7870 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 : 1.887 ------------------------------------------------------------------------------- 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: 7.9990 chunk 126 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 156 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 115 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 169 optimal weight: 5.9990 chunk 113 optimal weight: 10.0000 chunk 177 optimal weight: 0.4980 overall best weight: 4.6988 ------------------------------------------------------------------------------- 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 180 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 608 ASN B 62 GLN ** 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** ** D 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN D 234 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.126020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.083733 restraints weight = 48689.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.086709 restraints weight = 28648.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.088730 restraints weight = 18814.820| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3064 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3064 r_free = 0.3064 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3064 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.7062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 16386 Z= 0.303 Angle : 0.728 10.662 22134 Z= 0.385 Chirality : 0.044 0.188 2360 Planarity : 0.004 0.058 2818 Dihedral : 11.409 169.200 2242 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 20.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.18), residues: 1932 helix: 0.86 (0.15), residues: 1141 sheet: -0.63 (0.40), residues: 140 loop : 0.08 (0.24), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP C 44 HIS 0.012 0.002 HIS C 201 PHE 0.026 0.002 PHE A 378 TYR 0.039 0.002 TYR C 142 ARG 0.008 0.001 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.04209 ( 871) hydrogen bonds : angle 5.30912 ( 2571) covalent geometry : bond 0.00615 (16386) covalent geometry : angle 0.72763 (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 619 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 619 time to evaluate : 1.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 ASP cc_start: 0.9516 (t0) cc_final: 0.9216 (t70) REVERT: A 95 MET cc_start: 0.9030 (tpp) cc_final: 0.8475 (tpt) REVERT: A 116 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8624 (tt0) REVERT: A 124 ILE cc_start: 0.9801 (mm) cc_final: 0.9590 (mm) REVERT: A 143 LEU cc_start: 0.9569 (tp) cc_final: 0.9227 (tp) REVERT: A 172 LEU cc_start: 0.9296 (mp) cc_final: 0.8947 (mp) REVERT: A 195 LEU cc_start: 0.9691 (mt) cc_final: 0.9476 (mt) REVERT: A 204 SER cc_start: 0.9398 (m) cc_final: 0.8959 (p) REVERT: A 206 LEU cc_start: 0.9223 (mt) cc_final: 0.9019 (mt) REVERT: A 251 LEU cc_start: 0.9606 (tp) cc_final: 0.9309 (tp) REVERT: A 252 ASN cc_start: 0.9447 (t0) cc_final: 0.8864 (t0) REVERT: A 255 HIS cc_start: 0.8839 (t-90) cc_final: 0.8354 (t-90) REVERT: A 350 ARG cc_start: 0.8929 (mmm-85) cc_final: 0.8461 (mmm-85) REVERT: A 361 GLN cc_start: 0.9504 (tt0) cc_final: 0.9173 (tp40) REVERT: A 370 ASN cc_start: 0.9678 (m-40) cc_final: 0.9478 (m-40) REVERT: A 377 LYS cc_start: 0.9054 (mttt) cc_final: 0.8845 (UNCLASSIFIED) REVERT: A 394 TYR cc_start: 0.9191 (m-80) cc_final: 0.8355 (m-80) REVERT: A 406 ASP cc_start: 0.9006 (m-30) cc_final: 0.8652 (m-30) REVERT: A 418 ASN cc_start: 0.9633 (m-40) cc_final: 0.9073 (m-40) REVERT: A 421 GLU cc_start: 0.9306 (tm-30) cc_final: 0.9033 (tm-30) REVERT: A 468 LEU cc_start: 0.9676 (tp) cc_final: 0.9390 (tp) REVERT: A 472 LEU cc_start: 0.9769 (mt) cc_final: 0.9521 (mt) REVERT: A 493 MET cc_start: 0.9202 (tmm) cc_final: 0.8918 (tmm) REVERT: A 494 MET cc_start: 0.9438 (mtp) cc_final: 0.9034 (mtp) REVERT: A 499 SER cc_start: 0.9935 (t) cc_final: 0.9704 (p) REVERT: A 508 LYS cc_start: 0.9741 (tttt) cc_final: 0.9490 (tttp) REVERT: A 515 ASP cc_start: 0.9359 (m-30) cc_final: 0.9104 (m-30) REVERT: A 522 TYR cc_start: 0.9379 (m-80) cc_final: 0.8826 (m-10) REVERT: A 570 MET cc_start: 0.9328 (mtp) cc_final: 0.7697 (mtp) REVERT: A 575 ARG cc_start: 0.9491 (mtm110) cc_final: 0.8903 (ptp90) REVERT: A 602 GLU cc_start: 0.8801 (pm20) cc_final: 0.8160 (pm20) REVERT: A 615 MET cc_start: 0.9080 (mmp) cc_final: 0.8282 (mmp) REVERT: A 639 ASP cc_start: 0.9299 (m-30) cc_final: 0.9069 (m-30) REVERT: A 650 GLN cc_start: 0.8770 (mt0) cc_final: 0.8097 (mt0) REVERT: B 15 GLU cc_start: 0.9127 (tp30) cc_final: 0.8860 (tp30) REVERT: B 29 ASP cc_start: 0.9384 (t70) cc_final: 0.9020 (t0) REVERT: B 51 LEU cc_start: 0.9479 (tp) cc_final: 0.9201 (tp) REVERT: B 99 LYS cc_start: 0.9568 (mmmt) cc_final: 0.9308 (mmmm) REVERT: B 115 LEU cc_start: 0.9564 (mt) cc_final: 0.9334 (mt) REVERT: B 128 PHE cc_start: 0.9732 (t80) cc_final: 0.9517 (t80) REVERT: B 136 LYS cc_start: 0.9677 (mmtp) cc_final: 0.9360 (mmmm) REVERT: B 157 LEU cc_start: 0.9541 (tp) cc_final: 0.9267 (tp) REVERT: B 158 ASN cc_start: 0.9637 (m-40) cc_final: 0.9218 (p0) REVERT: B 161 ARG cc_start: 0.9160 (ttm110) cc_final: 0.8422 (mtp85) REVERT: B 211 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7587 (mm-30) REVERT: B 220 THR cc_start: 0.9147 (p) cc_final: 0.8892 (p) REVERT: B 227 MET cc_start: 0.9363 (mtm) cc_final: 0.9041 (mtm) REVERT: B 236 TYR cc_start: 0.9030 (t80) cc_final: 0.8619 (t80) REVERT: B 251 LEU cc_start: 0.9497 (tp) cc_final: 0.9208 (tp) REVERT: B 283 VAL cc_start: 0.9271 (t) cc_final: 0.9006 (t) REVERT: B 286 ASP cc_start: 0.8902 (m-30) cc_final: 0.8046 (m-30) REVERT: B 296 LYS cc_start: 0.9103 (mmpt) cc_final: 0.8781 (mtmm) REVERT: B 321 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8361 (tm-30) REVERT: B 322 MET cc_start: 0.9093 (mmm) cc_final: 0.8182 (mmm) REVERT: B 333 LYS cc_start: 0.9496 (ttmm) cc_final: 0.9152 (ttmm) REVERT: B 342 LEU cc_start: 0.9799 (tp) cc_final: 0.9516 (tp) REVERT: B 346 LEU cc_start: 0.9732 (mt) cc_final: 0.9522 (mt) REVERT: B 350 ARG cc_start: 0.8860 (mtp85) cc_final: 0.8142 (mtp85) REVERT: B 359 MET cc_start: 0.9217 (ttm) cc_final: 0.8889 (ttm) REVERT: B 362 ASP cc_start: 0.9178 (m-30) cc_final: 0.8037 (m-30) REVERT: B 398 ASP cc_start: 0.8986 (t70) cc_final: 0.8773 (t70) REVERT: B 407 ILE cc_start: 0.8940 (mt) cc_final: 0.8687 (mt) REVERT: B 413 SER cc_start: 0.9422 (m) cc_final: 0.9079 (t) REVERT: B 414 LEU cc_start: 0.9780 (mt) cc_final: 0.9529 (mt) REVERT: B 437 THR cc_start: 0.9763 (m) cc_final: 0.9553 (m) REVERT: B 494 MET cc_start: 0.9526 (mtt) cc_final: 0.8858 (mtt) REVERT: B 615 MET cc_start: 0.9072 (mmp) cc_final: 0.8644 (mmp) REVERT: B 636 LYS cc_start: 0.9708 (mptt) cc_final: 0.9455 (mmmt) REVERT: B 639 ASP cc_start: 0.9380 (m-30) cc_final: 0.9039 (m-30) REVERT: B 646 GLN cc_start: 0.9564 (pt0) cc_final: 0.9257 (pm20) REVERT: B 667 LEU cc_start: 0.9470 (tp) cc_final: 0.9232 (tt) REVERT: B 668 ASN cc_start: 0.9529 (m-40) cc_final: 0.9043 (m-40) REVERT: B 677 ARG cc_start: 0.9619 (mmm160) cc_final: 0.9319 (mmm-85) REVERT: B 683 TYR cc_start: 0.8672 (t80) cc_final: 0.8417 (t80) REVERT: C 98 ASN cc_start: 0.7502 (p0) cc_final: 0.7242 (p0) REVERT: C 100 VAL cc_start: 0.8642 (t) cc_final: 0.8439 (t) REVERT: C 261 ARG cc_start: 0.5394 (mtm110) cc_final: 0.5026 (ptp90) REVERT: D 22 TYR cc_start: 0.5658 (t80) cc_final: 0.5281 (t80) REVERT: D 25 ASN cc_start: 0.8153 (m-40) cc_final: 0.7919 (m-40) REVERT: D 69 GLN cc_start: 0.9463 (tp-100) cc_final: 0.9042 (tm-30) REVERT: D 91 ASN cc_start: 0.8412 (m110) cc_final: 0.8168 (m110) REVERT: D 100 VAL cc_start: 0.5374 (t) cc_final: 0.5000 (t) outliers start: 0 outliers final: 0 residues processed: 619 average time/residue: 0.2834 time to fit residues: 259.2832 Evaluate side-chains 530 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 530 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 39 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 161 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 175 optimal weight: 0.4980 chunk 24 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 14 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 447 ASN C 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 = 0.3782 r_free = 0.3782 target = 0.132671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.088473 restraints weight = 45777.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.091638 restraints weight = 27081.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.093783 restraints weight = 18104.329| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 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 = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.7240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16386 Z= 0.131 Angle : 0.620 12.274 22134 Z= 0.326 Chirality : 0.043 0.188 2360 Planarity : 0.003 0.050 2818 Dihedral : 10.993 171.914 2242 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: 0.84 (0.19), residues: 1932 helix: 1.08 (0.15), residues: 1141 sheet: -0.30 (0.42), residues: 128 loop : 0.00 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 124 HIS 0.012 0.001 HIS C 201 PHE 0.022 0.002 PHE A 378 TYR 0.023 0.002 TYR A 612 ARG 0.007 0.001 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.03833 ( 871) hydrogen bonds : angle 4.96153 ( 2571) covalent geometry : bond 0.00281 (16386) covalent geometry : angle 0.62006 (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 650 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 650 time to evaluate : 1.905 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 17 MET cc_start: 0.9087 (mpp) cc_final: 0.8708 (mpp) REVERT: A 29 ASP cc_start: 0.9451 (t0) cc_final: 0.9139 (t70) REVERT: A 95 MET cc_start: 0.8950 (tpp) cc_final: 0.8389 (tpt) REVERT: A 116 GLU cc_start: 0.8707 (mt-10) cc_final: 0.8307 (tt0) REVERT: A 124 ILE cc_start: 0.9741 (mm) cc_final: 0.9515 (mm) REVERT: A 139 GLU cc_start: 0.9252 (mt-10) cc_final: 0.9015 (pt0) REVERT: A 172 LEU cc_start: 0.9283 (mp) cc_final: 0.9004 (mp) REVERT: A 180 ASN cc_start: 0.9136 (m110) cc_final: 0.8821 (t0) REVERT: A 188 ILE cc_start: 0.9603 (mt) cc_final: 0.9388 (mt) REVERT: A 195 LEU cc_start: 0.9643 (mt) cc_final: 0.9439 (mt) REVERT: A 204 SER cc_start: 0.9364 (m) cc_final: 0.8839 (p) REVERT: A 206 LEU cc_start: 0.9130 (mt) cc_final: 0.8869 (mt) REVERT: A 252 ASN cc_start: 0.9393 (t0) cc_final: 0.8780 (t0) REVERT: A 255 HIS cc_start: 0.8770 (t-90) cc_final: 0.8406 (t-90) REVERT: A 307 TYR cc_start: 0.9645 (t80) cc_final: 0.9148 (t80) REVERT: A 322 MET cc_start: 0.8945 (tpp) cc_final: 0.8660 (mmm) REVERT: A 350 ARG cc_start: 0.8958 (mmm-85) cc_final: 0.8460 (mmm-85) REVERT: A 359 MET cc_start: 0.9338 (ptt) cc_final: 0.8583 (ppp) REVERT: A 361 GLN cc_start: 0.9405 (tt0) cc_final: 0.9117 (tp40) REVERT: A 370 ASN cc_start: 0.9547 (m-40) cc_final: 0.9223 (m110) REVERT: A 387 GLN cc_start: 0.9016 (mt0) cc_final: 0.8653 (mp10) REVERT: A 394 TYR cc_start: 0.9243 (m-80) cc_final: 0.8376 (m-80) REVERT: A 406 ASP cc_start: 0.9070 (m-30) cc_final: 0.8797 (m-30) REVERT: A 407 ILE cc_start: 0.9122 (mt) cc_final: 0.8690 (mt) REVERT: A 418 ASN cc_start: 0.9658 (m-40) cc_final: 0.9076 (m-40) REVERT: A 421 GLU cc_start: 0.9298 (tm-30) cc_final: 0.9006 (tm-30) REVERT: A 468 LEU cc_start: 0.9623 (tp) cc_final: 0.9355 (tp) REVERT: A 472 LEU cc_start: 0.9737 (mt) cc_final: 0.9523 (mt) REVERT: A 493 MET cc_start: 0.9183 (tmm) cc_final: 0.8829 (tmm) REVERT: A 494 MET cc_start: 0.9385 (mtp) cc_final: 0.9061 (mtp) REVERT: A 496 ASN cc_start: 0.9615 (t0) cc_final: 0.9061 (t0) REVERT: A 499 SER cc_start: 0.9928 (t) cc_final: 0.9717 (p) REVERT: A 500 ILE cc_start: 0.9727 (mt) cc_final: 0.9281 (mt) REVERT: A 508 LYS cc_start: 0.9735 (tttt) cc_final: 0.9511 (tttp) REVERT: A 515 ASP cc_start: 0.9255 (m-30) cc_final: 0.8978 (m-30) REVERT: A 522 TYR cc_start: 0.9351 (m-80) cc_final: 0.8788 (m-10) REVERT: A 570 MET cc_start: 0.9471 (mtp) cc_final: 0.7912 (ttm) REVERT: A 575 ARG cc_start: 0.9421 (mtm110) cc_final: 0.8418 (ptp90) REVERT: A 602 GLU cc_start: 0.8756 (pm20) cc_final: 0.7543 (pm20) REVERT: A 612 TYR cc_start: 0.8519 (m-80) cc_final: 0.8249 (m-10) REVERT: A 615 MET cc_start: 0.9055 (mmp) cc_final: 0.8503 (mmp) REVERT: A 632 MET cc_start: 0.9115 (mtm) cc_final: 0.8593 (mtm) REVERT: A 639 ASP cc_start: 0.9266 (m-30) cc_final: 0.8850 (m-30) REVERT: A 640 MET cc_start: 0.9334 (ttm) cc_final: 0.9045 (ttm) REVERT: A 650 GLN cc_start: 0.8597 (mt0) cc_final: 0.7958 (mt0) REVERT: A 668 ASN cc_start: 0.9676 (m110) cc_final: 0.9438 (m-40) REVERT: B 15 GLU cc_start: 0.9142 (tp30) cc_final: 0.8861 (tp30) REVERT: B 17 MET cc_start: 0.8868 (mpp) cc_final: 0.8561 (mpp) REVERT: B 29 ASP cc_start: 0.9378 (t70) cc_final: 0.9167 (t70) REVERT: B 51 LEU cc_start: 0.9489 (tp) cc_final: 0.9228 (tp) REVERT: B 99 LYS cc_start: 0.9605 (mmmt) cc_final: 0.8991 (mmmt) REVERT: B 115 LEU cc_start: 0.9566 (mt) cc_final: 0.9356 (mt) REVERT: B 128 PHE cc_start: 0.9729 (t80) cc_final: 0.9528 (t80) REVERT: B 136 LYS cc_start: 0.9679 (mmtp) cc_final: 0.9334 (mmmm) REVERT: B 144 MET cc_start: 0.9107 (mtm) cc_final: 0.8656 (mtm) REVERT: B 157 LEU cc_start: 0.9614 (tp) cc_final: 0.9327 (tp) REVERT: B 158 ASN cc_start: 0.9613 (m-40) cc_final: 0.9192 (p0) REVERT: B 161 ARG cc_start: 0.8992 (ttm110) cc_final: 0.8211 (mtp85) REVERT: B 200 SER cc_start: 0.9179 (t) cc_final: 0.8943 (t) REVERT: B 211 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7628 (mm-30) REVERT: B 217 GLU cc_start: 0.9272 (pp20) cc_final: 0.9052 (pp20) REVERT: B 227 MET cc_start: 0.9383 (mtm) cc_final: 0.9126 (mtm) REVERT: B 251 LEU cc_start: 0.9456 (tp) cc_final: 0.9135 (tp) REVERT: B 283 VAL cc_start: 0.9182 (t) cc_final: 0.8747 (t) REVERT: B 286 ASP cc_start: 0.8715 (m-30) cc_final: 0.7886 (m-30) REVERT: B 296 LYS cc_start: 0.8937 (mmpt) cc_final: 0.8632 (mtmm) REVERT: B 321 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8417 (tm-30) REVERT: B 322 MET cc_start: 0.9110 (mmm) cc_final: 0.7976 (mmm) REVERT: B 333 LYS cc_start: 0.9526 (ttmm) cc_final: 0.9197 (ttmm) REVERT: B 350 ARG cc_start: 0.8707 (mtp85) cc_final: 0.7962 (mtp85) REVERT: B 362 ASP cc_start: 0.9172 (m-30) cc_final: 0.8149 (m-30) REVERT: B 393 SER cc_start: 0.9436 (t) cc_final: 0.8727 (t) REVERT: B 396 ASP cc_start: 0.8767 (m-30) cc_final: 0.8477 (m-30) REVERT: B 402 GLU cc_start: 0.8580 (mp0) cc_final: 0.8188 (mp0) REVERT: B 413 SER cc_start: 0.9499 (m) cc_final: 0.9169 (t) REVERT: B 414 LEU cc_start: 0.9812 (mt) cc_final: 0.9609 (mt) REVERT: B 421 GLU cc_start: 0.9416 (tm-30) cc_final: 0.9145 (tm-30) REVERT: B 458 MET cc_start: 0.9255 (mmp) cc_final: 0.8940 (mmp) REVERT: B 459 LYS cc_start: 0.9226 (mppt) cc_final: 0.8467 (mptt) REVERT: B 494 MET cc_start: 0.9470 (mtt) cc_final: 0.8837 (mtt) REVERT: B 500 ILE cc_start: 0.9795 (mt) cc_final: 0.9585 (mt) REVERT: B 501 GLN cc_start: 0.9547 (mt0) cc_final: 0.8969 (mt0) REVERT: B 570 MET cc_start: 0.9292 (mtp) cc_final: 0.9044 (mtp) REVERT: B 603 GLU cc_start: 0.8062 (tm-30) cc_final: 0.7755 (tm-30) REVERT: B 615 MET cc_start: 0.9162 (mmp) cc_final: 0.8746 (mmp) REVERT: B 632 MET cc_start: 0.8382 (mmp) cc_final: 0.7946 (mmp) REVERT: B 636 LYS cc_start: 0.9698 (mptt) cc_final: 0.9420 (mmmt) REVERT: B 639 ASP cc_start: 0.9337 (m-30) cc_final: 0.8982 (m-30) REVERT: B 667 LEU cc_start: 0.9445 (tp) cc_final: 0.9174 (tt) REVERT: B 668 ASN cc_start: 0.9381 (m-40) cc_final: 0.8947 (m-40) REVERT: B 671 ASP cc_start: 0.9298 (m-30) cc_final: 0.9097 (m-30) REVERT: B 677 ARG cc_start: 0.9586 (mmm160) cc_final: 0.9321 (mmm-85) REVERT: B 679 ILE cc_start: 0.9726 (mm) cc_final: 0.9507 (mm) REVERT: C 45 LYS cc_start: 0.8646 (mptt) cc_final: 0.8305 (pttp) REVERT: C 100 VAL cc_start: 0.8774 (t) cc_final: 0.8445 (p) REVERT: C 101 HIS cc_start: 0.8393 (m90) cc_final: 0.8043 (m90) REVERT: C 261 ARG cc_start: 0.5036 (mtm110) cc_final: 0.4722 (ptp90) REVERT: D 69 GLN cc_start: 0.9417 (tp-100) cc_final: 0.9028 (tm-30) REVERT: D 100 VAL cc_start: 0.5194 (t) cc_final: 0.4808 (t) outliers start: 0 outliers final: 0 residues processed: 650 average time/residue: 0.2765 time to fit residues: 263.9391 Evaluate side-chains 559 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 559 time to evaluate : 1.675 ------------------------------------------------------------------------------- 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: 0.6980 chunk 30 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 159 optimal weight: 20.0000 chunk 72 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 29 optimal weight: 0.2980 chunk 183 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 180 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN A 180 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 ASN B 372 HIS ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 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 = 0.3792 r_free = 0.3792 target = 0.133506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.089938 restraints weight = 45489.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.092906 restraints weight = 26722.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.095020 restraints weight = 17969.496| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.7482 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= 0.134 Angle : 0.631 7.999 22134 Z= 0.333 Chirality : 0.043 0.184 2360 Planarity : 0.004 0.055 2818 Dihedral : 10.898 174.444 2242 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.19), residues: 1932 helix: 1.09 (0.15), residues: 1140 sheet: -0.30 (0.43), residues: 128 loop : -0.00 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 124 HIS 0.009 0.001 HIS C 201 PHE 0.026 0.002 PHE C 320 TYR 0.037 0.002 TYR C 142 ARG 0.009 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.03804 ( 871) hydrogen bonds : angle 5.01481 ( 2571) covalent geometry : bond 0.00290 (16386) covalent geometry : angle 0.63128 (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 627 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 627 time to evaluate : 1.814 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 17 MET cc_start: 0.9050 (mpp) cc_final: 0.8620 (mpp) REVERT: A 29 ASP cc_start: 0.9471 (t0) cc_final: 0.9162 (t70) REVERT: A 95 MET cc_start: 0.9007 (tpp) cc_final: 0.8457 (tpt) REVERT: A 116 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8281 (tt0) REVERT: A 124 ILE cc_start: 0.9811 (mm) cc_final: 0.9544 (mm) REVERT: A 147 GLN cc_start: 0.9248 (mm110) cc_final: 0.8833 (mm-40) REVERT: A 172 LEU cc_start: 0.9337 (mp) cc_final: 0.9031 (mp) REVERT: A 180 ASN cc_start: 0.9356 (m-40) cc_final: 0.9131 (m-40) REVERT: A 204 SER cc_start: 0.9385 (m) cc_final: 0.8852 (p) REVERT: A 206 LEU cc_start: 0.9109 (mt) cc_final: 0.8867 (mt) REVERT: A 235 ARG cc_start: 0.8848 (mtm110) cc_final: 0.8478 (mtm180) REVERT: A 251 LEU cc_start: 0.9583 (tp) cc_final: 0.9324 (tp) REVERT: A 252 ASN cc_start: 0.9412 (t0) cc_final: 0.8817 (t0) REVERT: A 255 HIS cc_start: 0.8764 (t-90) cc_final: 0.8441 (t-90) REVERT: A 301 PHE cc_start: 0.9261 (m-10) cc_final: 0.8783 (m-10) REVERT: A 307 TYR cc_start: 0.9662 (t80) cc_final: 0.9201 (t80) REVERT: A 322 MET cc_start: 0.8929 (tpp) cc_final: 0.8570 (mmm) REVERT: A 350 ARG cc_start: 0.8953 (mmm-85) cc_final: 0.8407 (mmm-85) REVERT: A 359 MET cc_start: 0.9353 (ptt) cc_final: 0.8635 (ppp) REVERT: A 361 GLN cc_start: 0.9434 (tt0) cc_final: 0.9130 (tp40) REVERT: A 370 ASN cc_start: 0.9541 (m-40) cc_final: 0.9192 (m110) REVERT: A 394 TYR cc_start: 0.9327 (m-80) cc_final: 0.8450 (m-80) REVERT: A 406 ASP cc_start: 0.9143 (m-30) cc_final: 0.8853 (m-30) REVERT: A 407 ILE cc_start: 0.9218 (mt) cc_final: 0.8744 (mt) REVERT: A 418 ASN cc_start: 0.9683 (m-40) cc_final: 0.9114 (m-40) REVERT: A 421 GLU cc_start: 0.9193 (tm-30) cc_final: 0.8915 (tm-30) REVERT: A 468 LEU cc_start: 0.9626 (tp) cc_final: 0.9407 (tp) REVERT: A 493 MET cc_start: 0.9176 (tmm) cc_final: 0.8826 (tmm) REVERT: A 496 ASN cc_start: 0.9629 (t0) cc_final: 0.9068 (t0) REVERT: A 499 SER cc_start: 0.9932 (t) cc_final: 0.9723 (p) REVERT: A 500 ILE cc_start: 0.9731 (mt) cc_final: 0.9374 (mt) REVERT: A 515 ASP cc_start: 0.9275 (m-30) cc_final: 0.9009 (m-30) REVERT: A 516 GLN cc_start: 0.9190 (tt0) cc_final: 0.8812 (tt0) REVERT: A 522 TYR cc_start: 0.9339 (m-80) cc_final: 0.8710 (m-10) REVERT: A 570 MET cc_start: 0.9473 (mtp) cc_final: 0.7965 (mtp) REVERT: A 575 ARG cc_start: 0.9443 (mtm110) cc_final: 0.9050 (ptp90) REVERT: A 601 ILE cc_start: 0.9482 (tt) cc_final: 0.8990 (tt) REVERT: A 602 GLU cc_start: 0.8853 (pm20) cc_final: 0.7719 (pm20) REVERT: A 603 GLU cc_start: 0.8636 (tp30) cc_final: 0.8380 (tp30) REVERT: A 612 TYR cc_start: 0.8451 (m-80) cc_final: 0.8090 (m-10) REVERT: A 615 MET cc_start: 0.9062 (mmp) cc_final: 0.8528 (mmp) REVERT: A 636 LYS cc_start: 0.9748 (mmtp) cc_final: 0.9316 (mmmm) REVERT: A 639 ASP cc_start: 0.9256 (m-30) cc_final: 0.8837 (m-30) REVERT: A 640 MET cc_start: 0.9266 (ttm) cc_final: 0.8967 (ttm) REVERT: A 650 GLN cc_start: 0.8715 (mt0) cc_final: 0.8512 (mt0) REVERT: A 668 ASN cc_start: 0.9609 (m110) cc_final: 0.9399 (m-40) REVERT: B 15 GLU cc_start: 0.9124 (tp30) cc_final: 0.8804 (tp30) REVERT: B 99 LYS cc_start: 0.9585 (mmmt) cc_final: 0.9226 (mmmt) REVERT: B 136 LYS cc_start: 0.9667 (mmtp) cc_final: 0.9300 (mmmm) REVERT: B 144 MET cc_start: 0.9139 (mtm) cc_final: 0.8739 (mtm) REVERT: B 157 LEU cc_start: 0.9599 (tp) cc_final: 0.9369 (tp) REVERT: B 161 ARG cc_start: 0.8950 (ttm110) cc_final: 0.7929 (mtp85) REVERT: B 191 GLN cc_start: 0.9141 (mm-40) cc_final: 0.8729 (mm-40) REVERT: B 211 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7639 (mm-30) REVERT: B 227 MET cc_start: 0.9299 (mtm) cc_final: 0.9095 (mtm) REVERT: B 251 LEU cc_start: 0.9425 (tp) cc_final: 0.9164 (tp) REVERT: B 258 ILE cc_start: 0.9552 (tp) cc_final: 0.9352 (tp) REVERT: B 286 ASP cc_start: 0.8682 (m-30) cc_final: 0.7934 (m-30) REVERT: B 290 GLU cc_start: 0.9193 (pp20) cc_final: 0.8423 (pp20) REVERT: B 291 LEU cc_start: 0.9602 (mt) cc_final: 0.9357 (mt) REVERT: B 294 GLU cc_start: 0.9525 (mp0) cc_final: 0.9061 (mp0) REVERT: B 296 LYS cc_start: 0.8908 (mmpt) cc_final: 0.8608 (mtmm) REVERT: B 321 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8162 (tm-30) REVERT: B 322 MET cc_start: 0.9114 (mmm) cc_final: 0.8632 (mmm) REVERT: B 333 LYS cc_start: 0.9532 (ttmm) cc_final: 0.9195 (ttmm) REVERT: B 350 ARG cc_start: 0.8713 (mtp85) cc_final: 0.7974 (mtp85) REVERT: B 362 ASP cc_start: 0.9132 (m-30) cc_final: 0.8066 (m-30) REVERT: B 393 SER cc_start: 0.9491 (t) cc_final: 0.8955 (t) REVERT: B 396 ASP cc_start: 0.8621 (m-30) cc_final: 0.8333 (m-30) REVERT: B 402 GLU cc_start: 0.8603 (mp0) cc_final: 0.8248 (mp0) REVERT: B 413 SER cc_start: 0.9567 (m) cc_final: 0.9212 (t) REVERT: B 414 LEU cc_start: 0.9801 (mt) cc_final: 0.9594 (mt) REVERT: B 421 GLU cc_start: 0.9366 (tm-30) cc_final: 0.9074 (tm-30) REVERT: B 440 SER cc_start: 0.9696 (t) cc_final: 0.9421 (p) REVERT: B 494 MET cc_start: 0.9465 (mtt) cc_final: 0.8786 (mtt) REVERT: B 615 MET cc_start: 0.9124 (mmp) cc_final: 0.8713 (mmp) REVERT: B 636 LYS cc_start: 0.9697 (mptt) cc_final: 0.9332 (mmmt) REVERT: B 639 ASP cc_start: 0.9287 (m-30) cc_final: 0.8876 (m-30) REVERT: B 667 LEU cc_start: 0.9453 (tp) cc_final: 0.9171 (tt) REVERT: B 668 ASN cc_start: 0.9341 (m-40) cc_final: 0.8895 (m-40) REVERT: B 677 ARG cc_start: 0.9575 (mmm160) cc_final: 0.9295 (mmm-85) REVERT: B 679 ILE cc_start: 0.9753 (mm) cc_final: 0.9542 (mm) REVERT: C 45 LYS cc_start: 0.8664 (mptt) cc_final: 0.8315 (pttp) REVERT: C 98 ASN cc_start: 0.6690 (p0) cc_final: 0.6418 (p0) REVERT: C 100 VAL cc_start: 0.8616 (t) cc_final: 0.8394 (p) REVERT: C 101 HIS cc_start: 0.8422 (m90) cc_final: 0.7822 (m90) REVERT: C 261 ARG cc_start: 0.4911 (mtm110) cc_final: 0.4529 (ptp-170) REVERT: D 25 ASN cc_start: 0.8145 (m-40) cc_final: 0.7941 (m-40) REVERT: D 69 GLN cc_start: 0.9407 (tp-100) cc_final: 0.9021 (tm-30) REVERT: D 91 ASN cc_start: 0.8034 (m110) cc_final: 0.7557 (m110) outliers start: 0 outliers final: 0 residues processed: 627 average time/residue: 0.2700 time to fit residues: 251.6100 Evaluate side-chains 558 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 558 time to evaluate : 1.755 ------------------------------------------------------------------------------- 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: 7.9990 chunk 102 optimal weight: 0.9980 chunk 182 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 188 optimal weight: 6.9990 chunk 27 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 516 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 668 ASN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 210 GLN D 233 ASN D 234 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.132424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.089350 restraints weight = 47902.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.092360 restraints weight = 28114.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.094385 restraints weight = 18755.456| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3125 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3125 r_free = 0.3125 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3125 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.7740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16386 Z= 0.214 Angle : 0.684 8.083 22134 Z= 0.363 Chirality : 0.045 0.232 2360 Planarity : 0.004 0.049 2818 Dihedral : 11.022 169.015 2242 Min Nonbonded Distance : 1.811 Molprobity Statistics. All-atom Clashscore : 18.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.19), residues: 1932 helix: 0.98 (0.15), residues: 1140 sheet: -0.63 (0.41), residues: 140 loop : 0.01 (0.24), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 44 HIS 0.014 0.002 HIS D 201 PHE 0.022 0.002 PHE C 320 TYR 0.038 0.002 TYR C 142 ARG 0.008 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.04126 ( 871) hydrogen bonds : angle 5.22745 ( 2571) covalent geometry : bond 0.00446 (16386) covalent geometry : angle 0.68418 (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 620 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 620 time to evaluate : 1.717 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 17 MET cc_start: 0.9063 (mpp) cc_final: 0.8672 (mpp) REVERT: A 29 ASP cc_start: 0.9514 (t0) cc_final: 0.9015 (t0) REVERT: A 91 PHE cc_start: 0.9583 (m-80) cc_final: 0.9042 (m-80) REVERT: A 95 MET cc_start: 0.9058 (tpp) cc_final: 0.8570 (tpt) REVERT: A 116 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8429 (tt0) REVERT: A 143 LEU cc_start: 0.9579 (tp) cc_final: 0.9369 (tp) REVERT: A 147 GLN cc_start: 0.9263 (mm110) cc_final: 0.8963 (mm-40) REVERT: A 190 MET cc_start: 0.9570 (mmm) cc_final: 0.9280 (mmm) REVERT: A 203 LEU cc_start: 0.9728 (mt) cc_final: 0.9527 (mt) REVERT: A 204 SER cc_start: 0.9390 (m) cc_final: 0.8987 (p) REVERT: A 206 LEU cc_start: 0.9199 (mt) cc_final: 0.8990 (mt) REVERT: A 251 LEU cc_start: 0.9537 (tp) cc_final: 0.9337 (tp) REVERT: A 252 ASN cc_start: 0.9438 (t0) cc_final: 0.8892 (t0) REVERT: A 255 HIS cc_start: 0.8823 (t-90) cc_final: 0.8477 (t-90) REVERT: A 307 TYR cc_start: 0.9640 (t80) cc_final: 0.9098 (t80) REVERT: A 322 MET cc_start: 0.8829 (tpp) cc_final: 0.8494 (mmm) REVERT: A 350 ARG cc_start: 0.9037 (mmm-85) cc_final: 0.8569 (mmm-85) REVERT: A 359 MET cc_start: 0.9121 (ptt) cc_final: 0.8484 (ppp) REVERT: A 370 ASN cc_start: 0.9628 (m-40) cc_final: 0.9260 (m110) REVERT: A 394 TYR cc_start: 0.9327 (m-80) cc_final: 0.8499 (m-80) REVERT: A 407 ILE cc_start: 0.9211 (mt) cc_final: 0.8825 (mt) REVERT: A 468 LEU cc_start: 0.9723 (tp) cc_final: 0.9492 (tp) REVERT: A 493 MET cc_start: 0.9169 (tmm) cc_final: 0.8819 (tmm) REVERT: A 499 SER cc_start: 0.9936 (t) cc_final: 0.9715 (p) REVERT: A 515 ASP cc_start: 0.9309 (m-30) cc_final: 0.9034 (m-30) REVERT: A 516 GLN cc_start: 0.9156 (tt0) cc_final: 0.8753 (tt0) REVERT: A 522 TYR cc_start: 0.9341 (m-80) cc_final: 0.8905 (m-10) REVERT: A 570 MET cc_start: 0.9434 (mtp) cc_final: 0.7965 (mtp) REVERT: A 575 ARG cc_start: 0.9484 (mtm110) cc_final: 0.9016 (ptp90) REVERT: A 602 GLU cc_start: 0.8925 (pm20) cc_final: 0.7874 (pm20) REVERT: A 612 TYR cc_start: 0.8500 (m-80) cc_final: 0.8155 (m-10) REVERT: A 615 MET cc_start: 0.9109 (mmp) cc_final: 0.8266 (mmp) REVERT: A 636 LYS cc_start: 0.9767 (mmtp) cc_final: 0.9334 (mmmm) REVERT: A 639 ASP cc_start: 0.9279 (m-30) cc_final: 0.8906 (m-30) REVERT: A 640 MET cc_start: 0.9388 (ttm) cc_final: 0.9144 (ttm) REVERT: A 650 GLN cc_start: 0.8680 (mt0) cc_final: 0.8051 (mt0) REVERT: A 680 LYS cc_start: 0.8497 (mttt) cc_final: 0.8061 (mttt) REVERT: A 682 ILE cc_start: 0.9498 (mp) cc_final: 0.9208 (mp) REVERT: B 15 GLU cc_start: 0.9146 (tp30) cc_final: 0.8822 (tp30) REVERT: B 17 MET cc_start: 0.8968 (mpp) cc_final: 0.8359 (mpp) REVERT: B 99 LYS cc_start: 0.9648 (mmmt) cc_final: 0.9251 (mmmm) REVERT: B 104 TYR cc_start: 0.8974 (m-80) cc_final: 0.8645 (m-80) REVERT: B 128 PHE cc_start: 0.9728 (t80) cc_final: 0.9524 (t80) REVERT: B 136 LYS cc_start: 0.9675 (mmtp) cc_final: 0.9285 (mmmm) REVERT: B 144 MET cc_start: 0.9181 (mtm) cc_final: 0.8727 (mtm) REVERT: B 158 ASN cc_start: 0.9667 (m-40) cc_final: 0.9202 (p0) REVERT: B 184 ARG cc_start: 0.9493 (mmm-85) cc_final: 0.8788 (mmm-85) REVERT: B 191 GLN cc_start: 0.9180 (mm-40) cc_final: 0.8882 (mm110) REVERT: B 211 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7613 (mm-30) REVERT: B 220 THR cc_start: 0.9200 (p) cc_final: 0.8953 (p) REVERT: B 227 MET cc_start: 0.9255 (mtm) cc_final: 0.9036 (mtm) REVERT: B 232 ASN cc_start: 0.9265 (m110) cc_final: 0.8965 (m110) REVERT: B 251 LEU cc_start: 0.9431 (tp) cc_final: 0.9144 (tp) REVERT: B 258 ILE cc_start: 0.9516 (tp) cc_final: 0.9294 (tp) REVERT: B 286 ASP cc_start: 0.8771 (m-30) cc_final: 0.7993 (m-30) REVERT: B 296 LYS cc_start: 0.8900 (mmpt) cc_final: 0.8613 (mtmm) REVERT: B 321 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8279 (tm-30) REVERT: B 322 MET cc_start: 0.9149 (mmm) cc_final: 0.8711 (mmm) REVERT: B 333 LYS cc_start: 0.9492 (ttmm) cc_final: 0.9170 (ttmm) REVERT: B 342 LEU cc_start: 0.9776 (tp) cc_final: 0.9495 (tp) REVERT: B 346 LEU cc_start: 0.9682 (mt) cc_final: 0.9479 (mt) REVERT: B 350 ARG cc_start: 0.8851 (mtp85) cc_final: 0.8028 (mtp85) REVERT: B 362 ASP cc_start: 0.9139 (m-30) cc_final: 0.8155 (m-30) REVERT: B 375 LYS cc_start: 0.9068 (mmtm) cc_final: 0.8556 (mmtm) REVERT: B 393 SER cc_start: 0.9472 (t) cc_final: 0.9032 (t) REVERT: B 402 GLU cc_start: 0.8519 (mp0) cc_final: 0.8151 (mp0) REVERT: B 403 ILE cc_start: 0.9169 (mm) cc_final: 0.8803 (tp) REVERT: B 413 SER cc_start: 0.9581 (m) cc_final: 0.9223 (t) REVERT: B 414 LEU cc_start: 0.9820 (mt) cc_final: 0.9616 (mt) REVERT: B 421 GLU cc_start: 0.9415 (tm-30) cc_final: 0.9163 (tm-30) REVERT: B 615 MET cc_start: 0.9152 (mmp) cc_final: 0.8820 (mmm) REVERT: B 636 LYS cc_start: 0.9703 (mptt) cc_final: 0.9376 (mmmt) REVERT: B 639 ASP cc_start: 0.9343 (m-30) cc_final: 0.8944 (m-30) REVERT: B 658 LEU cc_start: 0.9627 (mm) cc_final: 0.9399 (mm) REVERT: B 667 LEU cc_start: 0.9455 (tp) cc_final: 0.9172 (tt) REVERT: B 668 ASN cc_start: 0.9427 (m-40) cc_final: 0.8986 (m-40) REVERT: B 677 ARG cc_start: 0.9580 (mmm160) cc_final: 0.9278 (mmm-85) REVERT: B 683 TYR cc_start: 0.8743 (t80) cc_final: 0.8417 (t80) REVERT: C 42 LEU cc_start: 0.9256 (mt) cc_final: 0.8999 (mt) REVERT: C 45 LYS cc_start: 0.8651 (mptt) cc_final: 0.8267 (pttp) REVERT: C 101 HIS cc_start: 0.8604 (m90) cc_final: 0.7909 (m90) REVERT: C 261 ARG cc_start: 0.5089 (mtm110) cc_final: 0.4707 (ptp-170) REVERT: D 25 ASN cc_start: 0.8306 (m-40) cc_final: 0.8073 (m-40) REVERT: D 69 GLN cc_start: 0.9495 (tp-100) cc_final: 0.9132 (tm-30) REVERT: D 100 VAL cc_start: 0.5108 (t) cc_final: 0.4818 (t) REVERT: D 205 VAL cc_start: 0.9178 (t) cc_final: 0.8776 (p) outliers start: 0 outliers final: 0 residues processed: 620 average time/residue: 0.2818 time to fit residues: 259.3926 Evaluate side-chains 541 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 541 time to evaluate : 1.800 ------------------------------------------------------------------------------- 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: 0.0470 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 160 optimal weight: 20.0000 chunk 106 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 148 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 chunk 68 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 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 = 0.3802 r_free = 0.3802 target = 0.136172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.092448 restraints weight = 46363.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.095682 restraints weight = 27124.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.097851 restraints weight = 18127.892| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3234 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3234 r_free = 0.3234 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3234 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.7886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16386 Z= 0.136 Angle : 0.672 14.660 22134 Z= 0.353 Chirality : 0.045 0.210 2360 Planarity : 0.004 0.066 2818 Dihedral : 10.766 167.140 2242 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % 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: 0.65 (0.19), residues: 1932 helix: 1.00 (0.15), residues: 1139 sheet: -0.56 (0.41), residues: 144 loop : -0.16 (0.24), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 124 HIS 0.008 0.001 HIS D 201 PHE 0.026 0.002 PHE B 487 TYR 0.023 0.002 TYR D 262 ARG 0.014 0.001 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.03946 ( 871) hydrogen bonds : angle 5.18322 ( 2571) covalent geometry : bond 0.00293 (16386) covalent geometry : angle 0.67162 (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 619 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 619 time to evaluate : 1.729 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: 0.9019 (mpp) cc_final: 0.8753 (mpp) REVERT: A 91 PHE cc_start: 0.9483 (m-80) cc_final: 0.9037 (m-80) REVERT: A 95 MET cc_start: 0.8984 (tpp) cc_final: 0.8439 (tpt) REVERT: A 116 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8355 (tt0) REVERT: A 139 GLU cc_start: 0.9545 (mt-10) cc_final: 0.9342 (mt-10) REVERT: A 143 LEU cc_start: 0.9605 (tp) cc_final: 0.9294 (tp) REVERT: A 144 MET cc_start: 0.9314 (mmp) cc_final: 0.8912 (mmp) REVERT: A 190 MET cc_start: 0.9599 (mmm) cc_final: 0.9182 (mmm) REVERT: A 204 SER cc_start: 0.9426 (m) cc_final: 0.8975 (p) REVERT: A 235 ARG cc_start: 0.8853 (mtm110) cc_final: 0.8491 (mtm180) REVERT: A 251 LEU cc_start: 0.9589 (tp) cc_final: 0.9361 (tp) REVERT: A 252 ASN cc_start: 0.9381 (t0) cc_final: 0.8922 (t0) REVERT: A 283 VAL cc_start: 0.9252 (t) cc_final: 0.8994 (t) REVERT: A 307 TYR cc_start: 0.9650 (t80) cc_final: 0.9165 (t80) REVERT: A 322 MET cc_start: 0.8920 (tpp) cc_final: 0.8560 (mmm) REVERT: A 350 ARG cc_start: 0.9035 (mmm-85) cc_final: 0.8770 (mmm-85) REVERT: A 359 MET cc_start: 0.9082 (ptt) cc_final: 0.8466 (ppp) REVERT: A 370 ASN cc_start: 0.9551 (m-40) cc_final: 0.9084 (m110) REVERT: A 373 ILE cc_start: 0.9422 (mt) cc_final: 0.9191 (mt) REVERT: A 377 LYS cc_start: 0.8669 (mttt) cc_final: 0.8378 (mttp) REVERT: A 387 GLN cc_start: 0.9242 (mt0) cc_final: 0.8497 (mp10) REVERT: A 394 TYR cc_start: 0.9377 (m-80) cc_final: 0.8509 (m-80) REVERT: A 406 ASP cc_start: 0.8975 (m-30) cc_final: 0.8562 (m-30) REVERT: A 407 ILE cc_start: 0.9146 (mt) cc_final: 0.8807 (mt) REVERT: A 415 ASN cc_start: 0.9526 (t0) cc_final: 0.9061 (t0) REVERT: A 418 ASN cc_start: 0.9582 (m-40) cc_final: 0.9121 (m-40) REVERT: A 421 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8847 (tm-30) REVERT: A 468 LEU cc_start: 0.9639 (tp) cc_final: 0.9417 (tp) REVERT: A 493 MET cc_start: 0.9178 (tmm) cc_final: 0.8835 (tmm) REVERT: A 496 ASN cc_start: 0.9606 (t0) cc_final: 0.9095 (t0) REVERT: A 499 SER cc_start: 0.9932 (t) cc_final: 0.9698 (p) REVERT: A 500 ILE cc_start: 0.9721 (mt) cc_final: 0.9421 (mt) REVERT: A 515 ASP cc_start: 0.9283 (m-30) cc_final: 0.9043 (m-30) REVERT: A 516 GLN cc_start: 0.9206 (tt0) cc_final: 0.8915 (tt0) REVERT: A 522 TYR cc_start: 0.9317 (m-80) cc_final: 0.8841 (m-10) REVERT: A 570 MET cc_start: 0.9506 (mtp) cc_final: 0.7274 (mtp) REVERT: A 575 ARG cc_start: 0.9385 (mtm110) cc_final: 0.8953 (ptp90) REVERT: A 603 GLU cc_start: 0.8634 (tp30) cc_final: 0.8385 (tp30) REVERT: A 612 TYR cc_start: 0.8476 (m-80) cc_final: 0.8210 (m-10) REVERT: A 615 MET cc_start: 0.9116 (mmp) cc_final: 0.8573 (mmp) REVERT: A 636 LYS cc_start: 0.9719 (mmtp) cc_final: 0.9343 (mmmm) REVERT: A 639 ASP cc_start: 0.9242 (m-30) cc_final: 0.8766 (m-30) REVERT: A 640 MET cc_start: 0.9390 (ttm) cc_final: 0.8581 (tpp) REVERT: A 680 LYS cc_start: 0.8524 (mttt) cc_final: 0.8021 (mttt) REVERT: A 686 ARG cc_start: 0.8225 (mmt180) cc_final: 0.7898 (mmt180) REVERT: B 15 GLU cc_start: 0.9128 (tp30) cc_final: 0.8761 (tp30) REVERT: B 99 LYS cc_start: 0.9606 (mmmt) cc_final: 0.9238 (mmmt) REVERT: B 136 LYS cc_start: 0.9672 (mmtp) cc_final: 0.9376 (mmmm) REVERT: B 144 MET cc_start: 0.9050 (mtm) cc_final: 0.8642 (mtm) REVERT: B 157 LEU cc_start: 0.9613 (tp) cc_final: 0.9370 (tp) REVERT: B 158 ASN cc_start: 0.9546 (m-40) cc_final: 0.9156 (p0) REVERT: B 161 ARG cc_start: 0.8928 (ttm110) cc_final: 0.8498 (mtp85) REVERT: B 184 ARG cc_start: 0.9515 (mmm-85) cc_final: 0.8924 (mmm-85) REVERT: B 191 GLN cc_start: 0.9126 (mm-40) cc_final: 0.8798 (mm110) REVERT: B 200 SER cc_start: 0.9105 (t) cc_final: 0.8881 (t) REVERT: B 211 GLU cc_start: 0.8366 (mm-30) cc_final: 0.7719 (mm-30) REVERT: B 220 THR cc_start: 0.9144 (p) cc_final: 0.8938 (p) REVERT: B 228 LYS cc_start: 0.9062 (mmtt) cc_final: 0.8732 (mmtt) REVERT: B 232 ASN cc_start: 0.9242 (m110) cc_final: 0.8972 (m110) REVERT: B 258 ILE cc_start: 0.9526 (tp) cc_final: 0.9301 (tp) REVERT: B 283 VAL cc_start: 0.9036 (t) cc_final: 0.8028 (t) REVERT: B 286 ASP cc_start: 0.8716 (m-30) cc_final: 0.8267 (m-30) REVERT: B 290 GLU cc_start: 0.9246 (pp20) cc_final: 0.8752 (pp20) REVERT: B 291 LEU cc_start: 0.9608 (mt) cc_final: 0.9350 (mt) REVERT: B 296 LYS cc_start: 0.8814 (mmpt) cc_final: 0.8527 (mtmm) REVERT: B 321 GLU cc_start: 0.9058 (tm-30) cc_final: 0.8458 (tm-30) REVERT: B 322 MET cc_start: 0.9169 (mmm) cc_final: 0.8728 (mmm) REVERT: B 333 LYS cc_start: 0.9535 (ttmm) cc_final: 0.9239 (ttmm) REVERT: B 350 ARG cc_start: 0.8791 (mtp85) cc_final: 0.8144 (mtp85) REVERT: B 362 ASP cc_start: 0.9214 (m-30) cc_final: 0.8226 (m-30) REVERT: B 375 LYS cc_start: 0.9011 (mmtm) cc_final: 0.8536 (mmtt) REVERT: B 393 SER cc_start: 0.9440 (t) cc_final: 0.8754 (t) REVERT: B 396 ASP cc_start: 0.8600 (m-30) cc_final: 0.8367 (m-30) REVERT: B 402 GLU cc_start: 0.8569 (mp0) cc_final: 0.8101 (mp0) REVERT: B 403 ILE cc_start: 0.9164 (mm) cc_final: 0.8806 (tp) REVERT: B 413 SER cc_start: 0.9619 (m) cc_final: 0.9303 (t) REVERT: B 421 GLU cc_start: 0.9365 (tm-30) cc_final: 0.9072 (tm-30) REVERT: B 500 ILE cc_start: 0.9801 (mt) cc_final: 0.9581 (mt) REVERT: B 501 GLN cc_start: 0.9568 (mt0) cc_final: 0.9304 (mt0) REVERT: B 598 MET cc_start: 0.8472 (ttt) cc_final: 0.8212 (tpp) REVERT: B 615 MET cc_start: 0.9092 (mmp) cc_final: 0.8824 (mmm) REVERT: B 636 LYS cc_start: 0.9679 (mptt) cc_final: 0.9319 (mmmt) REVERT: B 639 ASP cc_start: 0.9300 (m-30) cc_final: 0.8845 (m-30) REVERT: B 658 LEU cc_start: 0.9566 (mm) cc_final: 0.9355 (mm) REVERT: B 667 LEU cc_start: 0.9463 (tp) cc_final: 0.9200 (tt) REVERT: B 668 ASN cc_start: 0.9334 (m-40) cc_final: 0.8915 (m-40) REVERT: B 677 ARG cc_start: 0.9559 (mmm160) cc_final: 0.9279 (mmm-85) REVERT: B 679 ILE cc_start: 0.9740 (mm) cc_final: 0.9538 (mm) REVERT: C 45 LYS cc_start: 0.8693 (mptt) cc_final: 0.8366 (pttp) REVERT: C 101 HIS cc_start: 0.7962 (m90) cc_final: 0.7296 (m90) REVERT: C 261 ARG cc_start: 0.5025 (mtm110) cc_final: 0.4658 (ptp-170) REVERT: D 25 ASN cc_start: 0.8259 (m-40) cc_final: 0.8037 (m-40) REVERT: D 69 GLN cc_start: 0.9432 (tp40) cc_final: 0.9063 (tm-30) REVERT: D 91 ASN cc_start: 0.8187 (m110) cc_final: 0.7793 (m110) REVERT: D 93 MET cc_start: 0.8932 (mtm) cc_final: 0.8729 (mtm) REVERT: D 100 VAL cc_start: 0.5010 (t) cc_final: 0.4662 (t) REVERT: D 205 VAL cc_start: 0.9120 (t) cc_final: 0.8889 (p) outliers start: 0 outliers final: 0 residues processed: 619 average time/residue: 0.2668 time to fit residues: 243.6328 Evaluate side-chains 547 residues out of total 1716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 547 time to evaluate : 1.658 ------------------------------------------------------------------------------- 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: 1.9990 chunk 16 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 105 optimal weight: 0.9980 chunk 179 optimal weight: 20.0000 chunk 190 optimal weight: 9.9990 chunk 58 optimal weight: 0.2980 chunk 180 optimal weight: 0.9990 chunk 108 optimal weight: 0.0970 chunk 43 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 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 = 0.3806 r_free = 0.3806 target = 0.138007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.094689 restraints weight = 46971.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.097768 restraints weight = 27585.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.099755 restraints weight = 18329.242| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7727 moved from start: 0.8059 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= 0.137 Angle : 0.670 14.812 22134 Z= 0.355 Chirality : 0.044 0.249 2360 Planarity : 0.004 0.051 2818 Dihedral : 10.648 169.762 2242 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.19), residues: 1932 helix: 0.88 (0.15), residues: 1141 sheet: -0.61 (0.42), residues: 144 loop : -0.12 (0.24), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP C 30 HIS 0.006 0.001 HIS D 201 PHE 0.035 0.002 PHE B 360 TYR 0.037 0.002 TYR C 142 ARG 0.012 0.001 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 871) hydrogen bonds : angle 5.17765 ( 2571) covalent geometry : bond 0.00298 (16386) covalent geometry : angle 0.66994 (22134) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6740.31 seconds wall clock time: 118 minutes 43.07 seconds (7123.07 seconds total)